Contacts of the helix formed by residues 15 - 37 (chain A) in PDB entry 1QI9
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 PRO 15 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A CYS* 3.6 24.2 - - - -
4A SER 3.2 15.9 - - - +
5A THR 3.6 12.1 - - - +
6A SER* 3.7 8.1 - - - +
7A ASP* 3.6 29.2 - - - +
13A THR 3.7 0.6 - - - -
14A PRO* 1.3 82.8 - - + -
16A ASN* 1.3 57.6 + - - +
17A GLU 3.1 4.7 + - - -
18A ARG* 3.3 35.0 + - - +
19A ASP* 4.4 2.8 + - - +
38B GLY 4.6 0.5 - - - +
39B THR* 3.8 18.5 - - + +
40B VAL 4.1 9.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
4A SER* 2.9 36.0 + - - +
5A THR* 4.0 17.3 - - - +
14A PRO* 3.6 12.6 - - - +
15A PRO* 1.3 72.4 - - - +
17A GLU* 1.3 68.2 + - - +
19A ASP* 3.3 13.0 - - - +
20A ASP* 3.8 6.8 - - - +
39B THR* 3.4 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.7 12.4 - - + +
14A PRO* 2.8 40.2 + - + +
16A ASN* 1.3 85.2 - - - +
18A ARG* 1.3 62.0 + - - +
19A ASP* 3.2 5.4 - - - -
20A ASP* 3.3 11.6 + - + +
21A GLU* 3.0 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP* 2.8 43.8 + - - -
9A ALA* 4.0 1.4 + - - +
11A ASP* 3.3 29.2 + - - +
13A THR* 2.8 38.3 + - + -
14A PRO 3.2 8.5 + - - +
15A PRO* 3.3 25.9 + - - +
17A GLU* 1.3 77.7 - - - +
19A ASP* 1.3 61.3 + - - +
21A GLU* 3.6 3.7 + - - +
22A ALA* 3.2 23.9 + - - +
40B VAL 4.0 8.1 + - - -
42B GLN* 3.7 10.5 - - - +
117B ALA* 5.6 0.9 - - - +
118B PHE* 6.2 1.6 - - + -
119B SER* 3.4 29.0 + - - +
339B TYR* 3.5 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO 4.4 1.4 + - - -
16A ASN* 3.3 25.8 - - - +
17A GLU 3.7 0.3 - - - -
18A ARG* 1.3 75.8 - - - +
20A ASP* 1.4 76.4 + - - +
22A ALA* 3.3 6.3 + - - +
23A PHE* 3.1 18.4 + - - +
34B LEU* 3.5 31.6 - - + +
37B THR* 4.2 16.3 - - + +
38B GLY* 3.4 40.4 + - - +
39B THR* 5.2 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN 3.8 16.1 - - - +
17A GLU* 3.3 12.1 + - + +
19A ASP* 1.4 90.8 + - - +
21A GLU* 1.3 57.3 + - + +
23A PHE* 3.4 5.9 + - - +
24A ALA* 2.9 29.7 + - - +
34B LEU* 3.7 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 2.8 39.8 + - + +
17A GLU* 3.0 28.2 + - + +
18A ARG* 4.0 4.5 - - - +
20A ASP* 1.3 73.1 - - + +
22A ALA* 1.3 64.7 + - - +
24A ALA* 3.9 6.1 - - - +
25A SER* 3.1 24.8 + - - -
111B ILE* 3.6 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG 3.2 18.0 + - - +
19A ASP* 3.3 5.6 + - - +
20A ASP 3.3 0.2 - - - -
21A GLU* 1.3 72.7 - - - +
23A PHE* 1.3 67.1 + - - +
25A SER* 3.4 2.9 + - - -
26A ARG* 3.2 38.3 + - - +
111B ILE* 3.8 19.7 - - + +
117B ALA* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP 3.1 16.1 + - - +
20A ASP* 3.7 5.2 - - - +
22A ALA* 1.3 75.9 - - - +
24A ALA* 1.3 67.1 + - + +
26A ARG* 3.1 8.0 + - - +
27A VAL* 2.9 51.1 + - + +
27B VAL* 3.9 13.7 - - + -
30B ALA* 3.6 27.1 - - + +
31B LYS* 3.5 35.9 - - + -
34B LEU* 4.1 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASP 2.9 17.6 + - - +
21A GLU* 3.9 7.4 - - - +
23A PHE* 1.3 82.4 - - + +
25A SER* 1.3 57.9 + - - +
27A VAL* 3.4 5.3 + - - +
28A ALA* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU 3.1 18.4 + - - -
22A ALA 3.6 4.9 - - - -
23A PHE 3.3 0.2 - - - -
24A ALA* 1.3 75.7 - - - +
26A ARG* 1.3 56.8 + - - +
28A ALA* 3.5 6.7 + - - +
29A ALA* 3.0 27.0 + - - +
512A THR* 5.1 5.7 - - - +
111B ILE* 3.6 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 3.2 21.2 + - - +
23A PHE* 3.1 8.3 + - - +
25A SER* 1.3 73.2 - - - +
27A VAL* 1.3 66.8 + - - +
29A ALA* 3.2 7.5 + - - +
30A ALA* 3.0 25.7 + - - +
113A ILE* 5.1 1.8 - - + -
26B ARG 6.6 0.2 - - - -
30B ALA* 3.9 25.9 + - + +
33B GLU* 3.8 25.7 - - - +
111B ILE* 3.9 12.3 - - + +
112B ASP* 2.9 26.4 + - - +
113B ILE* 3.3 34.8 + - + +
114B SER 4.2 0.4 + - - -
115B GLY 3.0 27.8 + - - -
116B PRO 3.8 0.6 - - - -
117B ALA* 3.3 31.8 - - - +
508B GLN* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 2.9 56.6 + - + +
24A ALA* 3.8 6.5 - - - +
26A ARG* 1.3 76.2 - - - +
28A ALA* 1.3 63.9 + - - +
30A ALA* 3.3 5.9 + - - +
31A LYS* 2.8 27.7 + - + +
23B PHE* 4.0 17.2 - - + -
27B VAL* 4.4 17.9 - - + +
30B ALA* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 3.0 17.1 + - - +
25A SER* 3.6 7.4 - - - +
27A VAL* 1.3 78.7 - - - +
29A ALA* 1.3 61.3 + - - +
31A LYS* 3.2 9.3 + - - +
32A ARG* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 3.0 18.7 + - - +
26A ARG* 3.2 7.1 + - - +
28A ALA* 1.3 74.8 - - - +
30A ALA* 1.3 57.0 + - - +
32A ARG* 3.3 11.1 + - - +
33A GLU* 3.1 26.9 + - - +
508A GLN* 4.2 19.1 + - + +
113B ILE* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG 3.0 16.0 + - - +
27A VAL* 3.6 5.8 - - - +
29A ALA* 1.3 73.7 - - - +
31A LYS* 1.3 59.8 + - - +
33A GLU* 3.2 8.5 + - - +
34A LEU* 2.8 27.9 + - - +
508A GLN* 5.5 0.2 - - - +
23B PHE* 3.5 20.4 - - + +
26B ARG* 4.0 35.2 + - + +
27B VAL* 5.0 2.2 - - + -
113B ILE* 4.4 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 2.8 23.1 + - + +
28A ALA* 3.2 10.1 + - - +
30A ALA* 1.3 74.8 - - - +
32A ARG* 1.3 58.5 + - - +
34A LEU* 3.2 7.0 + - + +
35A GLU* 2.9 68.6 + - + +
23B PHE* 3.6 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA 3.0 12.1 + - - +
29A ALA* 3.4 12.1 - - - +
30A ALA 3.3 0.2 - - - -
31A LYS* 1.3 73.6 - - - +
33A GLU* 1.4 59.8 + - + +
35A GLU* 4.9 1.3 - - - -
36A GLY* 2.9 27.9 + - - -
507A HIS* 5.9 0.8 - - - -
511A MET* 3.9 32.1 - - - +
534A ASP 4.0 5.9 + - - -
535A GLY* 3.0 40.5 + - - -
547A LEU* 3.2 47.9 + - + +
548A VAL* 3.9 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 3.1 16.7 + - - +
30A ALA* 3.2 5.8 + - - +
32A ARG* 1.4 72.8 - - + +
34A LEU* 1.3 66.9 + - - +
37A THR* 2.8 35.0 + - - +
115A GLY 4.4 3.3 - - - +
116A PRO* 3.6 19.4 - - - +
117A ALA 4.5 2.1 + - - -
504A ARG* 2.7 52.6 + - - +
508A GLN* 4.1 19.9 + - - +
548A VAL* 4.1 9.0 - - - +
26B ARG* 3.7 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 2.8 14.2 + - - +
31A LYS* 3.2 14.8 + - + +
33A GLU* 1.3 79.4 - - - +
35A GLU* 1.3 71.0 + - + +
37A THR* 3.9 1.3 - - - -
38A GLY* 3.2 19.6 + - - -
19B ASP* 3.5 43.4 - - + +
20B ASP* 3.6 19.3 - - - +
23B PHE* 3.9 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 2.9 59.3 + - + +
32A ARG* 5.0 0.9 - - - -
34A LEU* 1.3 82.8 - - + +
36A GLY* 1.3 61.3 + - - +
37A THR 3.4 0.3 + - - -
38A GLY* 4.1 6.1 + - - -
547A LEU* 3.5 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG 2.9 19.2 + - - -
33A GLU 3.9 0.4 - - - -
35A GLU* 1.3 75.9 - - - +
37A THR* 1.3 62.0 + - - +
547A LEU* 3.7 18.1 + - - +
548A VAL* 3.7 29.4 - - - +
550A THR* 4.6 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.8 27.5 + - - +
34A LEU* 3.9 2.0 - - - -
35A GLU 4.5 0.2 - - - -
36A GLY* 1.3 79.8 - - - +
38A GLY* 1.3 75.0 + - - +
39A THR 3.7 2.4 + - - +
40A VAL* 3.6 27.6 - - + +
120A ALA* 4.0 19.8 - - + +
504A ARG* 3.4 21.2 + - - +
19B ASP* 4.2 13.9 - - + +
----------------------------------------------------------
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