Contacts of the strand formed by residues 94 - 105 (chain A) in PDB entry 3OV6
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 PHE 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A SER* 4.0 0.2 - - - -
18A PHE* 3.1 75.6 + + + +
81A ILE* 3.6 24.5 - - + -
84A HIS 6.1 1.1 - - - -
92A TYR* 4.5 22.9 - + - -
93A PRO* 1.3 77.2 - - - +
95A GLU* 1.3 65.0 + - - +
96A VAL* 3.9 13.2 - - + -
118A PHE* 3.2 41.5 - + + -
119A ASN* 3.3 16.4 - - - +
1000A PRO* 5.7 0.4 - - - -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.9 2.5 - - + -
16A PHE 3.5 5.4 - - - +
17A SER* 3.2 20.4 + - - +
25A ARG* 4.5 1.0 + - - -
94A PHE* 1.3 77.0 - - - +
96A VAL* 1.3 69.4 + - - +
97A GLN* 5.3 4.5 - - + +
118A PHE* 3.6 2.8 - - - -
119A ASN* 2.7 43.8 + - - +
120A GLY 4.6 0.4 + - - -
1031A HIS* 3.6 20.6 + - + +
1032A PRO* 3.7 12.4 - - - +
1033A SER* 2.5 52.3 + - - -
1034A ASP* 4.2 1.4 + - - +
1062A PHE* 3.7 7.8 - - - -
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.5 4.0 - - - +
16A PHE* 2.8 59.2 + - + +
18A PHE* 4.9 2.9 - - + -
77A LEU* 5.9 2.0 - - + -
81A ILE* 5.5 1.3 - - + -
94A PHE* 3.9 18.1 - - + -
95A GLU* 1.3 80.5 - - - +
97A GLN* 1.3 68.6 - - - +
98A VAL* 4.4 4.7 - - + -
116A VAL* 3.9 22.0 - - + -
117A ALA 3.6 3.1 - - - +
118A PHE* 3.8 21.3 - - + -
1104A D12 4.0 21.3 - - + -
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Residues in contact with GLN 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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14A GLN 3.3 5.6 - - - +
15A ILE* 4.6 2.5 - - + -
95A GLU* 5.3 3.0 - - + +
96A VAL* 1.3 83.2 - - - +
98A VAL* 1.3 61.5 + - - +
116A VAL* 3.2 7.3 - - - +
117A ALA* 2.9 32.8 + - + +
119A ASN 5.4 0.2 + - - -
120A GLY* 3.6 13.3 + - - -
1031A HIS* 2.9 26.0 + - - -
1056A PHE* 3.2 30.2 - - + -
1060A TRP* 2.8 46.4 + - + +
1062A PHE* 3.4 25.1 - - + -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL 3.8 0.2 - - - +
13A ILE* 3.6 1.7 - - - -
14A GLN* 2.9 64.3 + - + +
16A PHE* 4.5 5.4 - - + -
73A TYR* 4.3 5.6 - - - +
77A LEU* 5.9 1.3 - - + -
96A VAL* 4.4 9.6 - - + -
97A GLN* 1.3 78.6 - - - +
99A LYS* 1.3 69.2 + - - +
100A ALA* 4.3 3.6 - - + +
114A PHE* 3.7 31.2 - - + -
115A GLN 3.4 3.6 - - - +
116A VAL* 4.1 20.0 - - + -
1056A PHE* 3.4 8.8 - - - -
1060A TRP* 4.8 0.2 - - - -
1104A D12 5.1 5.4 - - + -
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Residues in contact with LYS 99 (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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11A HIS* 4.4 30.6 - - + -
12A VAL 3.6 3.4 - - - -
13A ILE* 4.8 2.5 - - + -
98A VAL* 1.3 73.2 - - - +
100A ALA* 1.3 60.2 + - - +
113A PHE* 3.9 22.7 - - + -
114A PHE* 3.3 1.7 - - - -
115A GLN* 2.8 72.3 + - + +
1056A PHE* 3.9 29.4 - - + -
1057A SER 5.5 0.6 - - - -
1058A LYS* 4.2 33.6 - - - +
1060A TRP* 4.2 4.3 - - + -
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Residues in contact with ALA 100 (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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11A HIS* 3.3 1.0 - - - -
12A VAL* 2.7 40.5 + - - +
98A VAL* 4.1 4.0 - - + -
99A LYS* 1.3 75.4 - - - +
101A GLY* 1.3 59.6 + - - +
113A PHE* 3.4 8.5 - - - +
114A PHE* 3.4 33.7 - - + +
163A ILE* 5.1 0.9 - - + -
1105A MK0 3.7 29.1 - - + +
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Residues in contact with GLY 101 (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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10A PHE 3.5 9.0 - - - -
11A HIS* 4.3 0.4 - - - -
100A ALA* 1.3 74.4 - - - +
102A CYS* 1.3 62.3 + - - +
112A GLY* 3.2 4.5 - - - -
113A PHE* 2.8 43.9 + - - +
163A ILE* 3.4 12.5 - - - +
167A CYS* 3.6 10.8 - - - -
1105A MK0 4.3 6.1 - - - -
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Residues in contact with CYS 102 (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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9A SER* 3.5 2.8 - - - -
10A PHE 3.0 34.4 + - - +
101A GLY* 1.3 72.5 - - - -
103A GLU* 1.3 63.1 + - - +
111A GLU 3.3 10.1 - - - +
112A GLY* 4.5 0.2 - - - -
113A PHE* 3.5 8.5 - - - -
163A ILE 3.4 17.7 - - - +
167A CYS* 2.0 57.0 - - - -
168A PRO* 3.4 13.2 - - + -
171A LEU* 3.9 12.2 - - - +
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Residues in contact with GLU 103 (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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7A HIS* 2.8 35.4 + - + -
8A VAL 3.4 7.9 - - - +
9A SER* 4.3 7.0 - - - +
102A CYS* 1.3 77.0 - - - +
104A LEU* 1.3 61.1 + - - +
105A HIS* 3.1 20.4 + - + +
110A PRO* 3.3 5.5 - - - +
111A GLU* 2.8 62.1 + - - +
113A PHE* 3.6 18.8 - - + -
168A PRO* 5.6 0.3 - - - +
171A LEU* 4.9 0.9 - - - -
1058A LYS* 5.8 1.7 + - - -
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Residues in contact with LEU 104 (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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7A HIS* 3.0 21.5 - - - +
8A VAL* 2.8 21.9 + - + +
103A GLU* 1.3 73.9 - - - +
105A HIS* 1.3 66.3 + - - +
108A GLY* 3.6 33.2 - - - +
109A SER 3.9 5.4 - - - +
110A PRO* 4.1 10.5 - - + -
168A PRO* 4.8 11.7 - - + +
171A LEU* 4.3 15.7 - - + +
172A LEU* 3.6 42.8 - - + -
175A LEU* 5.9 2.0 - - + -
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Residues in contact with HIS 105 (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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6A GLU 3.6 7.2 - - - +
7A HIS* 3.5 22.4 + + + +
103A GLU* 3.1 38.3 + - + +
104A LEU* 1.3 80.6 - - - +
106A SER* 1.3 59.1 + - - +
108A GLY* 2.8 31.2 + - - -
109A SER* 2.9 27.0 + - - +
111A GLU* 2.8 32.7 + - + +
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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