Contacts of the strand formed by residues 87 - 95 (chain B) in PDB entry 1OXC
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 LEU 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A VAL* 4.2 8.7 - - + -
93A GLY* 3.3 22.7 - - - +
101A ASP 3.9 10.3 - - - +
102A TYR* 3.3 31.9 - - + +
103A ASN* 4.0 14.6 - - + -
106A VAL* 4.5 7.6 - - + -
81B VAL 3.7 1.0 - - - +
82B ILE* 3.3 3.1 - - - -
83B LEU* 2.8 43.1 + - + +
84B THR* 5.0 0.2 - - + -
86B GLU* 1.3 81.4 - - - +
88B ASN* 1.3 64.2 + - - +
89B PHE* 3.6 28.9 - - + -
110B ASN* 6.0 2.5 - - + +
111B TRP 4.1 10.5 - - - +
112B PRO* 4.7 1.3 - - + +
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Residues in contact with ASN 88 (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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80B GLN* 3.0 24.4 + - - +
81B VAL 3.6 3.1 - - - -
82B ILE* 3.2 21.0 - - - +
86B GLU* 3.1 21.2 + - - +
87B LEU* 1.3 76.6 - - - +
89B PHE* 1.3 65.6 + - - +
109B ILE 4.4 0.2 - - - -
110B ASN* 3.3 7.6 - - - +
111B TRP* 2.9 76.6 + - + +
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Residues in contact with PHE 89 (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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91A LEU* 3.7 42.4 - - + -
92A VAL 4.2 6.5 - - - -
106A VAL* 3.5 33.7 - - + -
107A VAL 4.9 0.2 - - - -
108A VAL* 4.3 4.9 - - + -
79B ALA 4.0 0.5 - - - +
80B GLN* 3.2 7.0 - - - +
81B VAL* 2.9 53.9 + - + +
83B LEU* 3.9 16.4 - - + -
87B LEU* 3.6 36.3 - - + -
88B ASN* 1.3 78.7 - - - +
90B ALA* 1.3 60.6 + - - +
91B LEU* 3.9 8.9 + - + -
108B VAL* 4.4 15.3 - - + -
109B ILE 3.3 4.9 - - - +
110B ASN* 4.6 5.8 - - + -
111B TRP* 4.9 0.7 - - - -
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Residues in contact with ALA 90 (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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6B PHE* 3.7 37.2 - - + -
79B ALA 3.7 5.4 - - - -
80B GLN* 4.3 2.0 - - + +
88B ASN 4.3 0.2 - - - -
89B PHE* 1.3 73.2 - - - +
91B LEU* 1.3 61.3 + - - +
92B VAL* 5.1 0.5 - - - +
107B VAL 3.8 0.9 - - - +
108B VAL* 3.6 3.5 - - - -
109B ILE* 2.8 55.1 + - + +
111B TRP* 4.1 11.6 - - + -
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Residues in contact with LEU 91 (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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81A VAL* 4.3 17.5 - - + -
83A LEU* 4.7 3.6 - - + -
89A PHE* 3.8 52.9 - - + -
91A LEU* 4.1 19.3 - - + -
6B PHE* 3.7 0.7 - - - -
78B SER* 3.0 30.0 - - - -
79B ALA* 2.8 21.9 + - + +
81B VAL* 4.5 6.3 - - + -
89B PHE* 4.0 19.3 - - + +
90B ALA* 1.3 78.8 - - - +
92B VAL* 1.3 64.2 + - - +
107B VAL 3.7 1.3 - - - -
108B VAL* 4.1 18.4 - - + -
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Residues in contact with VAL 92 (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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83A LEU* 5.2 0.2 - - - -
89A PHE* 4.1 5.2 - - - -
4B GLY* 4.2 2.2 - - - -
6B PHE* 3.7 26.2 - - + -
65B VAL* 4.1 28.9 - - + -
67B VAL* 5.1 1.8 - - + -
76B LEU* 4.1 22.7 - - + -
77B VAL 3.3 7.9 - - - +
78B SER* 4.1 3.8 - - - -
90B ALA 5.1 0.9 - - - +
91B LEU* 1.3 80.8 - - - +
93B GLY* 1.3 74.6 + - - +
105B ALA 5.5 0.2 - - - +
106B VAL* 3.4 9.4 - - - +
107B VAL* 2.9 46.6 + - + +
109B ILE* 5.8 0.4 - - + -
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Residues in contact with GLY 93 (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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83A LEU* 4.8 0.4 - - - +
87A LEU* 3.5 16.7 - - - +
76B LEU* 3.4 3.5 - - - -
77B VAL* 2.8 36.7 + - - +
92B VAL* 1.3 79.7 - - - +
94B SER* 1.3 64.2 + - - -
102B TYR 3.4 13.2 - - - -
105B ALA 3.7 4.0 - - - -
106B VAL* 4.6 1.3 - - - -
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Residues in contact with SER 94 (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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26B GLN* 4.4 1.0 + - - -
67B VAL* 3.6 8.1 - - - +
74B SER* 3.9 10.7 - - - -
75B ASP 3.1 7.4 - - - -
76B LEU* 3.6 21.3 - - - -
93B GLY* 1.3 76.2 - - - -
95B GLU* 1.3 61.0 + - - +
102B TYR* 3.1 27.1 + - - -
104B ASP* 3.2 12.5 + - - +
105B ALA* 2.7 39.1 + - - +
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Residues in contact with GLU 95 (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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74B SER* 3.4 5.1 - - - -
75B ASP* 2.9 31.9 + - + +
94B SER* 1.3 74.8 - - - +
96B ASP* 1.3 58.9 + - - +
97B GLY* 2.7 40.3 + - - +
99B ASP* 3.1 9.2 - - - +
100B ASN* 3.8 18.4 - - - +
101B ASP 3.0 6.9 + - - -
102B TYR* 2.9 52.0 + - + +
104B ASP* 3.0 0.7 - - - +
116B CA 2.4 31.5 - - - -
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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
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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