Contacts of the helix formed by residues 25 - 41 (chain E) in PDB entry 6AHU
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 ASP 25 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LEU* 1.3 78.0 - - - +
26E ASP* 1.3 79.9 + - - +
27E ARG* 3.3 24.8 + - - +
28E VAL* 3.3 23.2 + - + +
29E LEU* 2.9 30.5 + - - +
58E LEU* 4.1 7.4 - - - +
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Residues in contact with ASP 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ASP* 1.3 84.0 + - - +
27E ARG* 1.3 58.6 + - + +
29E LEU* 4.3 4.2 - - - +
30E SER* 3.1 29.1 + - - -
55E VAL* 3.8 32.9 - - + +
58E LEU* 3.4 28.3 - - - +
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Residues in contact with ARG 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ASP* 3.3 18.2 + - - +
26E ASP* 1.3 80.5 - - + +
28E VAL* 1.3 62.8 + - + +
30E SER* 4.2 3.6 - - - -
31E SER* 3.3 22.5 + - - -
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Residues in contact with VAL 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E SER 5.3 7.0 - - - +
24E LEU* 5.6 1.3 - - + -
25E ASP* 3.3 28.1 + - + +
27E ARG* 1.3 80.1 - - + +
29E LEU* 1.3 60.0 + - - +
31E SER* 3.2 6.0 + - - -
32E LEU* 2.8 27.0 + - - +
87E LEU* 4.1 27.4 - - + -
88E GLU 5.9 1.6 - - - +
89E ASN* 6.4 0.7 - - - +
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Residues in contact with LEU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E LEU* 6.2 4.9 - - + -
25E ASP 2.9 17.7 + - - +
26E ASP* 4.3 3.6 - - - +
28E VAL* 1.3 78.7 - - - +
30E SER* 1.3 58.0 + - - +
32E LEU* 4.2 9.0 - - + -
33E VAL* 3.1 44.4 + - + +
53E PHE* 5.0 0.2 - - - -
55E VAL* 3.9 23.6 - - + -
57E TYR 5.9 0.2 - - - +
58E LEU* 4.1 26.0 - - + -
65E VAL* 3.8 28.0 - - + -
66E LEU 5.6 0.2 - - - +
67E LEU* 4.4 1.8 - - + -
97E PHE* 3.9 28.3 - - + -
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Residues in contact with SER 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ASP 3.1 19.7 + - - -
27E ARG* 4.4 3.8 - - - -
29E LEU* 1.3 77.6 - - - +
31E SER* 1.3 58.2 + - - +
32E LEU 3.3 0.2 - - - -
34E ARG* 3.4 57.0 + - - +
53E PHE* 4.6 12.1 - - - -
55E VAL* 5.0 9.6 - - - +
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Residues in contact with SER 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ARG 3.3 17.9 + - - -
28E VAL* 3.2 7.7 + - - -
30E SER* 1.3 77.9 - - - +
32E LEU* 1.3 58.5 + - - +
34E ARG* 5.2 0.9 - - - -
35E ASP* 3.3 24.0 - - - +
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Residues in contact with LEU 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E VAL* 2.8 16.7 + - + +
29E LEU* 3.2 12.9 + - + +
31E SER* 1.3 79.1 - - - +
33E VAL* 1.3 62.1 + - + +
34E ARG 3.4 0.2 - - - -
35E ASP* 3.4 3.4 + - + +
36E THR* 3.1 32.5 + - - +
84E ILE* 4.0 28.7 - - + -
85E THR 5.3 3.6 - - - +
86E TYR 5.2 3.8 - - - +
87E LEU* 3.7 41.5 - - + -
95E PRO* 6.2 1.3 - - + -
97E PHE* 4.1 18.6 - - + -
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Residues in contact with VAL 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LEU* 3.1 34.1 + - + +
32E LEU* 1.3 78.5 - - + +
34E ARG* 1.3 62.8 + - - +
36E THR* 3.3 9.5 - - + +
37E ILE* 3.2 40.3 + - + +
53E PHE* 3.6 33.0 - - + -
67E LEU* 4.4 15.3 - - + -
77E VAL* 4.8 7.0 - - + -
80E ALA* 6.3 1.1 - - + -
81E LEU* 5.9 2.5 - - + -
84E ILE* 5.0 13.9 - - + -
97E PHE* 5.4 2.7 - - + -
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Residues in contact with ARG 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E SER* 3.4 36.9 + - - +
31E SER* 5.2 1.1 - - - -
32E LEU 3.4 0.6 - - - -
33E VAL* 1.3 77.2 - - - +
35E ASP* 1.3 60.7 + - - +
37E ILE* 4.2 8.6 + - + +
38E ALA* 3.8 15.9 + - - +
46E ALA* 4.8 12.1 - - - +
49E CYS 5.1 5.4 - - - +
50E SER* 4.0 32.0 + - - +
53E PHE* 3.0 52.6 + - + -
54E ALA* 4.9 2.4 - - - +
167J ARG* 5.3 3.6 + - - -
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Residues in contact with ASP 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E SER 3.3 21.6 + - - +
32E LEU* 3.4 6.0 + - + +
33E VAL 3.2 0.2 - - - -
34E ARG* 1.3 79.9 - - - +
36E THR* 1.3 59.2 + - - +
37E ILE 3.2 0.4 - - - -
38E ALA* 3.1 10.5 + - - +
39E ARG* 3.0 47.6 + - - +
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Residues in contact with THR 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 3.1 21.7 + - - +
33E VAL* 3.3 16.8 - - + +
35E ASP* 1.3 73.6 + - - +
37E ILE* 1.3 64.0 + - + +
39E ARG* 3.6 15.4 - - - +
40E VAL* 3.1 31.7 + - - +
80E ALA* 4.6 6.6 + - + +
83E PHE 3.3 23.0 + - - -
84E ILE* 3.7 29.0 - - + +
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Residues in contact with ILE 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 3.2 33.6 + - + +
34E ARG* 4.4 8.5 - - + +
35E ASP 3.2 0.2 - - - -
36E THR* 1.3 76.9 - - + +
38E ALA* 1.3 58.4 + - - +
40E VAL* 4.6 0.7 - - - +
41E HIS* 2.8 43.8 + - + +
42E GLY 4.2 0.6 - - - +
45E GLY* 3.4 34.3 - - - +
46E ALA* 3.9 4.3 - - - +
49E CYS* 4.3 16.2 - - + +
53E PHE* 6.1 1.1 - - + -
76E LEU* 4.9 3.4 - - + +
77E VAL* 4.3 25.8 - - + -
80E ALA* 4.0 21.3 - - + -
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Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ARG 3.8 10.3 + - - +
35E ASP* 3.1 15.4 + - - +
37E ILE* 1.3 78.1 - - - +
39E ARG* 1.3 58.1 + - - +
41E HIS 2.9 15.0 - - - +
42E GLY* 4.1 11.0 - - - +
43E THR* 6.3 0.4 - - + -
46E ALA* 4.1 8.6 - - + +
49H LYS 5.4 1.2 - - - +
167J ARG* 3.4 29.2 - - - +
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Residues in contact with ARG 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ASP* 3.0 37.0 + - - +
36E THR* 3.8 15.5 - - - +
37E ILE 3.2 0.6 - - - -
38E ALA* 1.3 81.0 - - + +
40E VAL* 1.3 65.1 + - + +
41E HIS 3.9 0.4 - - - +
49H LYS* 5.4 5.0 - - - +
54H GLU* 4.0 17.7 + - - +
166I ARG* 4.9 21.6 + - - +
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E THR* 3.1 21.2 + - - +
37E ILE* 4.4 1.1 - - - +
39E ARG* 1.3 79.6 - - + +
41E HIS* 1.3 74.3 + - + +
79E SER 5.6 1.1 - - - +
80E ALA* 5.2 11.4 - - + -
83E PHE* 3.7 47.6 - - + +
52H PHE 4.4 0.2 - - - +
53H GLY* 3.3 0.9 - - - -
54H GLU* 2.8 32.9 + - - +
55H VAL* 3.8 23.1 + - + +
166I ARG* 5.2 7.6 - - - +
209I LEU* 5.5 2.5 - - + -
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Residues in contact with HIS 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ILE* 2.8 36.6 + - + +
38E ALA 2.9 18.0 - - - +
39E ARG 3.9 0.5 - - - -
40E VAL* 1.3 94.0 + - + +
42E GLY* 1.3 63.4 + - - +
45E GLY* 4.8 9.2 - - - +
76E LEU* 3.6 49.2 + - + +
79E SER* 5.1 9.9 + - - -
80E ALA* 5.2 4.0 + - + +
49H LYS 4.5 0.9 - - - +
52H PHE* 3.6 16.1 + - - +
53H GLY* 3.5 5.0 - - - -
55H VAL* 5.3 7.7 - - + +
56H ASP* 5.2 5.6 + - - -
209I LEU* 5.0 12.0 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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