Contacts of the helix formed by residues 18 - 33 (chain A) in PDB entry 5I1U
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 HIS 18 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 2.8 21.8 + - - +
17A PRO* 1.3 91.8 + - + +
19A GLN* 1.3 64.4 + - - +
20A THR 3.3 3.2 + - - -
21A GLU* 3.3 14.0 + - - +
22A ALA* 2.9 21.7 + - - +
61A SER 3.4 17.4 + - - -
62A SER* 4.3 4.0 - - - -
63A ALA* 3.6 39.5 + - + +
66A LEU* 3.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 2.9 28.9 + - - +
16A ASN 3.3 12.0 + - - +
17A PRO 3.3 2.8 - - - -
18A HIS* 1.3 77.6 - - - +
20A THR* 1.3 58.7 + - - +
22A ALA* 3.4 1.0 + - - +
23A ALA* 2.9 29.9 + - + +
51A THR* 4.3 12.2 + - - +
52A GLU* 3.0 36.8 + - - +
55A SER* 3.1 24.0 + - - +
66A LEU* 3.7 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PRO 5.1 1.0 + - - -
18A HIS 3.3 0.6 - - - -
19A GLN* 1.3 78.5 - - - +
21A GLU* 1.3 65.2 + - - +
23A ALA* 3.2 7.7 + - - +
24A ASP* 3.1 34.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
18A HIS* 3.3 18.4 + - - +
20A THR* 1.3 80.0 - - - +
22A ALA* 1.3 63.8 + - - +
24A ASP* 3.2 11.6 + - - +
25A ARG* 3.2 35.0 + - + +
63A ALA* 3.5 28.5 - - + +
----------------------------------------------------------
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 HIS* 2.9 9.2 + - - +
19A GLN 4.0 1.8 - - - +
21A GLU* 1.3 76.5 - - - +
23A ALA* 1.3 53.1 + - - +
25A ARG* 3.1 10.1 + - - +
26A HIS* 2.8 35.7 + - - +
51A THR* 4.8 2.2 - - + -
63A ALA 4.0 5.8 + - - +
66A LEU* 3.5 40.8 - - + +
67A ALA* 3.7 20.5 - - - +
70A ALA* 5.5 2.2 - - + -
----------------------------------------------------------
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 GLN* 2.9 20.5 + - + +
20A THR* 3.2 7.4 + - + +
22A ALA* 1.3 76.1 - - - +
24A ASP* 1.3 58.9 + - - +
26A HIS* 3.3 2.1 + - - +
27A LEU* 3.0 29.1 + - - +
51A THR* 3.6 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 3.1 30.1 + - - +
21A GLU* 3.5 11.7 - - - +
23A ALA* 1.3 79.5 - - - +
25A ARG* 1.3 61.8 + - + +
27A LEU* 3.4 10.2 + - - +
28A GLU* 3.2 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.4 29.0 + - + +
22A ALA* 3.1 8.6 + - - +
24A ASP* 1.3 74.5 - - + +
26A HIS* 1.3 65.1 + - - +
28A GLU* 3.2 22.9 + - - +
29A TRP* 3.0 21.1 + - - +
32A ARG* 5.2 1.9 + - - -
63A ALA* 4.8 2.5 - - - +
64A GLU* 3.6 50.6 + - - +
67A ALA* 3.6 19.5 - - + +
71A ASP* 4.8 1.8 - - - +
126A ARG* 5.1 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA 2.8 19.7 + - - +
23A ALA 3.3 5.1 + - - +
25A ARG* 1.3 71.1 - - - +
27A LEU* 1.3 65.8 + - - +
29A TRP* 3.2 7.8 + + - +
30A LEU* 2.9 42.5 + - + +
45A TYR* 2.7 36.3 + + - -
50A ILE* 3.8 7.5 - - + +
51A THR* 3.8 20.6 - - + -
67A ALA* 4.9 1.1 - - - +
70A ALA* 3.3 31.4 - - + -
71A ASP* 2.8 36.1 + - - +
74A GLY* 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 3.0 13.7 + - - +
24A ASP* 3.6 12.6 - - - +
25A ARG 3.3 0.2 - - - -
26A HIS* 1.3 75.5 - - - +
28A GLU* 1.3 63.5 + - + +
30A LEU* 3.3 19.8 + - + -
31A GLN* 3.1 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 3.2 16.9 + - - +
25A ARG* 3.2 27.1 + - - +
26A HIS 3.2 0.6 - - - -
27A LEU* 1.3 79.3 - - + +
29A TRP* 1.3 61.4 + - - +
31A GLN* 3.2 20.0 + - - +
32A ARG* 3.0 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG 3.0 10.0 + - - +
26A HIS* 3.5 7.9 - + - +
28A GLU* 1.3 76.7 - - - +
30A LEU* 1.3 87.2 + - + +
32A ARG* 3.0 23.4 + - - +
33A HIS* 2.9 56.5 + + + -
36A LEU* 4.0 24.7 - - + -
71A ASP* 3.3 67.5 - - + +
74A GLY 4.9 1.6 - - - -
75A PHE* 4.3 11.9 - - + -
78A LEU* 5.0 1.1 - - + -
119A ALA* 4.1 14.1 - - + -
122A ASP* 3.1 20.8 + - - -
123A LEU* 4.2 13.6 - - + +
126A ARG* 3.5 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 2.9 38.2 + - + +
27A LEU* 3.6 24.0 - - + +
29A TRP* 1.3 95.1 - - + +
31A GLN* 1.3 57.4 + - + +
33A HIS* 3.2 5.8 - - - +
34A ARG* 3.1 26.9 + - - +
37A ALA* 4.0 25.3 - - + +
45A TYR* 3.7 39.0 - - + +
78A LEU* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.1 36.6 + - + +
28A GLU* 3.4 22.9 - - - +
29A TRP 3.1 0.2 - - - -
30A LEU* 1.3 76.5 - - - +
32A ARG* 1.3 64.5 + - + +
33A HIS 3.1 0.9 + - - -
34A ARG* 3.4 49.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
25A ARG 5.2 1.6 + - - -
28A GLU* 3.0 22.6 + - - +
29A TRP* 3.0 39.8 + - - +
31A GLN* 1.3 77.5 - - + +
33A HIS* 1.3 60.0 + - + +
34A ARG 3.5 0.8 + - - -
71A ASP* 5.2 1.0 + - - -
118A ARG* 2.8 44.3 + - - +
122A ASP* 4.2 16.2 + - - -
126A ARG* 5.0 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TRP* 2.9 63.1 + + + +
30A LEU* 3.2 7.2 - - - +
31A GLN 3.1 0.2 - - - -
32A ARG* 1.3 88.7 + - + +
34A ARG* 1.3 62.8 + - - +
35A GLU 3.2 2.9 - - - -
36A LEU* 3.0 29.0 + - + +
37A ALA* 3.0 11.6 + - - +
115A PRO 5.0 1.0 + - - -
118A ARG* 3.3 39.8 + - + +
119A ALA* 3.7 30.5 + - + +
122A ASP* 4.2 14.1 - - + -
----------------------------------------------------------
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