Contacts of the strand formed by residues 66 - 78 (chain B) in PDB entry 4OWW
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 ASP 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 4.4 2.6 - - - +
22B ILE* 3.4 1.7 - - - -
23B VAL* 2.9 28.9 + - + +
61B LEU 4.0 4.2 - - - +
62B ILE* 3.7 6.4 - - - -
63B GLN* 2.7 50.7 + - - +
64B PRO 3.4 0.7 - - - +
65B GLY* 1.3 76.3 - - - +
67B ILE* 1.3 60.7 + - - +
68B ILE* 3.8 20.4 + - + -
94B LYS* 2.8 39.9 + - + +
96B GLY 3.7 3.8 - - - -
97B GLU* 3.9 4.7 - - - +
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE* 3.9 19.3 - - + -
21B PHE 3.6 5.2 - - - +
22B ILE* 4.3 5.4 - - + -
65B GLY 3.4 2.7 + - - +
66B ASP* 1.3 73.6 - - - +
68B ILE* 1.3 61.6 + - - +
94B LYS* 3.5 3.8 - - - -
95B ILE* 2.9 43.4 + - + -
96B GLY* 2.8 20.0 + - - +
97B GLU 3.7 32.3 - - - +
98B PHE 4.1 0.7 - - - +
99B CYS* 3.7 14.1 - - + +
100B MET* 3.7 32.8 - - + -
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.8 6.1 - - + -
19B LEU 3.9 1.0 - - - +
20B ILE* 3.4 4.5 - - - -
21B PHE* 2.8 58.0 + - + +
23B VAL* 3.6 27.4 - - + -
62B ILE* 3.6 28.9 - - + -
66B ASP* 3.9 15.9 - - + +
67B ILE* 1.3 81.5 - - - +
69B ARG* 1.3 63.9 + - - +
70B LEU 3.9 0.2 + - - -
92B LEU* 3.7 25.1 - - + -
93B GLN 3.3 10.5 - - - +
94B LYS* 4.1 11.9 - - + +
95B ILE* 4.9 0.7 - - - -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA* 4.3 5.7 - - - +
18B ASN* 6.4 0.2 - - + -
19B LEU 3.6 4.3 - - - +
20B ILE* 4.0 24.7 - - + +
67B ILE 4.4 0.2 + - - -
68B ILE* 1.3 74.5 - - - +
70B LEU* 1.3 70.3 + - - +
71B THR* 4.1 14.8 + - + +
91B ASP* 3.6 3.6 - - - +
92B LEU* 3.7 0.9 - - - -
93B GLN* 2.8 65.7 + - + +
95B ILE* 3.4 36.7 - - + +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU 4.0 1.8 - - - +
18B ASN* 3.3 4.0 - - - +
19B LEU* 2.8 48.6 + - + +
21B PHE* 4.0 10.5 - - + -
52B ILE* 4.6 2.9 - - + -
68B ILE 3.9 0.6 + - - -
69B ARG* 1.3 75.6 - - - +
71B THR* 1.3 79.1 + - - +
73B GLY* 3.7 27.1 - - - -
84B LEU* 3.8 34.1 - - + -
85B TYR 4.2 1.6 - - - +
86B THR* 3.7 18.6 - - - +
91B ASP 3.6 7.0 - - - +
92B LEU* 3.6 25.1 - - + -
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASN* 3.2 14.1 - - + +
69B ARG* 4.5 21.1 - - + +
70B LEU* 1.3 82.3 - - - +
72B LYS* 1.3 73.4 + - - +
73B GLY 3.2 2.3 + - - -
86B THR* 4.7 0.5 - - - +
89B GLY 5.1 0.9 + - - -
90B GLY* 3.1 21.7 - - - -
91B ASP* 2.7 37.9 + - - +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASN* 3.9 36.1 + - + +
17B LEU 3.1 2.2 + - - -
18B ASN* 2.8 19.0 + - - +
71B THR* 1.3 77.4 - - - +
73B GLY* 1.3 63.4 + - - +
74B TYR* 5.2 0.2 - - - +
87B GLY* 3.0 25.5 + - - -
88B ARG 3.8 12.1 - - - +
89B GLY* 3.3 30.3 - - - +
90B GLY* 3.7 7.0 - - - +
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Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASN 3.2 9.0 + - - -
17B LEU* 2.7 43.1 + - - +
70B LEU* 3.7 17.9 - - - -
71B THR 3.2 2.4 - - - -
72B LYS* 1.3 76.8 - - - +
74B TYR* 1.3 59.7 + - - +
85B TYR 3.1 15.5 - - - -
87B GLY 4.0 0.2 - - - -
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Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU 3.3 13.9 - - - +
15B LYS* 3.9 13.5 - - + -
17B LEU* 3.8 6.5 - - - +
73B GLY* 1.3 73.5 - - - +
75B ALA* 1.3 65.3 + - - +
76B SER* 3.8 15.5 - - - -
84B LEU* 3.6 1.9 - - - +
85B TYR* 2.8 58.4 + + + +
86B THR 3.4 14.8 - - - -
87B GLY* 3.5 20.0 - - - -
4L T 3.6 16.3 + - + -
5L T 3.5 39.0 - - - -
6L T 3.3 34.1 + - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.5 26.9 - - + -
11B LYS 3.4 20.9 - - - +
12B PRO* 4.2 0.2 - - - -
13B GLY* 2.9 26.4 + - - -
14B LEU 2.9 8.2 + - - +
17B LEU* 3.9 3.8 - - + +
74B TYR* 1.3 78.4 - - - +
76B SER* 1.3 65.0 + - - +
82B LEU* 3.9 7.6 - - + -
83B THR 3.3 9.4 - - - +
84B LEU* 4.8 0.7 - - + -
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PRO* 4.5 6.3 - - - -
13B GLY 4.6 1.1 - - - +
74B TYR* 3.8 11.2 - - - -
75B ALA* 1.3 76.5 - - - +
77B VAL* 1.3 67.9 - - - +
82B LEU* 3.7 3.8 - - - +
83B THR* 2.8 32.0 + - - +
85B TYR* 3.2 23.9 - - - -
5L T 4.3 14.7 + - - -
6L T 4.4 3.1 + - - -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PRO* 3.9 25.7 - - + +
76B SER* 1.3 79.2 - - - +
78B PHE* 1.3 63.6 + - - +
79B LYS 4.2 0.4 + - - -
80B GLY* 3.8 32.5 - - - +
81B CYS 3.6 4.9 - - - +
82B LEU* 4.5 8.3 - - + +
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Residues in contact with PHE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B THR* 6.3 2.2 - - + -
53B SER* 5.4 2.2 - - - -
76B SER 3.8 0.6 + - - -
77B VAL* 1.3 74.1 - - - +
79B LYS* 1.3 107.2 + - + +
80B GLY 3.2 0.4 - - - -
81B CYS* 2.8 26.1 + - - +
83B THR* 3.8 10.2 + - + +
85B TYR* 3.3 18.4 - - - +
7L T 3.3 68.0 - + + -
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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