Contacts of the strand formed by residues 167 - 173 (chain B) in PDB entry 2CX9
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 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ALA* 5.5 1.1 - - + -
100B ILE* 4.0 20.0 - - + -
112B PHE* 3.9 24.5 - - + +
115B LYS* 5.5 0.4 - - + -
116B LEU* 3.8 29.4 - - + -
121B ALA* 4.2 8.3 - - + -
122B LEU 3.2 1.9 + - - +
123B GLY* 3.3 3.7 - - - -
124B ALA 2.9 24.8 + - - -
165B ALA* 3.4 3.3 - - - +
166B GLY* 1.3 86.4 - - - +
168B TYR* 1.3 72.8 + - - +
169B VAL* 5.0 1.3 - - + -
192B PHE 3.6 6.3 - - - +
193B PHE* 3.9 24.5 - - + -
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Residues in contact with TYR 168 (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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124B ALA* 3.4 26.7 - - + +
126B GLY 6.3 0.2 - - - -
162B GLY 2.6 30.0 + - - -
165B ALA* 3.5 31.0 + - + +
167B VAL* 1.3 78.1 - - - +
169B VAL* 1.3 65.3 + - - +
170B VAL* 4.4 6.1 - - + -
190B PHE 3.5 1.4 - - - +
191B ALA* 3.1 4.2 - - - +
192B PHE* 2.8 58.4 + + + -
194B ARG* 3.9 33.3 + - + -
199B LEU* 3.5 31.5 - - + +
201B VAL* 4.5 3.6 - - - +
218B LEU* 3.8 20.6 - - + -
220B LEU* 6.5 0.2 - - + -
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 3.8 28.9 - - + +
99B HIS* 3.6 29.4 - - + +
100B ILE* 3.9 21.8 - - + -
124B ALA 3.0 7.1 + - - +
125B TRP* 3.5 14.3 - - + +
126B GLY 2.8 25.8 + - - -
167B VAL* 5.0 0.4 - - + -
168B TYR* 1.3 79.3 - - - +
170B VAL* 1.3 61.9 + - - +
171B MET* 4.0 7.0 - - - +
189B ALA* 4.6 2.5 - - + -
190B PHE 3.1 6.7 - - - +
191B ALA* 4.0 4.7 - - + -
231B LEU* 4.0 12.8 - - + -
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLY* 3.7 8.5 - - - +
141B THR* 4.5 4.3 - - + -
152B LEU* 4.8 6.5 - - + -
156B LYS* 3.7 25.6 - - + -
168B TYR* 4.4 9.0 - - + -
169B VAL* 1.3 81.2 - - - +
171B MET* 1.3 71.4 + - - +
172B ALA* 5.1 1.1 - - + -
189B ALA* 3.5 1.0 - - - -
190B PHE* 2.7 42.4 + - + -
192B PHE* 3.9 28.9 - - + -
218B LEU* 5.3 6.7 - - + -
220B LEU* 3.8 27.4 - - + -
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Residues in contact with MET 171 (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 HIS* 3.8 13.2 - - - -
125B TRP* 3.4 40.8 - - + +
126B GLY 3.1 33.3 + - - +
127B LEU* 3.8 13.5 - - + -
139B LEU* 3.5 21.3 - - + +
141B THR* 3.8 0.9 - - - -
156B LYS* 2.7 31.2 + - - -
169B VAL* 4.0 5.6 - - - +
170B VAL* 1.3 75.2 - - - +
172B ALA* 1.3 62.3 - - - +
187B ILE* 4.3 6.5 - - + -
188B SER 3.3 9.0 - - - +
189B ALA* 3.7 20.9 - - + -
237B GLY 5.3 0.4 - - - +
241B VAL* 3.6 19.7 - - + -
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Residues in contact with ALA 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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139B LEU* 4.2 2.6 - - - +
141B THR* 3.5 25.4 - - + -
142B LYS 3.8 15.3 - - - -
143B ALA* 3.9 4.7 - - + -
152B LEU* 3.8 16.6 - - + -
170B VAL* 3.8 1.7 + - + +
171B MET* 1.3 75.2 - - - +
173B ARG* 1.3 64.6 + - - +
174B THR* 3.3 4.3 + - - +
187B ILE* 4.5 3.8 - - - -
188B SER* 2.8 31.9 + - - +
190B PHE* 4.4 4.0 - - + -
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Residues in contact with ARG 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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137B ALA 3.4 17.4 + - - -
138B ALA* 5.3 0.6 - - - +
139B LEU* 4.8 19.5 + - + +
140B LYS 5.6 0.2 - - - -
141B THR 2.9 19.0 + - - +
142B LYS* 3.5 11.2 - - + +
143B ALA 2.8 24.9 + - - +
172B ALA* 1.3 69.8 - - - +
174B THR* 1.3 60.3 + - - +
175B ASP 3.0 24.9 - - - +
176B PRO* 4.5 1.3 - - + -
177B PRO* 2.9 28.1 - - - +
183B LYS* 2.9 36.3 + - - +
185B GLN 2.9 17.4 + - - -
186B GLY* 3.5 14.6 - - - -
187B ILE* 3.6 12.2 - - + +
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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