Contacts of the helix formed by residues 30 - 51 (chain G) in PDB entry 3O65
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 SER 30 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E GLU* 2.6 36.0 + - - -
17G GLN* 4.2 3.6 - - - +
28G TYR 5.6 0.2 - - - -
29G PHE* 1.3 75.3 - - - +
31G PRO* 1.3 79.7 - - - +
32G VAL* 3.6 11.8 - - - +
33G GLU* 2.8 22.8 + - - +
34G LEU* 3.1 14.5 + - - +
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Residues in contact with PRO 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 4.7 19.7 - - + -
17G GLN* 3.5 21.6 - - - +
30G SER* 1.3 91.0 - - - +
32G VAL* 1.3 63.5 + - - +
33G GLU 3.1 0.3 + - - -
34G LEU* 3.2 9.3 + - + +
35G ALA* 2.9 23.8 + - - +
76G PHE* 4.8 5.3 - - + -
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Residues in contact with VAL 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E GLN 4.6 4.3 - - - +
26E GLY* 4.4 8.5 - - - -
27E GLU* 4.0 13.9 - - + +
28E TYR* 3.8 39.4 + - + +
30G SER* 3.6 15.0 - - - +
31G PRO* 1.3 80.8 - - - +
33G GLU* 1.3 68.6 - - - +
35G ALA* 3.4 8.4 - - + +
36G SER* 3.1 24.1 + - - +
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Residues in contact with GLU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR* 3.0 26.4 - - + +
29E PHE* 4.8 1.6 - - - -
33E GLU* 3.1 21.4 - - - +
88E TRP* 3.3 38.3 + - + -
28G TYR 3.2 17.0 - - - +
29G PHE* 3.5 21.9 - - + -
30G SER* 2.8 25.8 + - - +
32G VAL* 1.3 82.0 - - + +
34G LEU* 1.3 66.2 + - - +
36G SER 3.2 9.5 + - - -
37G ILE* 3.2 17.5 + - + +
87G PHE* 4.0 7.8 - - - -
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Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU* 6.4 0.4 - - + -
16G ALA* 4.4 2.7 - - + +
17G GLN* 3.6 41.5 - - + +
20G LEU* 3.9 26.5 - - + -
29G PHE* 4.4 14.8 - - + -
30G SER 3.1 12.5 + - - +
31G PRO* 3.7 7.2 - - + +
33G GLU* 1.3 76.0 - - - +
35G ALA* 1.3 68.2 + - - +
37G ILE* 3.1 12.7 + - + +
38G ALA* 3.0 22.5 + - - +
76G PHE* 3.7 34.7 - - + -
80G VAL* 4.1 19.3 - - + +
81G ILE* 6.1 0.7 - - + -
84G ALA* 4.7 0.2 - - + -
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Residues in contact with ALA 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G PRO 2.9 14.2 + - - +
32G VAL* 3.4 14.8 - - + +
34G LEU* 1.3 79.0 - - - +
36G SER* 1.3 58.5 + - - +
38G ALA* 3.0 4.3 + - - +
39G HIS* 2.9 39.8 + - + +
70G MSE 4.0 30.7 - - + -
76G PHE* 4.1 2.2 - - + -
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Residues in contact with SER 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR* 2.8 27.6 + - - -
88E TRP* 3.9 15.9 - - - -
171E PRO* 3.7 16.4 - - - +
172E ASP 4.7 4.9 + - - -
32G VAL* 3.1 10.6 + - - +
33G GLU 3.2 4.4 + - - -
35G ALA* 1.3 78.7 - - - +
37G ILE* 1.3 60.9 + - - +
39G HIS* 3.6 13.6 + - - +
40G GLN* 3.2 26.8 + - - +
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Residues in contact with ILE 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E TRP* 3.8 15.5 - - + -
29G PHE* 4.5 6.3 - - + -
33G GLU 3.2 16.8 + - - +
34G LEU* 3.1 17.6 + - + +
36G SER* 1.3 73.9 - - - +
38G ALA* 1.3 67.8 + - - +
40G GLN* 3.0 15.9 + - - +
41G LEU* 2.8 37.4 - - + +
80G VAL* 4.1 14.4 - - + +
83G ASN* 3.8 18.4 - - + -
84G ALA* 4.0 31.0 - - + -
87G PHE* 4.2 15.5 - - + -
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Residues in contact with ALA 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G LEU 3.0 12.1 + - - +
35G ALA 3.1 10.1 - - - +
37G ILE* 1.3 76.9 - - - +
39G HIS* 1.3 59.2 + - - +
41G LEU* 3.2 4.4 + - - +
42G ASP* 2.9 34.7 + - - +
69G ASN* 3.8 4.2 - - + +
70G MSE 3.9 31.9 - - + -
76G PHE* 4.5 1.8 - - + -
80G VAL* 3.6 25.7 - - + +
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Residues in contact with HIS 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E ASP* 5.7 12.3 - - + +
35G ALA* 2.9 31.2 + - + +
36G SER* 3.8 13.0 - - - +
37G ILE 3.1 0.2 - - - -
38G ALA* 1.3 74.4 - - - +
40G GLN* 1.3 64.4 + - - +
42G ASP* 3.2 18.5 + - - +
43G GLU* 3.0 21.7 + - - +
67G SER* 4.9 7.1 - - - -
70G MSE 4.2 20.7 - - + +
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Residues in contact with GLN 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E PHE 5.3 3.5 - - - +
88E TRP* 3.8 39.3 + - - +
169E ASP 5.8 1.2 + - - -
171E PRO* 5.4 7.3 - - - +
36G SER* 3.2 15.0 + - - +
37G ILE* 3.0 13.9 + - - +
39G HIS* 1.3 72.1 - - - +
41G LEU* 1.3 73.7 + - + +
43G GLU* 2.9 19.2 + - - +
44G GLU* 3.1 22.9 + - + +
83G ASN* 5.7 1.6 + - - -
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Residues in contact with LEU 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ILE* 2.8 41.3 + - + +
38G ALA* 3.4 5.4 - - - +
40G GLN* 1.3 84.8 - - + +
42G ASP* 1.3 62.1 + - - +
44G GLU* 3.4 15.8 + - - +
45G GLU* 3.2 24.1 + - - +
69G ASN* 3.1 22.9 - - - +
79G GLN* 4.4 26.9 - - + +
80G VAL 4.9 0.7 - - - +
83G ASN* 3.1 37.7 - - + +
8H LEU* 4.3 24.8 - - + +
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Residues in contact with ASP 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ALA* 2.9 22.2 + - - +
39G HIS* 3.4 21.5 + - - +
40G GLN 3.0 0.2 - - - -
41G LEU* 1.3 77.5 - - - +
43G GLU* 1.3 63.4 + - - +
45G GLU* 3.0 10.5 + - - +
46G ARG* 2.9 22.3 + - - +
66G PRO 5.0 4.5 - - - +
67G SER* 2.9 29.6 - - - -
68G GLU 2.4 29.2 + - - +
69G ASN* 2.8 13.0 - - - +
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Residues in contact with GLU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G HIS 3.0 11.9 + - - +
40G GLN* 2.9 12.7 + - - +
42G ASP* 1.3 76.0 - - - +
44G GLU* 1.3 64.7 + - + +
46G ARG* 3.1 38.5 + - - +
47G MSE 3.1 29.7 + - + +
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Residues in contact with GLU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G GLN* 3.1 21.7 + - + +
41G LEU* 3.5 23.2 - - - +
43G GLU* 1.3 78.1 - - + +
45G GLU* 1.3 60.8 + - - +
47G MSE 3.3 13.8 + - - +
48G ARG* 3.2 36.0 + - - +
83G ASN* 4.9 4.3 + - - -
8H LEU* 3.3 37.7 - - + +
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Residues in contact with GLU 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LEU 3.2 8.9 + - - +
42G ASP* 3.0 11.1 + - - +
44G GLU* 1.3 73.6 - - - +
46G ARG* 1.3 66.5 + - - +
48G ARG* 3.4 9.0 + - - +
49G MSE 3.0 37.5 + - + +
68G GLU* 4.5 8.9 - - - +
69G ASN* 3.5 20.6 - - - +
79G GLN* 3.7 14.4 + - - -
8H LEU* 3.8 17.2 - - + +
42H ARG* 3.5 23.1 + - - -
70H VAL* 3.7 23.5 - - + +
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Residues in contact with ARG 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G ASP 2.9 12.4 + - - +
43G GLU* 3.1 36.7 + - - +
45G GLU* 1.3 76.6 - - - +
47G MSE 1.3 92.0 + - - +
49G MSE 3.8 5.9 - - - +
50G ALA* 3.2 38.0 + - - +
62G PHE* 5.4 16.4 - - + -
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Residues in contact with MSE 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G GLU* 3.1 22.9 + - + +
44G GLU* 3.4 15.5 - - - +
45G GLU 3.1 0.6 - - - -
46G ARG* 1.3 101.5 - - - +
48G ARG* 1.3 83.1 + - - +
49G MSE 2.9 3.1 + - - -
50G ALA* 3.0 14.0 + - - +
51G GLU* 3.6 19.1 + - - +
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Residues in contact with ARG 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G GLU* 3.2 28.3 + - - +
45G GLU* 3.4 8.9 + - - +
47G MSE 1.3 95.9 - - - +
49G MSE 1.3 57.6 + - - +
51G GLU* 3.2 18.7 - - - +
6H LYS* 5.0 12.1 - - - +
8H LEU* 4.0 24.9 - - + +
44H ILE* 4.4 22.3 - - + +
47H GLY* 3.1 21.9 + - - -
68H HIS* 2.8 48.2 + - + +
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Residues in contact with MSE 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G GLU* 3.0 27.4 + - + +
46G ARG* 3.8 6.3 - - - +
47G MSE 2.9 1.0 + - - -
48G ARG* 1.3 74.5 - - - +
50G ALA* 1.3 64.1 + - - +
51G GLU 3.1 4.1 + - - -
52G GLY 3.8 2.4 + - - -
53G GLY 4.3 8.0 + - - +
54G VAL* 4.7 3.2 - - + +
58G GLU* 3.6 31.8 - - - +
42H ARG* 6.4 0.4 - - - -
44H ILE* 3.5 32.8 - - + -
47H GLY* 3.5 33.2 - - - +
49H GLN* 3.5 44.0 - - + +
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Residues in contact with ALA 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G ARG* 3.2 31.3 + - + +
47G MSE 3.0 7.1 + - - +
49G MSE 1.3 74.6 - - - +
51G GLU* 1.3 67.2 + - - +
52G GLY 3.4 0.2 - - - -
53G GLY* 2.9 15.3 + - - -
54G VAL* 4.5 15.5 - - + +
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Residues in contact with GLU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G MSE 3.6 15.6 - - - +
48G ARG* 3.2 22.1 - - - +
49G MSE 3.1 0.6 - - - -
50G ALA* 1.3 81.0 - - - +
52G GLY* 1.3 59.1 + - - +
53G GLY 3.3 2.1 + - - -
46H ALA* 3.3 26.2 - - + +
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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