Contacts of the helix formed by residues 6 - 24 (chain T) 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 SER 6 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40S THR* 3.5 21.3 - - - -
41S GLU* 2.8 35.0 + - - -
4T LYS 3.7 1.4 + - - -
5T MET* 1.3 77.6 - - - +
7T GLN* 1.3 65.7 + - - +
8T LEU 3.4 2.4 + - - -
9T GLU* 2.8 27.4 + - - +
10T ARG* 2.9 23.7 + - - +
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Residues in contact with GLN 7 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11S SER* 2.8 38.3 + - - +
14S ASP* 3.9 15.8 + - - +
15S VAL* 3.4 14.9 - - + +
18S LYS* 3.1 29.7 + - - +
41S GLU* 3.7 5.6 + - - +
6T SER* 1.3 72.7 - - - +
8T LEU* 1.3 63.6 + - - +
10T ARG* 3.1 26.3 + - - +
11T ASN* 2.9 27.7 + - - +
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Residues in contact with LEU 8 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S ILE* 4.0 32.8 - - + -
15S VAL* 3.9 12.3 - - + +
37S LEU* 5.1 3.6 - - + -
41S GLU* 3.3 31.0 + - + +
71S PHE* 4.4 22.7 - - + -
75S VAL* 4.4 9.9 - - + -
78S MET* 3.7 28.9 - - + -
6T SER* 3.3 3.3 - - - +
7T GLN* 1.3 78.4 - - - +
9T GLU* 1.3 57.6 + - - +
11T ASN* 3.2 5.6 + - - +
12T ILE* 3.0 47.8 + - + +
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Residues in contact with GLU 9 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41S GLU 3.6 11.6 - - - +
42S SER 4.7 0.6 - - - -
43S PRO* 3.4 38.9 - - + +
78S MET* 4.7 4.0 - - + -
4T LYS 4.3 2.4 - - - +
5T MET* 3.5 26.4 - - + +
6T SER* 2.8 44.0 + - - +
8T LEU* 1.3 77.1 - - - +
10T ARG* 1.3 58.1 + - - +
12T ILE* 3.4 9.0 + - - +
13T GLU* 2.9 28.4 + - - +
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Residues in contact with ARG 10 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T MET* 2.7 55.0 + - + -
6T SER* 2.9 15.1 + - - +
7T GLN* 3.1 28.5 + - - +
9T GLU* 1.3 77.3 - - - +
11T ASN* 1.3 61.8 + - - +
13T GLU* 3.3 10.2 + - - +
14T THR* 3.0 31.7 + - - -
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Residues in contact with ASN 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S ALA* 3.5 26.7 - - + +
11S SER* 2.6 54.1 + - - -
12S ILE* 3.5 14.8 - - + +
15S VAL* 4.1 2.6 - - - +
7T GLN* 2.9 26.2 + - - +
8T LEU* 3.2 6.1 + - - +
10T ARG* 1.3 76.4 - - - +
12T ILE* 1.3 66.1 + - - +
14T THR* 3.2 6.4 + - - -
15T ILE* 3.1 25.7 + - - +
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Residues in contact with ILE 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12S ILE* 5.0 0.9 - - + -
75S VAL* 4.4 15.0 - - + +
78S MET* 3.7 43.3 - - + +
79S GLY* 3.8 22.0 - - - +
82S ALA* 4.0 10.5 - - + -
8T LEU* 3.0 33.0 + - + +
9T GLU* 3.7 6.5 - - - +
11T ASN* 1.3 73.9 - - - +
13T GLU* 1.3 66.3 + - - +
15T ILE* 3.1 16.1 + - + +
16T ILE* 2.9 40.3 + - + +
76T PHE* 5.8 0.2 - - + -
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Residues in contact with GLU 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T MET* 3.5 30.9 - - + +
9T GLU 2.9 17.8 + - - +
10T ARG* 3.4 12.5 - - - +
11T ASN 3.2 0.2 - - - -
12T ILE* 1.3 77.6 - - - +
14T THR* 1.3 56.7 + - - +
16T ILE* 3.2 10.0 + - + +
17T ASN* 2.7 56.2 + - - +
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Residues in contact with THR 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S GLU* 3.7 37.6 + - + +
5S LEU* 4.0 10.8 - - - -
8S ALA* 3.8 12.2 - - + +
10T ARG 3.0 14.3 + - - -
11T ASN* 3.2 10.0 + - - -
13T GLU* 1.3 75.6 - - - +
15T ILE* 1.3 56.3 + - - +
17T ASN* 3.7 8.7 + - - +
18T THR* 2.7 43.2 + - - +
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Residues in contact with ILE 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5S LEU* 3.9 22.2 - - + -
8S ALA* 4.9 1.8 - - + -
9S LEU* 3.8 24.7 - - + -
12S ILE* 3.9 16.2 - - + -
75S VAL* 5.7 2.5 - - + -
11T ASN 3.1 14.8 + - - +
12T ILE* 3.1 16.9 + - + +
14T THR* 1.3 77.2 - - - +
16T ILE* 1.3 62.2 + - - +
18T THR* 3.3 1.7 + - - -
19T PHE* 3.0 22.9 + - - +
76T PHE* 3.9 23.3 - - + -
79T PHE* 4.2 6.9 - - + -
80T ILE* 4.9 8.3 - - + -
83T MET* 3.7 28.0 - - + -
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Residues in contact with ILE 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79S GLY 4.1 1.1 - - - +
82S ALA* 3.6 19.5 - - + +
83S HIS* 3.5 35.2 - - + +
86S SER* 4.4 10.5 - - - +
12T ILE* 2.9 26.2 + - + +
13T GLU* 3.7 9.9 - - + +
15T ILE* 1.3 74.8 - - - +
17T ASN* 1.3 68.6 + - - +
19T PHE* 3.4 2.8 + - - +
20T HIS* 3.0 49.8 + - + +
76T PHE* 3.7 26.7 - - + -
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Residues in contact with ASN 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T GLU* 2.7 46.6 + - - +
14T THR* 3.7 7.1 - - - +
16T ILE* 1.3 76.7 - - - +
18T THR* 1.3 62.3 + - - +
20T HIS* 3.3 8.1 + - - +
21T GLN* 3.0 40.8 + - - +
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Residues in contact with THR 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4S GLU* 6.1 0.2 - - - +
5S LEU* 4.1 23.0 + - + +
14T THR* 2.7 35.6 + - - +
15T ILE 3.9 3.1 - - - -
17T ASN* 1.3 69.8 - - - +
19T PHE* 1.3 65.5 + - - +
21T GLN* 3.3 17.0 + - - +
22T TYR* 3.2 31.0 - - + -
40T LEU* 4.2 7.4 - - + -
44T ASP* 3.5 39.3 - - + +
79T PHE* 6.1 0.7 - - - -
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Residues in contact with PHE 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S HIS* 4.4 0.4 - - - -
15T ILE 3.0 17.0 + - - +
16T ILE 3.4 4.0 + - - +
18T THR* 1.3 74.2 - - - +
20T HIS* 1.3 70.8 + + - +
22T TYR 3.2 3.6 + - - -
23T SER* 2.9 36.9 + - - -
30T ASP* 3.3 42.2 - - - -
31T THR* 4.1 2.5 - - - -
32T LEU* 3.7 26.7 - - + +
40T LEU* 4.2 9.8 - - - +
74T LEU 3.6 17.5 - - - -
75T SER 3.8 3.1 - - - -
76T PHE* 3.5 46.0 - + + -
79T PHE* 3.7 25.5 - + + -
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Residues in contact with HIS 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S HIS* 3.5 2.7 + + - -
86S SER* 3.6 11.4 - - - -
87S HIS* 3.1 15.1 + + - -
16T ILE* 3.0 41.4 + - + +
17T ASN* 3.3 9.6 + - - +
19T PHE* 1.3 80.3 - + - +
21T GLN* 1.3 64.4 + - + +
22T TYR 3.1 3.3 + - - -
23T SER* 3.4 13.9 + - - -
24T VAL* 3.2 28.1 + - + +
29T PRO 5.0 2.5 - - - -
30T ASP* 3.8 0.9 - - - -
202T MN 2.3 36.0 + - - -
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Residues in contact with GLN 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17T ASN* 3.0 34.4 + - - +
18T THR* 3.7 19.6 + - - +
19T PHE 3.3 0.4 - - - -
20T HIS* 1.3 76.0 - - + +
22T TYR* 1.3 74.6 + - + +
24T VAL* 3.8 8.4 - - - +
25T LYS* 3.5 23.0 - - - +
44T ASP* 4.9 2.3 - - - +
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Residues in contact with TYR 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T THR* 3.2 25.6 - - + -
19T PHE 3.2 2.3 + - - +
21T GLN* 1.3 91.2 + - + +
23T SER* 1.3 65.0 + - - +
24T VAL 3.2 2.2 - - - -
25T LYS* 3.2 20.8 + - + +
32T LEU* 3.6 18.2 - - + -
36T GLU* 3.0 31.4 - - + +
39T GLU* 3.4 49.6 - - + -
40T LEU* 3.7 25.8 - - + -
43T LYS* 3.7 18.6 - - + +
44T ASP* 2.6 32.1 + - - -
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Residues in contact with SER 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T PHE* 2.9 31.9 + - - -
20T HIS* 3.3 26.2 + - - -
22T TYR* 1.3 76.8 - - - +
24T VAL* 1.3 59.1 + - - +
28T HIS 3.1 8.1 - - - +
29T PRO 2.8 20.4 + - - -
31T THR 3.6 21.3 - - - -
32T LEU* 3.5 6.9 - - - +
36T GLU* 3.1 3.1 - - - +
203T CA 2.4 26.2 - - - -
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Residues in contact with VAL 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20T HIS* 3.2 17.2 + - + +
21T GLN* 3.8 14.1 - - - +
23T SER* 1.3 80.9 + - - +
25T LYS* 1.3 70.5 + - + +
26T LEU 3.5 1.5 + - - +
27T GLY 5.3 0.9 - - - +
29T PRO* 3.5 28.2 - - + +
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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
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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