Contacts of the strand formed by residues 98 - 105 (chain B) in PDB entry 2O5F
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 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B LEU* 1.3 73.3 - - - +
99B TRP* 1.3 63.8 + - - +
121B LEU* 3.5 4.3 - - - +
122B ARG* 2.8 57.5 + - - +
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Residues in contact with TRP 99 (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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79B GLU* 3.7 35.9 - - + -
82B PHE* 3.8 21.5 - + + -
83B ARG* 4.6 3.4 - - - -
94B ILE* 3.1 51.9 + - + +
95B ASP* 4.7 4.8 + - - +
97B LEU 3.6 4.3 - - - -
98B SER* 1.3 78.4 + - - +
100B ARG* 1.3 88.0 + - - +
101B PRO* 4.1 14.6 - - + -
119B TYR* 3.9 22.0 - + - -
120B GLU 3.1 14.4 - - - +
121B LEU* 3.5 14.1 - - + -
122B ARG* 5.5 1.1 - - - -
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Residues in contact with ARG 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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42B ARG* 4.6 4.9 - - - +
99B TRP* 1.3 87.8 - - - +
101B PRO* 1.3 83.3 + - + +
102B LEU* 3.4 20.7 + - - +
119B TYR* 3.6 1.3 - - - -
120B GLU* 2.7 58.9 + - - +
122B ARG* 5.5 3.8 - - - +
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Residues in contact with PRO 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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99B TRP* 4.1 10.8 - - + -
100B ARG* 1.3 99.8 + - + +
102B LEU* 1.3 61.0 + - - +
103B ALA 5.1 1.6 - - - +
117B CYS* 4.8 7.6 - - - -
118B VAL 3.9 1.1 - - - +
119B TYR* 3.8 26.0 - - + -
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Residues in contact with LEU 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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40B PHE* 4.4 1.1 - - + -
100B ARG* 3.4 28.9 + - - +
101B PRO* 1.3 75.4 - - - +
103B ALA* 1.3 63.5 + - - +
118B VAL* 2.7 31.5 + - + +
119B TYR 4.2 7.0 - - - +
120B GLU* 4.3 18.8 - - + +
166B CYS* 3.8 39.3 - - + +
167B TYR* 3.7 27.4 - - + +
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Residues in contact with ALA 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 PRO* 3.8 1.2 - - - +
102B LEU* 1.3 83.7 - - + +
104B SER* 1.3 61.6 + - - +
105B PHE* 3.6 32.3 - - + -
117B CYS* 3.5 5.0 - - - -
118B VAL* 2.8 30.8 + - + +
165B ARG 5.9 0.2 - - - +
166B CYS* 4.4 9.4 - - - -
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Residues in contact with SER 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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103B ALA* 1.3 76.4 + - - +
105B PHE* 1.3 73.4 + - - +
116B MET 3.4 9.5 + - - -
117B CYS* 4.3 13.0 - - - +
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Residues in contact with PHE 105 (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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103B ALA* 3.6 28.0 - - + -
104B SER* 1.3 83.0 - - - +
106B SER* 1.3 59.0 + - - +
110B THR* 3.9 19.5 - - + +
112B LEU* 3.5 31.9 - - + -
114B SER 4.1 0.8 - - - +
115B PHE* 3.5 6.1 - - - -
116B MET* 3.0 39.5 + - + +
118B VAL* 4.0 19.1 - - + -
162B LEU* 4.4 2.7 - - + -
165B ARG* 3.9 37.5 - - + -
166B CYS* 3.8 18.2 - - - -
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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