Contacts of the strand formed by residues 96 - 103 (chain B) in PDB entry 2O6E
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 ARG 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B TYR 4.4 5.4 - - - +
95B LEU* 1.3 75.3 - - - +
97B VAL* 1.3 62.2 + - - +
98B VAL* 4.1 6.9 + - + +
143B GLU 3.6 2.9 - - - +
145B ALA* 2.9 48.7 + - + +
146B ALA 3.1 26.2 + - - +
147B PRO 3.9 1.4 + - - -
148B SER* 2.7 41.3 + - - +
151B GLU* 4.5 7.9 - - - +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA* 4.4 11.2 - - + -
75B ILE* 3.6 25.6 - - + -
95B LEU* 3.9 6.1 + - + -
96B ARG* 1.3 73.9 - - - +
98B VAL* 1.3 71.9 + - - +
113B MET* 3.9 0.9 - - - +
114B PHE* 3.0 55.5 + - + +
125B TYR* 3.8 27.7 - - + -
142B PHE* 4.7 6.3 - - + -
143B GLU 3.4 7.4 - - - +
144B ILE* 4.0 19.1 - - + -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ARG* 4.8 5.2 - - + +
97B VAL* 1.3 85.5 - - - +
99B ALA* 1.3 60.9 + - - +
100B PHE* 3.9 15.2 - - + -
111B LYS* 3.4 48.5 - - + +
112B VAL 3.5 10.3 - - - +
113B MET* 4.3 11.4 - - + -
114B PHE 4.5 0.2 - - - +
141B ARG 3.6 1.0 - - - +
142B PHE* 3.4 2.3 - - - -
143B GLU* 2.7 42.5 + - + +
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Residues in contact with ALA 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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71B ILE* 6.2 0.4 - - + -
98B VAL* 1.3 74.3 - - - +
100B PHE* 1.3 63.2 + - - +
101B LEU* 4.2 13.2 - - + -
110B GLN 3.7 0.5 - - - +
111B LYS* 3.5 2.9 - - - -
112B VAL* 2.8 45.3 + - + +
114B PHE* 3.7 31.1 - - + -
140B VAL* 5.2 0.2 - - + -
141B ARG 3.1 4.9 - - - +
142B PHE* 3.8 15.3 - - + -
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Residues in contact with PHE 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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98B VAL* 3.9 20.0 - - + -
99B ALA* 1.3 76.3 - - - +
101B LEU* 1.3 62.2 + - - +
102B GLN* 4.2 0.4 - - - -
109B VAL* 3.9 23.1 - - + -
110B GLN 3.4 4.3 - - - -
111B LYS* 3.7 37.2 - - + -
139B LYS 3.6 1.4 - - - +
140B VAL* 3.5 4.3 - - - -
141B ARG* 2.7 53.9 + - + +
143B GLU* 3.6 42.0 - - + -
312B CL 4.4 8.1 - - + -
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Residues in contact with LEU 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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71B ILE* 4.8 13.2 - - + -
99B ALA* 4.6 10.1 - - + -
100B PHE* 1.3 80.4 - - - +
102B GLN* 1.3 62.1 + - - +
108B LYS 4.0 0.5 - - - +
109B VAL* 3.5 4.4 - - - +
110B GLN* 2.8 66.5 + - + +
112B VAL* 4.0 11.0 - - + -
129B VAL* 4.0 22.0 - - + -
131B PHE* 4.1 15.9 - - + -
138B TYR* 4.1 16.9 - - + -
139B LYS 3.5 3.4 - - - -
140B VAL* 3.9 28.5 - - + -
142B PHE* 6.0 0.2 - - + -
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Residues in contact with GLN 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 PHE 4.2 0.2 - - - -
101B LEU* 1.3 75.2 - - - +
103B LYS* 1.3 64.7 + - - +
104B HIS 3.6 0.7 + - - -
106B SER 3.0 24.0 + - - +
107B GLU* 3.8 21.6 + - - +
108B LYS 3.4 16.8 - - - +
109B VAL* 3.7 15.4 - - + +
138B TYR* 3.7 3.7 - - - -
139B LYS* 2.9 50.1 + - + +
312B CL 3.2 27.3 - - + +
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Residues in contact with LYS 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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102B GLN* 1.3 74.3 + - - +
104B HIS* 1.3 76.0 + - - +
106B SER* 3.0 39.4 + - - +
108B LYS 4.4 3.4 + - - -
133B GLU* 3.0 39.8 + - + +
135B LEU 2.6 29.9 + - - +
136B GLY* 4.3 4.0 - - - -
137B THR 3.5 13.7 - - - +
138B TYR* 3.5 27.9 - - + +
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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