Contacts of the helix formed by residues 84 - 97 (chain A) in PDB entry 4UN7
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A TYR* 2.7 13.4 + - - +
38A VAL* 5.0 0.9 - - - +
65A VAL* 3.7 11.1 - - - +
67A SER* 3.4 12.7 + - - -
82A VAL* 3.5 12.2 + - - -
83A SER* 1.3 77.2 + - - +
85A LYS* 1.3 58.5 + - - +
86A LYS* 3.5 5.5 + - - +
87A LEU* 3.0 31.7 + - - +
88A TYR* 2.9 31.7 + - - +
5C C 3.5 9.7 + - - -
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Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.6 37.3 + - + +
84A SER* 1.3 72.1 + - - +
86A LYS* 1.3 64.2 + - - +
88A TYR* 3.7 0.3 - - - +
89A TYR* 3.1 52.4 + - + -
4C G 2.4 43.2 + - - +
5C C 2.8 25.1 + - - +
25E G 4.0 36.1 + - + +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 2.3 43.7 + - + +
64A ASN* 4.0 9.0 + - - +
65A VAL* 3.9 18.8 - - + -
84A SER* 3.3 6.2 + - - +
85A LYS* 1.3 79.8 - - - +
87A LEU* 1.3 58.1 + - - +
89A TYR* 3.4 2.1 + - - +
90A TYR* 2.9 28.1 + - + +
5C C 4.9 1.8 + - - -
25E G 3.3 66.6 + - + +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 3.6 13.7 - - + -
56A MET* 3.9 21.3 - - - -
59A LEU* 4.4 9.0 - - + -
60A ILE* 4.3 10.1 - - + -
63A LEU* 4.2 24.0 - - + -
65A VAL* 4.4 12.1 - - + -
82A VAL* 3.8 31.4 - - + -
84A SER* 3.0 20.9 + - - +
86A LYS* 1.3 74.6 - - - +
88A TYR* 1.3 65.9 + - - +
90A TYR* 3.5 5.7 - - + +
91A PHE* 3.2 40.0 + - + -
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Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.8 19.3 + - + +
25A TYR 3.7 35.4 - - - -
26A LYS* 3.7 22.4 + - + +
36A TYR* 3.6 28.3 - + + -
37A ARG 3.9 10.8 - - - -
38A VAL* 3.7 12.5 - - + +
84A SER 2.9 18.6 + - - +
85A LYS 3.7 1.6 - - - +
86A LYS 3.3 0.2 - - - -
87A LEU* 1.3 79.9 - - - +
89A TYR* 1.3 92.6 + + - +
91A PHE* 3.3 2.4 + - - +
92A ALA* 2.8 36.6 + - + +
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 4.0 15.6 - - + +
36A TYR* 3.8 28.4 + + - -
85A LYS* 3.1 31.0 + - + +
86A LYS 4.0 0.2 - - - +
88A TYR* 1.3 97.3 - + - +
90A TYR* 1.3 68.8 + - - +
92A ALA* 4.2 7.0 - - + -
93A ASN* 2.8 32.8 + - - +
25E G 3.3 66.9 + + + +
1F C 3.4 40.0 + + - -
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.7 12.0 - - + +
8A SER* 4.8 2.4 - - - -
11A SER* 2.5 39.9 + - - -
59A LEU* 4.2 5.4 - - + -
63A LEU* 3.7 39.3 - - + -
86A LYS* 2.9 21.1 + - + +
87A LEU* 3.5 9.6 - - + +
88A TYR 3.2 0.2 - - - -
89A TYR* 1.3 78.3 - - - +
91A PHE* 1.3 82.9 + + - +
93A ASN* 4.1 3.3 - - - +
94A MET* 3.2 31.3 + - + +
25E G 5.2 0.8 + - - -
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 3.4 25.6 - - - -
14A LEU* 4.1 11.9 - - + -
15A LEU* 3.8 24.8 - - + +
18A ILE* 3.7 24.0 - - + -
24A LEU* 4.0 18.6 - - + -
38A VAL* 3.9 13.9 - - + -
56A MET* 4.4 3.4 - - + -
59A LEU* 3.5 30.7 - - + -
87A LEU* 3.2 36.8 + - + +
88A TYR 3.9 2.0 - - - +
89A TYR 3.1 0.2 - - - -
90A TYR* 1.3 93.0 - + - +
92A ALA* 1.3 61.1 + - - +
94A MET* 3.1 7.6 + - - +
95A LEU* 2.8 30.1 + - - +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.9 15.6 - - + +
88A TYR* 2.8 39.4 + - + +
89A TYR* 4.1 11.2 - - + +
91A PHE* 1.3 73.1 - - - +
93A ASN* 1.3 64.4 + - - +
95A LEU* 3.3 7.4 + - - +
96A GLU* 3.1 23.7 + - - +
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Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TYR* 2.8 27.2 + - - +
90A TYR* 4.1 3.3 - - - +
92A ALA* 1.3 71.1 - - - +
94A MET* 1.3 64.9 - - - +
96A GLU* 3.2 23.8 + - - +
97A ARG* 3.3 17.7 + - - +
24E C 3.5 25.4 + - + -
25E G 2.8 27.0 + - - -
1F C 3.4 19.4 + - - -
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Residues in contact with MET 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 3.9 10.3 - - - +
11A SER* 3.8 21.1 - - - +
12A ALA* 3.5 29.4 - - + +
15A LEU* 4.1 10.8 - - + -
90A TYR* 3.2 25.1 + - + +
91A PHE* 3.1 12.9 + - - +
93A ASN* 1.3 78.6 - - - +
95A LEU* 1.3 61.4 + - - +
97A ARG* 3.3 29.0 + - - +
98A ILE 3.4 8.0 + - - -
101A PHE* 3.5 38.8 - - + -
105A GLU* 4.5 9.9 - - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 4.1 16.5 - - + +
19A ILE* 3.9 35.9 - - + -
24A LEU* 4.6 13.5 - - + -
91A PHE 2.8 16.0 + - - +
92A ALA* 3.5 7.2 - - - +
93A ASN 3.2 0.2 - - - -
94A MET* 1.3 76.2 - - - +
96A GLU* 1.3 63.4 + - - +
97A ARG 3.3 0.5 + - - -
98A ILE* 3.3 41.7 + - + +
109A PHE* 5.5 0.2 - - + -
134A LEU* 5.6 4.9 - - + -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ALA 3.1 13.6 + - - +
93A ASN* 3.2 22.2 + - - +
95A LEU* 1.3 77.6 - - - +
97A ARG* 1.3 57.8 + - + +
98A ILE 3.3 2.4 + - - -
99A ARG* 4.5 12.5 + - - -
1F C 5.3 8.0 + - - -
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 5.8 0.4 - - - -
93A ASN* 3.3 13.9 + - - +
94A MET* 3.6 25.4 - - - +
95A LEU 3.1 1.0 - - - -
96A GLU* 1.3 77.5 - - + +
98A ILE* 1.3 63.5 + - - +
99A ARG* 3.2 2.9 - - - -
100A LEU* 3.0 52.3 + - + +
101A PHE* 3.7 8.4 - - + -
102A ASN* 6.0 0.2 - - - +
105A GLU* 3.8 25.3 + - - -
23E G 5.0 14.9 + - - -
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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