Contacts of the helix formed by residues 5 - 20 (chain H) in PDB entry 3EXF
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 VAL 5 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H THR* 1.3 71.3 - - - +
6H ARG* 1.3 65.5 + - - +
8H ALA* 3.0 4.0 + - - +
9H ILE* 2.9 30.5 + - + +
147H PRO* 6.4 0.9 - - + -
148H TRP 4.1 7.2 - - - +
149H ASN* 3.9 4.3 - - - -
150H SER* 3.0 34.3 + - - +
153H ALA* 4.3 16.1 - - + +
175H MET* 3.4 34.1 - - + +
176H TYR* 3.7 16.2 - - + +
178H VAL 3.3 2.5 + - - +
180H PHE* 3.6 17.7 - - + -
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Residues in contact with ARG 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H THR* 4.0 4.5 + - - +
5H VAL* 1.3 73.2 - - - +
7H ASP* 1.3 73.9 + - - +
9H ILE* 3.4 4.9 + - - +
10H ASN* 3.1 22.3 + - + +
37H TYR* 2.9 31.7 + - - +
38H LYS* 4.0 15.7 - - - +
39H VAL* 3.9 27.6 - - + +
41H ARG* 4.2 13.7 - - - +
176H TYR* 2.8 44.5 + - + +
177H GLY* 3.6 23.4 - - - +
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Residues in contact with ASP 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H VAL* 3.9 15.2 - - + -
4H THR* 2.9 26.5 + - - +
6H ARG* 1.3 93.4 - - - +
8H ALA* 1.3 56.7 + - - +
10H ASN* 3.3 6.7 + - - +
11H GLN* 2.8 35.3 + - - +
41H ARG* 5.3 2.4 + - - -
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Residues in contact with ALA 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H VAL* 3.7 5.2 - - + +
4H THR 2.9 11.9 + - - +
5H VAL 3.5 7.0 - - - +
7H ASP* 1.3 72.7 - - - +
9H ILE* 1.3 61.8 + - - +
11H GLN* 3.8 6.9 - - - +
12H GLY* 2.9 23.0 + - - -
150H SER* 3.7 26.7 - - - +
153H ALA* 4.7 0.4 - - + -
154H LYS* 3.6 17.0 - - + +
182H PHE* 3.7 24.2 - - + -
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Residues in contact with ILE 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H VAL* 2.9 21.2 + - + +
6H ARG* 3.7 4.5 - - - +
8H ALA* 1.3 72.6 - - - +
10H ASN* 1.3 69.8 + - - +
12H GLY* 2.7 11.1 + - - -
13H MET* 3.0 23.7 + - + +
39H VAL* 3.8 17.7 - - + -
115H ARG* 4.5 0.4 - - - +
147H PRO* 5.9 1.3 - - + -
153H ALA* 3.8 20.9 - - + -
157H ILE* 3.2 28.9 - - + +
171H GLU* 3.1 34.3 - - + +
176H TYR* 3.9 22.2 - - + -
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Residues in contact with ASN 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ARG* 3.1 10.0 + - + +
7H ASP* 3.4 12.1 - - - +
9H ILE* 1.3 81.6 - - - +
11H GLN* 1.3 64.4 + - - +
13H MET* 3.3 7.2 + - - +
14H ASP* 2.9 27.2 + - - +
38H LYS 4.8 0.2 + - - -
39H VAL 2.5 29.8 + - - +
40H SER* 3.4 5.1 - - - +
41H ARG* 3.1 35.8 + - - +
43H LEU* 3.9 12.9 - - - +
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Residues in contact with GLN 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H VAL* 4.5 7.5 - - - +
7H ASP* 2.8 23.2 + - - +
8H ALA* 3.9 6.5 - - - +
10H ASN* 1.3 75.3 + - - +
12H GLY* 1.3 65.3 + - - +
14H ASP* 3.4 8.4 - - + +
15H GLU* 3.1 40.1 + - + +
154H LYS* 3.2 27.4 + - - -
182H PHE* 3.7 21.7 - - - -
187H GLN* 4.0 10.1 - - - +
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Residues in contact with GLY 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ALA 2.9 10.0 + - - -
9H ILE 2.7 10.9 + - - -
11H GLN* 1.3 80.8 - - - +
13H MET* 1.3 62.4 + - - -
15H GLU* 3.1 9.9 + - - +
16H GLU* 3.3 14.3 + - - +
154H LYS* 4.3 5.6 - - - -
157H ILE* 3.5 21.8 - - - -
158H LYS* 4.2 12.1 - - - +
161H ILE* 5.1 0.2 - - - -
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Residues in contact with MET 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ILE* 3.0 19.3 + - + +
10H ASN* 3.8 3.1 - - - +
12H GLY* 1.3 66.8 - - - -
14H ASP* 1.3 70.4 + - - +
16H GLU* 3.0 2.3 + - - +
17H LEU* 2.9 35.9 + - + +
25H LEU* 3.6 27.1 - - + -
39H VAL* 3.8 24.0 - - + +
40H SER* 3.8 12.6 - - - -
43H LEU* 4.2 7.2 - - + -
77H ILE* 4.5 19.5 - - + -
115H ARG* 3.4 42.2 - - - +
157H ILE* 4.1 6.7 - - + +
161H ILE* 4.4 14.1 - - + +
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Residues in contact with ASP 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ASN* 2.9 18.1 + - - +
11H GLN* 3.4 16.7 - - + +
12H GLY 3.1 0.2 + - - -
13H MET* 1.3 78.6 - - - +
15H GLU* 1.3 66.4 + - + +
17H LEU* 3.1 8.5 + - - +
18H GLU* 3.1 20.4 + - - +
43H LEU* 4.6 14.0 - - + +
46H LYS* 3.2 20.9 + - - +
47H TYR* 2.8 25.3 + - - -
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Residues in contact with GLU 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H GLN* 3.1 24.6 - - + +
12H GLY 3.1 6.1 + - - +
14H ASP* 1.3 80.1 - - + +
16H GLU* 1.3 59.1 + - - +
18H GLU* 3.4 7.0 - - - +
19H ARG* 2.9 30.2 + - - +
154H LYS* 3.1 36.9 + - - -
158H LYS* 3.4 25.2 + - - +
187H GLN 3.9 5.2 - - - +
189H LYS* 3.4 27.6 - - + +
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Residues in contact with GLU 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H GLY 3.3 8.7 + - - +
13H MET 3.0 5.5 + - - +
15H GLU* 1.3 77.0 - - - +
17H LEU* 1.3 57.8 + - - +
19H ARG* 3.5 28.5 + - - +
20H ASP* 3.3 19.1 + - - +
23H VAL* 3.4 16.1 - - + +
158H LYS* 2.6 43.8 + - + +
161H ILE* 3.8 43.8 - - + +
162H ARG* 3.0 26.7 + - - -
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Residues in contact with LEU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H MET* 2.9 36.3 + - + +
14H ASP* 3.4 5.6 - - - +
16H GLU* 1.3 75.8 - - - +
18H GLU* 1.3 67.0 + - - +
20H ASP 3.4 7.8 + - - -
21H GLU 4.0 0.9 + - - -
23H VAL* 3.8 21.8 - - + +
24H PHE* 4.1 14.6 - - - -
25H LEU* 4.9 2.9 - - + +
43H LEU* 4.3 12.6 - - + -
47H TYR* 3.7 33.9 - - + -
51H ARG* 3.1 49.5 + - + +
52H ILE* 4.5 9.4 - - + -
77H ILE* 5.4 2.2 - - + -
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Residues in contact with GLU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ASP* 3.1 9.9 + - - +
15H GLU* 3.4 13.9 - - - +
17H LEU* 1.3 79.4 - - - +
19H ARG* 1.3 66.5 + - - +
20H ASP* 3.0 2.3 + - - -
21H GLU 4.7 0.7 + - - -
46H LYS* 3.5 23.4 + - - -
47H TYR* 3.4 19.6 + - - -
189H LYS* 6.5 1.3 - - - -
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Residues in contact with ARG 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H GLU 2.9 15.0 + - - +
16H GLU* 3.5 16.7 + - - +
17H LEU 3.2 0.4 - - - -
18H GLU* 1.3 83.1 - - - +
20H ASP* 1.4 66.9 + - + +
161H ILE* 6.2 0.2 - - - +
162H ARG* 3.0 59.9 - - - +
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Residues in contact with ASP 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H GLU 3.3 6.7 + - - +
17H LEU 3.8 4.3 - - - -
18H GLU 3.0 3.8 + - - -
19H ARG* 1.4 91.9 + - + +
21H GLU* 1.3 57.5 + - - +
22H LYS* 2.4 55.1 + - - +
23H VAL* 2.8 29.2 + - + +
51H ARG* 3.8 0.7 + - - -
75H ARG* 3.6 18.0 - - - -
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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) + - + + + + + -
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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