Contacts of the strand formed by residues 170 - 178 (chain B) in PDB entry 1CPJ
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 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ALA* 4.2 6.7 - - - -
41B ARG* 3.8 14.8 - - - +
80B TRP* 5.6 0.2 - - - -
160B ILE* 4.8 2.2 - - + +
163B GLU* 4.0 18.6 - - + -
164B ILE* 4.0 14.6 - - + +
168B GLY 4.0 2.9 - - - +
169B PRO* 1.3 78.6 - - - +
171B GLU* 1.3 61.0 + - - +
202B ARG* 3.1 7.1 - - - +
203B ILE* 2.7 63.7 + - + +
246B ILE* 3.7 32.1 - - + -
247B VAL 3.9 2.9 - - - +
248B ALA* 4.2 7.9 - - + -
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Residues in contact with GLU 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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30B TRP* 3.0 22.2 - - - +
33B GLY* 3.5 15.4 - - - +
34B ALA* 3.1 23.3 + - - +
37B ALA* 4.2 3.4 - - - +
76B PRO* 3.4 25.6 - - + +
80B TRP* 2.9 28.5 + - + +
170B VAL* 1.3 77.6 - - - +
172B GLY* 1.3 67.0 + - - +
200B ALA* 3.8 10.4 - - - +
201B ILE 3.4 12.1 - - - +
203B ILE 5.3 0.2 - - - -
245B GLU 4.4 0.2 - - - -
246B ILE* 3.3 8.8 - - - +
247B VAL* 3.0 37.7 + - + +
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Residues in contact with GLY 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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76B PRO* 5.5 2.5 - - - -
171B GLU* 1.3 79.6 - - - +
173B ALA* 1.3 60.4 + - - +
200B ALA* 3.2 7.8 - - - +
201B ILE* 2.8 42.0 + - - +
203B ILE* 4.9 0.7 - - - -
245B GLU 3.2 14.8 - - - -
246B ILE* 4.0 11.9 - - - -
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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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76B PRO* 5.2 6.3 - - + -
172B GLY* 1.3 75.7 - - - +
174B PHE* 1.3 66.4 + - - +
198B GLY* 5.8 1.6 - - - -
199B HIS 3.2 16.6 - - - +
200B ALA* 4.1 8.3 - - + +
201B ILE* 4.2 1.0 - - - +
241B GLY 3.1 22.2 - - - +
242B ILE* 3.7 8.5 + - - +
245B GLU* 3.5 35.3 + - + +
246B ILE* 5.0 1.6 - - - +
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Residues in contact with PHE 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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173B ALA* 1.3 78.1 - - - +
175B THR* 1.3 76.9 + - - +
176B VAL* 3.4 22.7 + - + -
180B PHE* 3.8 39.5 - + - -
188B TYR* 5.4 1.6 - + - -
198B GLY* 3.5 3.1 - - - -
199B HIS* 2.9 53.5 + + + -
201B ILE* 3.8 24.9 - - + -
231B PHE* 3.8 9.9 - + - -
233B ILE* 3.9 19.3 - - + -
240B CYS* 3.2 18.6 - - + +
241B GLY* 4.5 0.4 - - - -
242B ILE* 3.7 18.8 - - + -
245B GLU* 5.7 0.2 - - - -
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Residues in contact with THR 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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75A TYR* 2.8 38.0 + - - +
174B PHE* 1.3 76.5 - - - +
176B VAL* 1.3 66.8 + - - +
177B PHE* 3.8 23.5 + - + -
188B TYR* 5.9 0.3 - - - -
195B VAL* 5.2 6.5 - - + -
197B GLY* 3.5 15.5 - - - +
198B GLY* 4.6 1.5 - - - -
240B CYS* 2.8 30.1 + - - +
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Residues in contact with VAL 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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174B PHE* 3.6 23.6 - - + +
175B THR* 1.3 75.6 - - - +
177B PHE* 1.3 70.2 + - - +
180B PHE* 3.9 20.2 - - + -
181B LEU* 4.5 11.4 - - + -
195B VAL* 3.8 1.7 - - - -
196B MET* 2.8 41.2 + - + -
197B GLY 2.6 20.2 + - - +
198B GLY 4.5 0.7 - - - +
199B HIS* 3.4 34.5 - - + -
221B TRP* 5.3 2.9 - - + -
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Residues in contact with PHE 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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69A ASP* 6.1 5.2 - - + -
75A TYR* 5.2 2.7 - - - -
175B THR* 3.9 26.2 - - + -
176B VAL* 1.3 81.9 - - - +
178B SER* 1.3 59.8 + - - +
179B ASP* 3.2 17.3 - - - +
180B PHE* 3.0 28.4 + - - +
181B LEU* 3.9 1.0 + - - +
188B TYR* 4.6 2.3 + - - -
190B HIS* 3.1 40.2 - + + -
193B GLY 3.5 13.5 - - - -
194B ASP 3.1 14.8 - - - +
195B VAL* 3.4 27.6 - - + -
196B MET* 4.1 1.8 - - - -
240B CYS* 3.8 20.9 - - - -
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Residues in contact with SER 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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177B PHE* 1.3 71.5 - - - +
179B ASP* 1.3 60.4 + - - +
180B PHE 3.2 0.2 - - - -
181B LEU* 3.4 35.1 + - - +
182B THR* 4.5 6.4 + - - +
193B GLY* 3.5 4.3 - - - -
194B ASP* 2.8 42.1 + - - +
196B MET* 3.9 10.7 - - - +
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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