Contacts of the helix formed by residues 31 - 42 (chain S) in PDB entry 4GGF
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 ARG 31 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K ARG* 5.0 16.6 - - - +
32K ASP* 5.6 0.8 + - - -
30S TYR* 1.3 73.4 - - - +
32S ASP* 1.3 62.4 + - - +
34S LEU* 3.3 4.0 + - - +
35S LYS* 3.3 19.8 + - - +
51S ALA* 5.6 2.9 - - + +
52S ASP* 3.0 48.2 + - - +
55S PHE* 3.5 51.5 - - + +
56S LYS* 5.2 2.4 - - - +
64S GLY 4.3 1.2 + - - -
103S GOL 2.9 46.8 + - - +
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Residues in contact with ASP 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K TYR* 3.8 20.9 - - - +
31K ARG* 5.1 9.7 + - + +
32K ASP* 5.8 2.5 - - - -
64K GLY* 4.6 6.1 - - - +
23S LYS* 2.9 34.1 + - - -
30S TYR* 3.5 12.5 - - - +
31S ARG* 1.3 79.3 - - - +
33S ASP* 1.3 77.1 + - - +
35S LYS* 3.3 16.6 + - - +
36S LYS* 3.4 16.6 + - - +
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Residues in contact with ASP 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19S TYR* 4.0 22.3 - - + +
22S ILE* 3.7 22.5 - - + +
23S LYS* 2.8 26.6 + - - +
28S ALA 4.2 1.0 - - - +
29S VAL* 3.6 16.6 - - + -
30S TYR* 3.0 38.8 + - - +
32S ASP* 1.3 81.5 + - - +
34S LEU* 1.3 59.8 + - - +
36S LYS* 3.1 11.5 + - - +
37S LEU* 2.9 26.9 + - - +
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Residues in contact with LEU 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S VAL* 3.4 17.9 - - + +
30S TYR 2.8 19.0 + - - +
31S ARG 3.6 5.6 - - - +
32S ASP 3.3 0.4 - - - -
33S ASP* 1.3 70.6 - - - +
35S LYS* 1.3 61.2 + - - +
37S LEU* 3.2 21.7 + - + +
38S LEU* 2.8 43.7 + - + +
51S ALA 4.0 6.5 - - - +
54S TRP 4.2 3.8 - - - -
55S PHE* 3.6 48.7 - - + +
58S LEU* 4.2 21.3 - - + -
66S VAL* 4.4 10.1 - - + -
71S PHE* 5.8 0.9 - - + -
74S LEU* 5.0 3.1 - - + -
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Residues in contact with LYS 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S ARG 3.3 9.1 + - - +
32S ASP* 3.6 11.0 - - - +
33S ASP 3.3 0.4 - - - -
34S LEU* 1.3 78.1 - - - +
36S LYS* 1.3 58.0 + - + +
38S LEU* 3.4 1.9 + - - +
39S GLU* 2.7 69.3 + - + +
51S ALA* 4.0 19.2 - - + +
102S GOL 2.7 39.0 - - - +
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Residues in contact with LYS 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ASN* 4.4 24.0 + - + +
71C ASP* 4.5 14.6 + - - +
19S TYR* 3.8 17.3 - - + -
22S ILE* 4.5 19.3 - - + +
32S ASP 3.4 11.1 + - - +
33S ASP* 3.1 12.2 + - - +
35S LYS* 1.3 74.6 - - + +
37S LEU* 1.3 65.1 + - - +
39S GLU* 3.5 10.3 + - - +
40S THR* 2.8 35.0 + - - +
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Residues in contact with LEU 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S VAL* 5.1 0.9 - - + +
16S TYR* 5.0 4.3 - - + -
19S TYR* 3.6 45.5 - - + -
29S VAL* 4.6 9.6 - - + -
33S ASP 2.9 12.8 + - - +
34S LEU* 3.2 21.7 + - + +
36S LYS* 1.3 75.1 - - - +
38S LEU* 1.3 63.8 + - + +
40S THR 3.2 0.9 + - - -
41S GLU* 2.8 47.2 + - + +
42S SER* 5.9 1.1 - - - -
71S PHE* 3.9 29.2 - - + -
74S LEU* 3.9 25.8 - - + -
78S MET* 6.2 0.2 - - - -
8T LEU* 5.1 2.7 - - + -
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Residues in contact with LEU 38 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S LEU* 2.8 31.7 + - + +
35S LYS* 3.9 2.7 - - - +
37S LEU* 1.3 80.1 - - + +
39S GLU* 1.3 63.7 + - + +
42S SER* 2.8 43.4 + - - +
46S ILE* 4.1 10.5 - - + +
47S ARG* 3.3 15.4 - - + +
50S GLY 5.0 0.2 - - - -
51S ALA* 3.7 33.0 - - + +
54S TRP* 3.9 33.9 - - + -
58S LEU* 6.1 0.2 - - + -
74S LEU* 4.1 24.2 - - + -
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Residues in contact with GLU 39 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S LYS* 2.7 57.8 + - + +
36S LYS* 3.9 10.5 - - - +
37S LEU 3.3 0.2 - - - -
38S LEU* 1.3 78.3 - - + +
40S THR* 1.3 60.0 + - - +
42S SER 4.6 1.4 - - - +
47S ARG* 3.6 31.9 + - + +
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Residues in contact with THR 40 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S LYS* 5.2 2.7 - - - +
19S TYR* 3.2 27.7 + - - +
36S LYS* 2.8 19.5 + - - +
39S GLU* 1.3 78.5 - - - +
41S GLU* 1.3 68.7 + - - +
42S SER 3.7 0.7 - - - -
6T SER* 3.5 15.1 - - - -
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Residues in contact with GLU 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S VAL* 3.7 15.9 - - + +
18S LYS* 2.8 26.3 + - - -
19S TYR* 2.7 33.5 + - + +
37S LEU* 2.8 24.0 + - + +
40S THR* 1.3 84.0 - - - +
42S SER* 1.3 60.9 + - - +
78S MET* 4.0 6.3 - - - +
6T SER* 2.8 27.6 + - - -
7T GLN* 3.7 4.2 + - - +
8T LEU* 3.3 40.6 + - + +
9T GLU* 3.6 9.5 - - - +
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Residues in contact with SER 42 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37S LEU* 5.9 1.1 - - - -
38S LEU* 2.8 31.9 + - - +
39S GLU 4.6 2.1 - - - +
40S THR 5.1 0.2 - - - -
41S GLU* 1.3 81.4 - - - +
43S PRO* 1.3 71.7 - - - +
46S ILE* 3.5 23.4 - - - +
47S ARG* 3.1 30.3 + - - +
78S MET* 4.0 13.0 - - - -
9T GLU* 4.6 2.5 - - - -
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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