Contacts of the strand formed by residues 136 - 145 (chain B) in PDB entry 2O6C
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 GLY 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B LYS* 4.2 9.6 - - - -
134B GLY 3.7 0.8 + - - -
135B LEU* 1.3 76.6 - - - +
137B THR* 1.3 62.6 + - - -
138B TYR* 3.6 9.5 - - - -
179B GLU* 3.8 1.3 - - - -
180B TRP 2.9 34.6 + - - +
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Residues in contact with THR 137 (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 LYS* 3.5 5.2 - - - +
104B HIS* 2.7 66.9 + - + +
136B GLY* 1.3 72.9 - - - -
138B TYR* 1.3 59.8 + - - +
177B ASP* 3.6 24.7 - - + +
178B PHE 3.2 11.0 - - - +
179B GLU* 3.6 20.1 + - + +
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Residues in contact with TYR 138 (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 LEU* 4.1 15.7 - - + -
102B GLN 3.4 11.7 - - - -
103B LYS* 3.5 35.2 - - + +
104B HIS* 4.0 1.6 - - - -
110B GLN* 5.6 2.2 - - - -
131B PHE* 3.8 23.5 - + + +
133B GLU* 3.5 14.2 + - + +
134B GLY 2.6 42.6 + - - -
136B GLY 3.6 21.5 - - - -
137B THR* 1.3 77.0 - - - +
139B LYS* 1.3 62.8 + - - +
140B VAL* 3.8 12.5 + - + -
176B ASP 3.3 9.7 - - - +
178B PHE* 2.6 49.6 + + + +
180B TRP* 4.1 14.1 - - + -
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Residues in contact with LYS 139 (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 3.6 1.0 - - - +
101B LEU* 3.5 4.7 - - - -
102B GLN* 2.8 53.5 + - + +
104B HIS* 3.7 17.7 - - + +
138B TYR* 1.3 73.2 - - - +
140B VAL* 1.3 58.6 + - - +
141B ARG* 4.2 0.9 - - - -
174B GLU* 4.9 11.6 + - - +
175B TRP 3.5 6.7 - - - +
176B ASP* 3.6 37.4 + - - +
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Residues in contact with VAL 140 (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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33B ILE* 4.1 23.3 - - + -
71B ILE* 5.9 3.1 - - + -
99B ALA* 5.1 0.4 - - + -
100B PHE 3.6 2.9 - - - +
101B LEU* 3.8 24.5 - - + -
138B TYR* 4.0 4.5 - - + -
139B LYS* 1.3 79.1 - - - +
141B ARG* 1.3 61.8 + - - +
142B PHE* 3.8 26.9 - - + -
174B GLU* 3.3 4.4 - - - +
175B TRP* 2.7 41.9 + - + +
178B PHE* 3.7 37.9 - - + -
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Residues in contact with ARG 141 (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 3.7 0.7 - - - +
99B ALA* 3.1 2.8 - - - -
100B PHE* 2.7 54.5 + - + +
139B LYS 5.7 0.2 - - - -
140B VAL* 1.3 74.0 - - - +
142B PHE* 1.3 64.2 + - - +
143B GLU* 2.8 34.0 + - + +
172B VAL* 3.5 37.1 - - + +
173B ALA 3.5 4.0 - - - -
174B GLU* 3.0 37.8 + - - +
303B CL 4.7 3.1 - - + -
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Residues in contact with PHE 142 (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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33B ILE* 3.9 19.7 - - + -
44B VAL* 4.1 10.3 - - + -
45B GLY 4.0 1.3 - - - -
46B GLY* 4.0 6.3 - - - -
71B ILE* 4.1 10.1 - - + -
72B GLU 4.4 0.4 - - - -
73B ALA* 3.7 31.4 - - + -
97B VAL* 4.7 4.9 - - + -
98B VAL 3.3 6.1 - - - +
99B ALA* 3.6 27.4 - - + -
114B PHE* 4.1 10.3 - + - -
140B VAL* 3.8 17.0 - - + -
141B ARG* 1.3 74.8 - - - +
143B GLU* 1.3 60.4 + - - +
144B ILE* 4.5 10.4 - - + +
171B LEU 3.6 0.9 - - - +
172B VAL* 3.3 9.0 - - - +
173B ALA* 2.7 39.6 + - + +
175B TRP* 3.7 32.8 - + - -
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Residues in contact with GLU 143 (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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96B ARG 3.6 1.7 - - - +
97B VAL* 3.5 4.3 - - - +
98B VAL* 2.7 39.9 + - + +
100B PHE* 3.6 28.9 - - + -
141B ARG* 2.8 41.0 + - + +
142B PHE* 1.3 74.9 - - - +
144B ILE* 1.3 60.5 + - - +
145B ALA 4.1 0.4 - - - -
170B PRO* 4.2 19.0 - - + +
171B LEU 3.5 3.6 - - - -
172B VAL* 4.2 9.0 - - + -
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Residues in contact with ILE 144 (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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39B VAL* 6.3 0.7 - - + -
42B LEU* 3.8 16.2 - - + -
44B VAL* 3.8 36.3 - - + -
75B ILE* 4.0 16.2 - - + -
95B LEU* 3.8 31.6 - - + -
96B ARG 3.6 2.7 - - - -
97B VAL* 4.1 19.1 - - + -
142B PHE* 4.5 11.4 - - + +
143B GLU* 1.3 77.6 - - - +
145B ALA* 1.3 61.4 + - - +
167B TRP* 3.0 11.5 + - + -
170B PRO* 3.2 2.6 - - - +
171B LEU* 2.8 47.5 + - + +
172B VAL 5.5 0.2 - - - -
173B ALA* 4.8 3.8 - - + -
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Residues in contact with ALA 145 (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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95B LEU* 3.5 9.0 - - - +
96B ARG* 2.9 52.9 + - + +
143B GLU 4.1 0.6 - - - -
144B ILE* 1.3 74.2 - - - +
146B ALA* 1.3 71.0 - - - +
167B TRP* 3.7 3.6 - - - +
168B SER 5.8 2.7 - - - +
170B PRO* 4.1 20.4 - - + +
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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