Contacts of the strand formed by residues 99 - 104 (chain B) in PDB entry 2OB2
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 VAL 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B PHE* 3.8 18.6 - - + -
93B LEU* 3.5 30.5 - - + -
96B ASN* 2.9 46.9 - - + +
97B GLU 3.6 2.5 + - - +
98B LYS* 1.3 72.9 - - - +
100B GLN* 1.3 77.1 + - - +
101B VAL* 4.4 1.6 - - + -
121B HIS 3.6 5.9 + - - +
122B LEU* 3.4 5.9 - - + -
123B ALA* 2.8 26.0 + - - +
194B ILE* 3.8 5.2 - - - -
195B PRO* 3.4 13.9 - - + +
197B ILE* 4.2 5.8 - - + -
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Residues in contact with GLN 100 (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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99B VAL* 1.3 78.7 - - - +
101B VAL* 1.3 62.9 + - - +
102B VAL* 4.9 0.9 - - + -
123B ALA* 3.1 16.6 - - + +
125B VAL* 5.8 1.6 - - + -
189B CYS 4.7 1.9 - - - +
190B THR* 3.4 23.0 - - + -
191B LYS* 2.7 41.4 + - - +
194B ILE* 3.5 25.0 + - + +
195B PRO 3.0 6.8 + - - +
196B THR* 2.7 39.0 + - + +
197B ILE 2.8 24.8 + - - +
223B PHE* 3.2 14.3 - - - -
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Residues in contact with VAL 101 (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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89B ILE* 5.2 3.6 - - + -
93B LEU* 4.5 3.6 - - + -
99B VAL* 4.4 1.3 - - + -
100B GLN* 1.3 75.4 - - - +
102B VAL* 1.3 64.7 + - - +
115B LEU* 5.6 0.9 - - + -
122B LEU* 3.3 24.0 - - + -
123B ALA 2.7 8.5 + - - +
124B TYR* 3.3 37.9 - - + -
125B VAL* 2.7 34.5 + - - +
197B ILE* 3.3 31.4 - - + +
199B ILE* 3.7 24.5 - - + -
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Residues in contact with VAL 102 (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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100B GLN* 4.9 1.1 - - + -
101B VAL* 1.3 77.5 - - - +
103B ASN* 1.3 60.7 + - - +
104B LEU* 3.6 18.0 + - + -
125B VAL* 3.4 8.3 - - + +
127B ILE* 3.6 30.1 - - + -
186B LEU* 4.0 11.2 - - + -
190B THR* 3.9 28.0 - - + -
196B THR* 4.1 18.8 - - + -
197B ILE 2.9 10.5 + - - +
198B VAL* 3.4 10.9 - - + +
199B ILE* 2.9 25.3 + - - +
219B ILE* 5.7 1.8 - - + -
223B PHE* 4.9 3.8 - - + -
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Residues in contact with ASN 103 (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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101B VAL 4.1 0.2 - - - -
102B VAL* 1.3 73.1 - - - +
104B LEU* 1.3 64.7 + - - +
105B GLY 4.4 0.7 - - - +
106B CYS* 3.4 20.1 - - - +
109B ASP* 3.0 25.3 + - - +
124B TYR* 2.8 29.7 + - + +
125B VAL 2.7 11.6 + - - +
126B ASP* 3.7 14.1 + - - +
127B ILE* 2.9 30.5 + - - +
199B ILE* 3.8 29.7 - - + +
201B GLU 5.3 0.3 + - - -
1802B SAH 4.6 4.3 + - - -
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Residues in contact with LEU 104 (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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102B VAL* 3.6 23.6 - - + -
103B ASN* 1.3 71.5 + - - +
105B GLY* 1.4 67.9 + - - +
127B ILE* 4.0 9.2 - - + -
176B LEU* 3.9 25.4 - - + -
182B THR* 5.5 0.4 - - + -
186B LEU* 5.6 0.2 - - + -
198B VAL* 3.3 30.1 - - + -
199B ILE 2.8 20.8 + - - +
200B SER* 4.1 3.9 - - - -
201B GLU 4.5 1.6 + - - -
203B LEU* 3.6 31.0 - - + +
215B LEU* 4.4 10.1 - - + -
219B ILE* 4.1 16.6 - - + -
228B TRP* 3.6 21.5 - - + -
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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