Contacts of the strand formed by residues 171 - 180 (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 LEU 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B VAL* 3.5 42.4 - - + +
40B GLY* 5.1 3.4 - - - -
41B PRO* 3.8 11.9 - - + -
42B LEU* 3.7 22.4 - - + -
142B PHE 3.6 0.9 - - - +
143B GLU* 3.5 3.8 - - - -
144B ILE* 2.8 45.5 + - + +
167B TRP* 3.7 39.3 - - + +
169B GLU 4.4 2.2 - - - +
170B PRO* 1.3 74.2 - - - +
172B VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 172 (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* 3.2 26.6 - - - +
141B ARG* 3.5 57.7 - - + +
142B PHE 3.3 2.2 - - - -
143B GLU* 4.2 11.9 - - + -
144B ILE* 5.5 0.7 - - - -
170B PRO 3.9 9.9 - - - +
171B LEU* 1.3 79.9 - - - +
173B ALA* 1.3 66.0 + - - +
174B GLU* 4.1 9.6 - - + +
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Residues in contact with ALA 173 (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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37B ARG* 4.1 16.6 - - + -
39B VAL* 4.6 2.0 - - + -
44B VAL* 3.8 34.8 - - + -
141B ARG* 3.5 1.4 - - - -
142B PHE* 2.7 40.0 + - + +
144B ILE* 4.8 2.4 - - + +
171B LEU 4.3 0.2 + - - -
172B VAL* 1.3 73.8 - - - +
174B GLU* 1.3 59.0 + - - +
175B TRP* 4.0 16.7 - - + -
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Residues in contact with GLU 174 (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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37B ARG* 2.9 29.3 + - - +
139B LYS* 4.9 12.5 + - - +
140B VAL 3.3 13.2 - - - +
141B ARG* 3.0 42.7 + - + +
172B VAL* 4.1 9.2 + - + +
173B ALA* 1.3 74.4 - - - +
175B TRP* 1.3 68.4 + - - +
176B ASP* 3.8 20.2 + - - +
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Residues in contact with TRP 175 (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* 3.7 32.1 - - + +
34B GLY* 3.3 26.9 - - - -
35B GLU 2.6 28.5 + - - -
37B ARG* 3.4 33.2 - - + +
44B VAL* 4.4 7.0 - - + -
45B GLY 4.5 2.0 - - - -
46B GLY* 4.1 19.3 - - - -
138B TYR 4.0 1.0 - - - +
139B LYS* 3.5 1.4 - - - -
140B VAL* 2.7 47.5 + - + +
142B PHE* 3.7 48.9 - + - -
173B ALA* 4.0 16.6 - - + -
174B GLU* 1.3 74.2 - - - +
176B ASP* 1.3 60.8 + - - +
177B ASP 3.6 3.1 - - - +
178B PHE* 5.2 2.7 - - + +
502B SO4 3.5 11.7 - - - +
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Residues in contact with ASP 176 (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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104B HIS* 2.6 35.0 + - - -
138B TYR 3.3 7.8 - - - +
139B LYS* 3.6 28.3 + - + +
174B GLU* 3.8 22.3 + - - +
175B TRP* 1.3 75.4 - - - +
177B ASP* 1.3 63.2 + - - +
502B SO4 4.4 5.5 + - - -
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Residues in contact with ASP 177 (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 5.5 0.9 - - - -
104B HIS* 3.2 19.8 - - - -
137B THR* 3.6 14.5 - - + +
175B TRP* 3.6 1.2 - - - +
176B ASP* 1.3 88.3 - - - +
178B PHE* 1.3 63.3 + - - +
179B GLU* 3.4 9.8 + - - +
502B SO4 5.3 2.4 + - - +
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Residues in contact with PHE 178 (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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32B PRO 4.4 1.6 - - - -
33B ILE* 3.7 41.3 - - + +
48B TYR* 3.4 46.9 - + + -
71B ILE* 5.6 3.4 - - + -
131B PHE* 3.8 29.8 - + - -
137B THR* 3.2 1.4 - - - -
138B TYR* 2.6 53.7 + + + +
140B VAL* 3.7 28.3 - - + -
175B TRP* 4.9 3.5 + - + +
177B ASP* 1.3 73.0 - - - +
179B GLU* 1.3 70.6 + - - +
180B TRP* 3.7 15.9 + + + -
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Residues in contact with GLU 179 (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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48B TYR* 4.2 9.2 + - - -
136B GLY 3.8 3.1 - - - +
137B THR* 3.6 25.9 + - + +
177B ASP* 3.4 7.4 + - - +
178B PHE* 1.3 87.7 - - - +
180B TRP* 1.3 60.1 + - - +
181B LYS* 3.7 34.7 + - + +
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Residues in contact with TRP 180 (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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48B TYR* 3.9 29.6 - + - -
68B ASP* 3.7 45.3 + - + -
69B CYS* 4.4 1.3 - - + -
131B PHE* 3.4 36.5 - + + +
134B GLY* 3.3 29.9 + - - -
135B LEU* 3.5 14.7 - - - +
136B GLY* 2.9 41.2 + - - +
138B TYR* 4.1 8.3 - - + -
178B PHE* 3.7 16.9 + + + -
179B GLU* 1.3 70.8 - - - +
181B LYS* 1.3 58.8 + - - +
182B GLY* 3.4 42.2 - - - -
183B PRO* 3.6 9.0 - - + -
185B TRP* 4.2 4.9 - + - -
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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