Contacts of the helix formed by residues 84 - 97 (chain G) in PDB entry 4UNA
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 84 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36G TYR 2.7 13.9 + - - -
38G VAL* 4.8 0.9 - - - +
65G VAL* 3.6 11.5 - - - +
67G SER* 3.4 18.6 - - - -
82G VAL* 3.3 6.7 + - - -
83G SER* 1.3 76.7 - - - +
85G LYS* 1.3 57.5 + - - +
86G LYS* 3.3 6.6 + - - +
87G LEU* 2.9 30.7 + - - +
88G TYR* 2.8 31.5 + - - +
5I C 3.6 8.5 + - - -
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Residues in contact with LYS 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B G 4.0 44.9 + - + +
36G TYR* 3.5 44.6 + - + +
84G SER* 1.3 70.9 - - - +
86G LYS* 1.3 59.0 + - - +
88G TYR* 3.4 2.1 + - - +
89G TYR* 3.0 40.3 + - + -
4I G 2.5 41.2 + - - +
5I C 2.8 25.1 + - - +
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Residues in contact with LYS 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B G 3.5 64.6 + - + +
63G LEU* 2.5 36.5 + - + -
64G ASN* 4.1 11.2 + - - +
65G VAL* 3.9 19.5 - - + -
84G SER* 3.1 7.0 + - - +
85G LYS* 1.3 78.0 - - - +
87G LEU* 1.3 61.9 + - - +
89G TYR* 3.4 1.9 + - - +
90G TYR* 2.9 30.4 + - + +
5I C 5.1 2.1 + - - +
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Residues in contact with LEU 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G VAL* 3.7 11.7 - - + -
56G MET* 3.9 21.8 - - - -
59G LEU* 4.2 9.4 - - + -
60G ILE* 4.6 9.4 - - + -
63G LEU* 3.9 26.9 - - + -
65G VAL* 4.4 11.8 - - + +
82G VAL* 3.7 32.5 - - + -
84G SER* 2.9 21.6 + - - +
86G LYS* 1.3 74.5 - - - +
88G TYR* 1.3 66.0 + - - +
90G TYR* 3.4 5.5 - - + +
91G PHE* 3.1 40.8 + - + -
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Residues in contact with TYR 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G LEU* 3.6 36.3 + - + +
25G TYR 3.7 20.4 - - - -
26G LYS* 3.5 40.6 + - + +
36G TYR* 3.6 19.3 - + + -
37G ARG 3.9 11.7 - - - -
38G VAL* 3.7 12.2 - - + +
84G SER 2.8 18.8 + - - +
85G LYS 3.4 4.0 - - - +
87G LEU* 1.3 77.0 - - - +
89G TYR* 1.3 85.1 + + - +
91G PHE* 3.8 2.1 - - - +
92G ALA* 2.8 40.7 + - + +
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Residues in contact with TYR 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B G 3.2 67.0 + + + +
1C C 3.4 35.5 + + - -
26G LYS* 2.3 38.4 + - - -
36G TYR* 4.0 7.3 - + - -
85G LYS* 3.0 42.5 + - + +
86G LYS 4.1 0.2 - - - +
88G TYR* 1.3 92.7 - + - +
90G TYR* 1.3 60.0 + - - +
92G ALA* 4.2 6.3 - - + -
93G ASN* 2.7 41.4 + - - +
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Residues in contact with TYR 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B G 5.2 0.6 + - - -
7G VAL* 4.0 9.9 + - - +
8G SER* 5.1 1.6 - - - -
11G SER* 2.5 37.3 + - - -
59G LEU* 3.9 17.9 - - + +
63G LEU* 3.9 35.7 - - + -
86G LYS* 2.9 20.1 + - + +
87G LEU* 3.4 13.2 - - + +
89G TYR* 1.3 78.6 - - - +
91G PHE* 1.3 77.3 + + - +
93G ASN* 4.0 3.0 - - - +
94G MET* 3.1 28.4 + - + +
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Residues in contact with PHE 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G SER 3.7 21.1 - - - -
14G LEU* 4.2 8.5 - - + -
15G LEU* 4.0 18.4 - - + +
18G ILE* 3.7 27.1 - - + -
24G LEU* 3.8 18.8 - - + -
38G VAL* 3.7 21.8 - - + -
56G MET* 4.3 4.9 - - - -
59G LEU* 3.4 27.1 - - + -
87G LEU* 3.1 46.1 + - + +
88G TYR 4.0 0.9 - - - +
90G TYR* 1.3 85.5 - + - +
92G ALA* 1.3 60.8 + - - +
94G MET* 3.1 8.5 + - - +
95G LEU* 2.7 30.8 + - - +
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Residues in contact with ALA 92 (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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24G LEU* 3.7 16.3 - - + +
88G TYR* 2.8 38.5 + - + +
89G TYR* 3.9 12.1 - - + +
91G PHE* 1.3 73.4 - - - +
93G ASN* 1.3 63.9 + - - +
95G LEU* 3.2 7.5 + - - +
96G GLU* 3.1 28.9 + - + +
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Residues in contact with ASN 93 (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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24B C 3.3 26.4 + - + -
25B G 2.9 26.4 + - - -
1C C 3.0 21.1 + - - -
89G TYR* 2.7 29.9 + - - +
90G TYR* 4.0 3.7 - - - +
92G ALA* 1.3 70.7 - - - +
94G MET* 1.3 65.1 + - - +
96G GLU* 3.5 17.2 + - - +
97G ARG* 3.3 30.0 + - + +
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Residues in contact with MET 94 (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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8G SER* 3.9 8.5 - - - +
11G SER* 3.8 29.2 - - - +
12G ALA* 3.7 26.5 - - + +
15G LEU* 4.2 9.0 - - + -
90G TYR* 3.1 26.3 + - + +
91G PHE* 3.1 13.8 + - - +
93G ASN* 1.3 78.4 - - - +
95G LEU* 1.3 61.0 + - - +
97G ARG* 3.1 16.6 + - - +
98G ILE 3.3 8.1 + - - -
101G PHE* 3.6 36.6 - - + -
105G GLU* 4.1 11.7 - - - +
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Residues in contact with LEU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 4.1 14.1 - - + +
19G ILE* 3.6 38.1 - - + -
24G LEU* 4.9 8.7 - - + -
91G PHE 2.7 16.1 + - - +
92G ALA* 3.2 11.4 + - - +
94G MET* 1.3 74.1 - - - +
96G GLU* 1.3 62.0 + - + +
98G ILE* 3.2 43.8 + - + +
134G LEU* 5.7 3.6 - - + -
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Residues in contact with GLU 96 (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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1C C 4.3 15.4 + - - -
92G ALA* 3.1 18.3 + - - +
93G ASN* 3.5 25.6 - - - +
95G LEU* 1.3 76.6 - - - +
97G ARG* 1.3 60.0 + - + +
98G ILE* 3.3 2.9 + - - +
99G ARG* 4.9 11.3 + - - +
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Residues in contact with ARG 97 (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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22B C 2.5 68.6 + - - +
23B G 4.5 11.4 + - - -
93G ASN* 3.3 16.6 - - - +
94G MET* 3.1 12.6 + - - +
96G GLU* 1.3 78.7 - - + +
98G ILE* 1.3 65.6 + - - +
99G ARG* 3.1 3.8 - - - -
100G LEU* 2.9 52.5 + - + +
101G PHE* 3.8 8.5 + - + -
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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
------------------------------------------------------------
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