Contacts of the helix formed by residues 3 - 19 (chain G) in PDB entry 4B86
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 PRO 3 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET 3.9 0.2 - - - +
2G ASN* 1.4 90.3 - - - +
4G VAL* 1.3 53.2 + - - +
5G ASN 3.6 1.8 - - - -
6G ALA* 4.4 3.6 - - + -
7G THR* 2.7 31.0 + - - +
63G GLN* 3.6 2.5 - - - +
65G TYR* 3.3 25.5 - - + +
93G ASN* 3.5 23.6 - - - +
95G GLN* 3.8 33.0 - - + +
96G LEU* 3.8 19.7 - - + -
99G LEU* 4.5 8.3 - - + -
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Residues in contact with VAL 4 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F GLN* 4.1 10.1 - - + +
241F GLN* 3.5 38.1 - - + +
2G ASN* 3.0 28.1 + - + +
3G PRO* 1.3 70.4 - - - +
5G ASN* 1.3 63.2 + - - +
7G THR* 3.0 6.1 + - - +
8G ALA* 2.9 34.7 + - + +
61G THR* 6.3 3.4 - - + -
63G GLN* 3.2 12.6 - - - +
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Residues in contact with ASN 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G VAL* 1.3 77.5 - - - +
6G ALA* 1.3 58.2 + - - +
8G ALA* 3.3 5.7 + - - +
9G LEU* 2.9 42.1 + - + +
41G SER* 4.8 9.4 - - - -
61G THR 5.5 0.2 + - - -
63G GLN* 2.8 36.7 + - + +
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Residues in contact with ALA 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G PRO* 4.1 10.2 + - + +
4G VAL 3.4 0.6 - - - -
5G ASN* 1.3 78.3 - - - +
7G THR* 1.3 58.6 + - - +
9G LEU* 3.5 0.4 + - - -
10G TYR* 2.9 28.4 + - - +
38G PHE* 3.4 6.6 - - - -
41G SER* 3.5 28.0 - - - +
42G LEU* 3.8 17.5 - - + -
63G GLN* 4.2 3.1 - - - +
65G TYR* 5.4 1.3 - - + -
96G LEU* 4.9 2.0 - - + -
99G LEU* 3.7 22.0 - - + -
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Residues in contact with THR 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E LEU* 4.6 6.7 - - + -
236E GLN* 4.1 20.4 - - - +
233F ILE* 4.8 2.0 - - + -
237F GLN* 3.7 22.0 + - - +
3G PRO 2.7 22.3 + - - +
4G VAL* 3.0 13.3 + - - -
6G ALA* 1.3 73.4 - - - +
8G ALA* 1.3 58.0 + - - +
10G TYR* 3.2 6.7 + - + +
11G ILE* 2.9 39.0 + - - +
95G GLN* 4.3 5.6 - - - +
99G LEU* 3.7 28.7 - - + -
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Residues in contact with ALA 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G VAL* 2.9 22.6 + - + +
5G ASN* 3.3 7.2 + - - +
7G THR* 1.3 76.5 + - - +
9G LEU* 1.3 58.6 + - + +
11G ILE* 3.3 11.1 + - - +
12G SER* 3.0 31.8 + - - -
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Residues in contact with LEU 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ASN* 2.9 26.8 + - + +
6G ALA 3.8 0.2 - - - +
8G ALA* 1.3 77.5 - - + +
10G TYR* 1.3 57.4 + - - +
12G SER* 3.7 5.1 - - - +
13G ALA* 2.9 31.7 + - - +
34G LEU* 4.0 26.2 - - + +
37G TYR* 3.3 40.8 - - + +
38G PHE* 3.6 20.6 - - + +
41G SER* 3.6 17.3 - - - +
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Residues in contact with TYR 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E ILE* 3.8 13.5 - - - +
229E GLN* 2.8 44.4 + - + +
232E LEU* 4.7 5.4 - - + -
230F LEU* 3.9 10.8 - - + -
233F ILE* 4.7 7.0 - - + -
6G ALA 2.9 18.5 + - - +
7G THR* 3.2 9.2 + - + +
9G LEU* 1.3 74.3 - - - +
11G ILE* 1.3 65.0 + - + +
13G ALA* 4.7 0.2 - - - -
14G SER* 2.9 48.1 + - - -
38G PHE* 3.4 31.6 - + + -
99G LEU* 4.4 15.3 - - + -
102G CYS* 3.5 39.8 - - + -
106G LEU* 4.5 6.5 - - + -
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Residues in contact with ILE 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F LEU* 4.0 26.2 - - + +
233F ILE* 4.3 14.6 - - + -
234F GLU* 3.8 35.9 - - + +
237F GLN* 5.3 3.6 - - + -
7G THR* 2.9 27.7 + - - +
8G ALA* 3.6 9.0 - - - +
10G TYR* 1.3 76.0 - - + +
12G SER* 1.3 58.9 + - - +
14G SER* 4.1 0.5 - - - -
15G ARG* 2.9 74.9 + - + +
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Residues in contact with SER 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ALA 3.0 18.9 + - - -
9G LEU* 3.7 4.6 - - - +
11G ILE* 1.3 76.9 - - - +
13G ALA* 1.3 58.3 + - - +
15G ARG* 3.8 3.4 - - - +
16G LEU* 2.9 39.4 + - - +
34G LEU* 3.3 27.5 - - - +
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Residues in contact with ALA 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G LEU 2.9 22.2 + - - +
10G TYR 3.9 2.5 - - - +
12G SER* 1.3 72.5 - - - +
14G SER* 1.3 57.4 + - - +
16G LEU* 3.2 4.7 + - - +
17G VAL* 2.9 36.0 + - + +
34G LEU* 3.3 14.6 - - + +
35G LEU* 3.9 27.4 - - + -
38G PHE* 4.4 8.7 - - + -
106G LEU* 4.1 9.2 - - + -
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Residues in contact with SER 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E ILE* 4.8 0.9 - - - +
229E GLN* 4.5 0.8 + - - -
230F LEU* 3.8 25.8 - - - -
10G TYR* 2.9 46.3 + - - -
13G ALA* 1.3 72.9 - - - +
15G ARG* 1.3 57.6 + - - +
17G VAL* 3.9 0.6 - - - +
18G LEU* 2.9 43.5 + - - +
106G LEU* 3.4 23.2 - - - +
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Residues in contact with ARG 15 (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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227F LEU* 4.3 16.1 - - + +
230F LEU* 4.1 17.2 - - + +
231F ASP* 2.6 43.5 + - - +
234F GLU* 2.9 39.6 + - - -
11G ILE* 2.9 41.7 + - - +
12G SER* 3.8 4.9 - - - +
14G SER* 1.3 76.4 - - - +
16G LEU* 1.3 60.2 + - + +
19G ASN* 3.1 39.1 + - - +
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Residues in contact with LEU 16 (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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12G SER* 2.9 25.7 + - - +
13G ALA* 3.2 5.8 + - - +
15G ARG* 1.3 79.3 - - + +
17G VAL* 1.3 63.7 + - - +
19G ASN* 4.2 0.6 - - - -
20G TYR* 3.6 18.7 + - - -
27G ALA* 5.4 1.9 - - + +
30G GLU* 3.7 44.0 - - + +
31G ILE* 3.7 37.6 - - + +
34G LEU* 3.8 24.7 - - + -
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Residues in contact with VAL 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ALA* 2.9 23.3 + - + +
14G SER* 4.0 5.2 - - - +
16G LEU* 1.3 76.6 - - - +
18G LEU* 1.3 62.3 - - + +
20G TYR* 3.5 15.2 - - - +
31G ILE* 4.3 24.0 - - + -
35G LEU* 5.5 1.1 - - + -
106G LEU* 4.8 7.4 - - + -
109G TYR* 3.7 34.5 + - + -
110G ILE* 3.8 36.1 - - + -
113G THR* 5.0 0.7 - - - +
115G LEU* 4.1 16.5 - - + +
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Residues in contact with LEU 18 (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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222E LEU* 4.1 2.0 - - + -
225E ILE* 5.7 1.1 - - + -
223F LYS* 3.9 35.3 + - + +
226F LEU* 3.4 41.1 - - + -
227F LEU* 4.4 16.4 - - + +
230F LEU* 4.4 5.8 - - + -
14G SER* 2.9 35.7 + - - +
17G VAL* 1.3 78.4 - - + +
19G ASN* 1.3 60.3 + - - +
20G TYR 3.2 7.2 + - - +
106G LEU* 5.2 5.8 - - + -
109G TYR* 3.7 36.1 - - + +
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Residues in contact with ASN 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F LEU* 3.4 37.8 - - - +
15G ARG* 3.1 22.7 + - - +
16G LEU 4.2 1.8 - - - -
18G LEU* 1.3 75.5 - - - +
20G TYR* 1.3 64.7 + - - +
21G ASP* 2.9 8.3 + - - +
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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
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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