Contacts of the helix formed by residues 3 - 21 (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 THR 3 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1S MET 5.2 0.9 - - - +
2S LEU* 1.3 75.7 - - - +
4S GLU* 1.3 59.7 + - - +
5S LEU 3.4 2.2 + - - -
6S GLU* 2.9 31.9 + - - +
7S LYS* 2.9 29.5 + - - +
43T LYS 3.4 25.6 - - - +
44T ASP* 2.7 33.4 + - - +
46T GLN* 3.8 19.3 - - + +
47T ASN* 4.1 1.6 - - - +
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Residues in contact with GLU 4 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S THR* 1.3 74.4 - - - +
5S LEU* 1.3 58.2 + - - +
7S LYS* 3.4 25.5 + - - +
8S ALA* 3.0 27.4 + - - +
14T THR* 3.7 17.4 + - + +
44T ASP* 5.6 0.4 + - - -
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Residues in contact with LEU 5 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S THR* 3.2 1.4 + - - +
4S GLU* 1.3 76.4 - - - +
6S GLU* 1.3 65.7 + - - +
8S ALA* 3.1 12.7 + - + +
9S LEU* 3.1 15.8 + - + +
14T THR* 4.0 6.9 - - + +
15T ILE* 3.9 38.4 - - + +
18T THR* 4.1 23.3 + - + +
40T LEU* 4.2 9.2 - - + -
44T ASP* 3.8 30.8 + - + +
45T LEU* 3.7 29.2 - - + -
79T PHE* 5.2 1.3 - - + -
83T MET* 4.0 20.2 - - - -
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Residues in contact with GLU 6 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S LEU* 3.5 8.8 - - + +
3S THR* 2.9 28.3 + - - +
5S LEU* 1.3 77.5 - - - +
7S LYS* 1.3 61.0 + - - +
9S LEU* 3.2 6.2 + - - +
10S ASN* 3.1 20.6 + - - +
44T ASP 3.5 7.6 - - - +
45T LEU* 3.2 15.7 - - + -
47T ASN* 2.8 58.7 + - - +
48T PHE* 2.9 49.7 + - + -
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Residues in contact with LYS 7 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1S MET* 3.4 34.2 - - - +
2S LEU* 3.5 32.3 + - + +
3S THR 2.9 17.6 + - - +
4S GLU* 3.6 25.7 + - - +
6S GLU* 1.3 75.2 - - - +
8S ALA* 1.3 56.9 + - - +
10S ASN* 3.4 6.9 + - - +
11S SER* 2.9 30.4 + - - -
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Residues in contact with ALA 8 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S GLU 3.0 14.2 + - - +
5S LEU* 3.1 12.7 + - + +
7S LYS* 1.3 76.2 - - - +
9S LEU* 1.3 63.3 + - - +
11S SER 3.3 0.9 + - - -
12S ILE* 3.1 27.0 + - - +
11T ASN* 3.5 34.0 - - + +
14T THR* 3.8 21.8 - - + +
15T ILE* 4.9 2.5 - - + -
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Residues in contact with LEU 9 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5S LEU* 3.1 14.2 + - + +
6S GLU* 3.2 6.3 + - - +
8S ALA* 1.3 74.6 - - - +
10S ASN* 1.3 62.5 + - - +
12S ILE* 3.1 19.1 + - + +
13S ILE* 3.4 8.1 + - - +
15T ILE* 3.8 33.2 - - + -
45T LEU* 4.6 9.9 - - + -
48T PHE* 3.9 27.8 - - + -
83T MET* 4.1 27.1 - - + +
86T LEU* 3.9 20.2 - - + -
87T THR* 3.5 31.4 - - - +
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Residues in contact with ASN 10 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S LEU* 3.3 31.1 - - - +
6S GLU 3.1 13.7 + - - +
7S LYS* 3.9 5.6 - - - +
9S LEU* 1.3 74.9 - - - +
11S SER* 1.3 56.3 + - - +
13S ILE* 3.2 16.2 - - - +
14S ASP* 3.0 30.8 + - - +
48T PHE* 3.7 9.0 - - - -
90T SER* 2.8 30.6 + - - -
94T MET* 3.7 12.9 - - + +
109T LEU 5.1 0.4 + - - -
111T GLU* 4.2 11.3 + - - -
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Residues in contact with SER 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S LYS 2.9 18.3 + - - -
8S ALA* 4.3 0.2 - - - -
9S LEU 3.2 0.2 - - - -
10S ASN* 1.3 72.9 - - - +
12S ILE* 1.3 53.6 + - - +
14S ASP* 3.1 12.8 + - - +
15S VAL* 2.8 35.2 + - - +
7T GLN* 2.8 25.6 + - - +
11T ASN* 2.6 37.4 + - - -
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Residues in contact with ILE 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S ALA 3.1 14.3 + - - +
9S LEU* 3.1 18.5 + - + +
11S SER* 1.3 71.8 - - - +
13S ILE* 1.3 65.3 + - - +
15S VAL* 3.3 6.6 + - - +
16S TYR 3.1 18.2 + - - -
68S PHE* 5.0 0.2 - - + -
71S PHE* 3.7 25.2 - - + -
72S LEU* 4.5 2.7 - - + -
75S VAL* 3.9 28.9 - - + -
8T LEU* 4.0 11.0 - - + -
11T ASN* 3.8 21.5 - - + +
12T ILE* 5.0 1.1 - - + -
15T ILE* 3.9 27.6 - - + -
87T THR* 4.1 16.2 - - + +
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Residues in contact with ILE 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S LEU 3.9 2.7 - - - +
10S ASN* 3.2 32.9 + - - +
12S ILE* 1.3 77.0 - - - +
14S ASP* 1.3 65.3 + - - +
16S TYR* 3.2 4.0 + - - +
17S HIS* 2.8 48.3 + - + +
68S PHE* 3.7 24.5 - - + -
87T THR* 3.6 26.0 - - + +
90T SER* 4.1 1.1 - - - +
91T HIS* 3.6 28.3 - - + +
94T MET* 3.8 13.5 - - + -
105T HIS* 3.9 10.8 - - + -
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Residues in contact with ASP 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S ASN* 3.0 21.6 + - - +
11S SER* 3.1 13.7 + - - +
13S ILE* 1.3 79.2 - - - +
15S VAL* 1.3 64.2 + - - +
17S HIS* 3.0 8.6 + - - +
18S LYS* 3.0 26.8 + - + +
7T GLN* 3.9 12.4 + - - +
94T MET* 5.9 1.7 - - - +
105T HIS* 5.3 5.5 + - - -
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Residues in contact with VAL 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S SER 2.8 21.5 + - - +
12S ILE* 3.6 9.2 - - - +
13S ILE 3.3 0.2 - - - -
14S ASP* 1.3 71.7 - - - +
16S TYR* 1.3 66.3 + - - +
18S LYS* 3.2 13.7 + - - +
19S TYR* 3.1 20.1 - - + -
37S LEU* 5.4 0.7 - - + -
41S GLU* 3.7 33.2 - - + +
71S PHE* 4.6 11.0 - - + -
7T GLN* 3.4 33.9 - - + +
8T LEU* 3.9 22.9 - - + +
11T ASN* 4.1 5.2 - - - +
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Residues in contact with TYR 16 (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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12S ILE 3.1 6.4 + - - +
13S ILE 3.2 8.0 + - - +
15S VAL* 1.3 75.4 - - - +
17S HIS* 1.3 69.1 + + - +
19S TYR* 3.0 11.6 + - - +
20S SER* 2.9 46.2 + - - -
27S HIS* 3.0 33.4 + + - -
28S ALA 3.4 0.9 + - - -
29S VAL* 3.4 18.6 + - + -
37S LEU* 5.0 1.6 - - + -
66S VAL* 2.7 25.7 + - + -
67S ASN* 3.2 19.1 - - - -
68S PHE* 3.6 28.3 - + + -
71S PHE* 3.5 44.1 - + + -
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Residues in contact with HIS 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S ILE* 2.8 28.3 + - + +
14S ASP* 3.0 10.3 + - - +
16S TYR* 1.3 87.5 - + - +
18S LYS* 1.3 66.1 + - - +
19S TYR 3.0 1.8 - - - -
20S SER* 3.3 16.6 - - - -
21S LEU* 3.0 40.9 + - + +
27S HIS* 3.3 7.3 + + - -
68S PHE* 5.0 1.1 - + - -
91T HIS* 3.2 25.5 + + - -
103T HIS* 3.3 20.4 - + - -
105T HIS* 3.5 11.4 - + + -
201T MN 2.3 29.0 + - - -
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Residues in contact with LYS 18 (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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14S ASP* 3.0 20.4 + - + +
15S VAL* 3.2 11.4 + - - +
17S HIS* 1.3 77.8 - - - +
19S TYR* 1.3 73.0 + - + +
21S LEU* 5.1 0.7 - - - +
22S ILE* 3.4 18.4 + - - +
40S THR* 5.2 3.2 - - - +
41S GLU* 2.8 32.7 + - - -
7T GLN* 3.1 29.9 + - - +
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Residues in contact with TYR 19 (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 3.1 20.0 - - - -
16S TYR 3.0 5.2 + - - +
18S LYS* 1.3 93.2 - - + +
20S SER* 1.3 63.3 + - - +
21S LEU 3.3 1.6 - - - -
22S ILE* 3.3 35.0 + - + +
29S VAL* 4.0 17.7 - - + -
33S ASP* 4.0 16.8 - - + +
36S LYS* 3.8 17.7 - - + -
37S LEU* 3.6 48.7 - - + -
40S THR* 3.2 22.1 - - - +
41S GLU* 2.7 38.1 + - + +
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Residues in contact with SER 20 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S TYR* 2.9 41.2 + - - -
17S HIS* 3.3 20.3 - - - -
19S TYR* 1.3 78.4 - - - +
21S LEU* 1.3 60.8 + - - +
22S ILE 3.2 1.4 + - - -
23S LYS 3.8 5.5 - - - +
24S GLY 5.1 0.2 - - - +
25S ASN 3.3 20.8 - - - +
26S PHE* 2.7 28.2 + - - +
28S ALA 3.6 14.3 - - - +
29S VAL* 3.7 3.8 - - - +
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Residues in contact with LEU 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17S HIS* 3.0 35.5 + - + +
18S LYS 5.1 1.1 - - - +
20S SER* 1.3 77.0 - - - +
22S ILE* 1.3 65.3 + - - +
23S LYS* 3.4 1.9 + - - -
26S PHE* 3.7 36.5 - - + +
103T HIS* 3.7 40.2 - - + +
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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