Contacts of the helix formed by residues 2 - 32 (chain A) in PDB entry 1UCU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 2 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 1.3 70.3 - - - +
3A VAL* 1.3 54.1 + - + +
4A ILE 3.1 2.9 - - - -
5A ASN* 2.9 24.6 + - + +
6A THR* 2.8 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 3 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA* 3.0 22.0 - - + +
2A GLN* 1.3 78.7 + - + +
4A ILE* 1.3 55.0 + - - +
6A THR* 3.4 17.3 - - + -
7A ASN* 2.7 51.5 + - + +
490A LEU* 4.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA 3.4 18.6 + - - +
2A GLN* 5.3 0.2 - - - -
3A VAL* 1.3 73.3 - - - +
5A ASN* 1.3 76.8 + - - +
7A ASN* 3.9 1.9 - - - +
8A SER* 3.0 25.3 + - - -
490A LEU* 4.2 37.3 - - + +
493A LEU* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLN* 2.9 26.2 + - + +
4A ILE* 1.3 93.3 - - - +
6A THR* 1.3 64.9 + - - +
7A ASN 3.1 1.8 - - - -
8A SER* 3.0 17.2 + - - -
9A LEU* 3.0 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLN* 2.8 28.3 + - - +
3A VAL* 3.4 32.1 - - + +
5A ASN* 1.3 73.1 - - - +
7A ASN* 1.3 62.9 + - - +
9A LEU* 3.0 29.6 - - - +
10A SER* 3.1 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 2.7 33.3 + - + +
4A ILE 3.9 1.1 - - - +
6A THR* 1.3 70.6 - - - +
8A SER* 1.3 53.8 + - - +
9A LEU 2.9 2.0 - - - -
10A SER* 2.7 15.5 + - - -
11A LEU* 2.6 67.5 + - - +
486A PRO* 3.4 14.1 - - - +
489A VAL* 5.4 7.3 - - - +
490A LEU* 3.4 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE 3.0 16.7 + - - -
5A ASN* 3.0 17.9 + - - -
7A ASN* 1.3 76.7 - - - +
9A LEU* 1.3 52.0 + - - +
11A LEU* 3.1 18.0 + - - +
12A LEU* 2.6 33.3 + - - +
15A ASN* 5.3 0.5 + - - -
490A LEU* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.0 27.7 + - + +
6A THR* 3.0 17.9 - - - +
7A ASN 2.9 0.4 - - - -
8A SER* 1.3 77.5 - - - +
10A SER* 1.3 54.9 + - - +
11A LEU 2.9 5.4 - - - -
12A LEU* 2.9 43.0 + - + +
13A THR* 3.0 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR 3.1 5.5 + - - -
7A ASN* 2.7 24.6 + - - -
9A LEU* 1.3 76.6 - - - +
11A LEU* 1.3 60.8 + - - +
13A THR* 2.6 23.3 + - - -
14A GLN* 3.2 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 2.6 41.5 + - - +
8A SER* 3.3 14.1 - - - +
9A LEU 2.9 0.2 - - - -
10A SER* 1.3 81.6 - - - +
12A LEU* 1.3 53.9 + - - +
13A THR 3.1 1.8 - - - -
14A GLN* 3.0 25.3 + - - +
15A ASN* 2.6 42.7 + - - +
483A ASN 5.5 0.4 - - - +
486A PRO* 3.1 33.2 - - + -
487A GLN* 4.6 13.0 - - + +
490A LEU* 4.5 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER 2.6 13.2 + - - +
9A LEU* 2.9 33.4 + - + +
11A LEU* 1.3 76.4 - - - +
13A THR* 1.3 52.7 + - + +
15A ASN* 3.2 21.1 + - + +
16A ASN* 2.6 43.7 + - - +
19A LYS* 5.4 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.0 14.1 + - + +
10A SER* 2.6 31.7 + - - -
12A LEU* 1.3 77.1 - - + +
14A GLN* 1.3 58.4 + - - +
16A ASN* 3.0 29.8 + - + +
17A LEU* 3.1 10.6 + - - +
479A LEU* 4.2 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 3.2 20.1 + - - +
11A LEU* 3.0 31.7 + - - +
13A THR* 1.3 76.9 + - - +
15A ASN* 1.3 59.7 + - - +
16A ASN 3.1 0.2 - - - -
17A LEU* 3.0 22.2 + - - +
18A ASN* 3.4 8.0 + - - -
479A LEU* 3.4 37.3 - - + +
482A ALA* 2.9 39.1 + - - +
483A ASN* 4.1 5.2 - - + -
486A PRO* 3.6 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER 5.3 0.4 + - - -
11A LEU* 2.6 30.4 + - - +
12A LEU* 3.3 23.5 - - + +
14A GLN* 1.3 70.6 - - - +
16A ASN* 1.3 60.7 + - - +
17A LEU 3.0 1.8 - - - -
18A ASN* 2.9 42.3 + - + +
19A LYS* 3.1 13.4 + - - +
483A ASN* 5.8 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 2.6 23.9 + - - +
13A THR* 3.0 22.0 + - + +
15A ASN* 1.3 76.4 - - - +
17A LEU* 1.3 52.7 + - - +
18A ASN 3.1 0.7 - - - -
19A LYS* 3.0 43.2 + - - +
20A SER* 2.7 33.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR 3.1 5.2 + - - +
14A GLN 3.0 14.7 + - - +
15A ASN 3.0 0.6 - - - -
16A ASN* 1.3 78.0 - - - +
18A ASN* 1.3 54.1 + - - +
19A LYS 3.0 0.4 - - - -
20A SER* 3.0 23.0 + - - +
21A GLN* 2.6 30.0 + - - +
24A LEU* 5.7 0.2 - - + -
472A GLN* 4.4 5.4 - - + +
475A GLY* 3.8 6.3 - - - +
476A THR* 3.5 37.9 + - - +
479A LEU* 3.4 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN 3.4 4.0 + - - -
15A ASN* 2.9 40.9 + - + +
17A LEU* 1.3 78.3 - - - +
19A LYS* 1.3 58.3 + - + +
21A GLN* 3.0 33.7 + - - +
22A SER* 2.9 21.8 + - - -
476A THR* 5.2 1.1 + - - -
483A ASN* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.4 10.2 - - - +
15A ASN* 3.1 11.6 + - - +
16A ASN* 3.0 47.0 + - - +
18A ASN* 1.3 77.4 - - + +
20A SER* 1.3 53.3 + - - +
21A GLN 3.0 5.6 - - - -
22A SER* 3.1 13.6 + - - -
23A ALA* 2.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN 2.7 17.8 + - - -
17A LEU* 3.0 36.1 + - - +
19A LYS* 1.3 73.8 - - - +
21A GLN* 1.3 55.0 + - - +
22A SER 3.2 0.7 - - - -
23A ALA* 3.1 15.1 + - - +
24A LEU* 2.8 33.0 + - - +
472A GLN* 4.2 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 2.6 11.7 + - - +
18A ASN* 3.0 35.5 + - - +
20A SER* 1.3 74.2 - - - +
22A SER* 1.3 55.9 + - - +
23A ALA 3.0 1.3 - - - -
24A LEU* 3.0 23.6 + - + +
25A GLY* 2.8 28.9 + - - -
476A THR* 3.8 17.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN 2.9 10.7 + - - -
19A LYS* 3.1 20.4 - - - -
21A GLN* 1.3 79.5 - - - +
23A ALA* 1.3 48.6 + - - -
25A GLY* 3.4 2.8 + - - +
26A THR* 2.7 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS 2.9 7.4 + - - +
20A SER* 3.1 22.7 - - - +
21A GLN 3.0 0.2 - - - -
22A SER* 1.3 77.3 - - - +
24A LEU* 1.3 53.1 + - - +
26A THR* 3.3 15.0 - - + +
27A ALA* 2.6 34.8 + - - +
472A GLN* 4.2 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 5.7 0.4 - - + -
20A SER 2.8 15.7 + - - +
21A GLN* 3.0 27.5 + - + +
23A ALA* 1.3 75.2 - - - +
25A GLY* 1.3 53.2 + - - +
27A ALA* 3.3 7.2 + - + +
28A ILE* 2.8 36.2 + - - +
469A GLN* 3.3 38.0 - - + +
472A GLN* 3.4 25.4 - - + +
473A GLN* 3.8 21.3 - - + +
476A THR* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN 2.8 13.7 + - - -
22A SER* 3.6 4.7 - - - -
24A LEU* 1.3 77.8 - - - +
26A THR* 1.3 52.4 + - - +
28A ILE* 3.2 15.1 + - - +
29A GLU* 2.7 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 2.7 21.1 + - - -
23A ALA* 3.2 17.7 + - + +
25A GLY* 1.3 70.6 - - - +
27A ALA* 1.3 59.3 + - + +
29A GLU* 3.2 10.6 + - - +
30A ARG* 2.8 72.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 2.6 20.9 + - - +
24A LEU* 3.4 9.6 - - + +
26A THR* 1.3 72.9 - - + +
28A ILE* 1.3 55.4 + - - +
29A GLU 3.0 1.1 - - - -
30A ARG* 2.9 12.0 + - - +
31A LEU* 2.7 52.2 + - + +
465A MET* 4.8 14.1 - - + +
469A GLN* 4.7 9.0 - - + -
472A GLN* 5.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 2.8 17.5 + - - +
25A GLY* 3.3 15.9 - - - +
27A ALA* 1.3 76.4 - - - +
29A GLU* 1.3 53.0 + - - +
31A LEU* 3.5 8.6 - - + +
32A SER* 2.7 36.2 + - - -
469A GLN* 3.9 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY 2.7 13.2 + - - +
26A THR* 3.2 15.9 - - - +
27A ALA 3.0 0.2 - - - -
28A ILE* 1.3 77.1 - - + +
30A ARG* 1.3 61.5 + - + +
31A LEU 3.1 1.6 - - - -
32A SER* 3.0 36.1 + - - -
33A SER* 3.5 5.7 + - - -
34A GLY 4.4 0.3 + - - -
35A LEU 5.5 0.2 - - - +
36A ARG* 4.3 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 2.8 49.4 + - - +
27A ALA* 3.5 8.9 - - - +
29A GLU* 1.3 73.3 - - + +
31A LEU* 1.3 59.1 + - + +
34A GLY* 2.9 34.5 - - - +
36A ARG* 5.5 11.0 - - + -
457A ASP* 5.0 4.8 - - - +
465A MET* 4.9 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 2.7 30.5 + - + +
28A ILE* 3.5 8.1 - - + +
30A ARG* 1.3 79.4 - - + +
32A SER* 1.3 64.7 - - - +
33A SER 3.4 1.6 + - - -
34A GLY* 3.9 6.0 + - - +
457A ASP* 3.6 31.3 - - + +
462A VAL* 3.5 33.2 - - + -
465A MET* 3.8 26.0 - - + +
469A GLN* 3.1 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 2.7 21.5 + - - -
29A GLU* 3.0 26.3 + - - -
31A LEU* 1.3 79.6 - - - +
33A SER* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il