Contacts of the strand formed by residues 169 - 174 (chain B) in PDB entry 5CEV
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 169 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B VAL* 3.4 16.8 - - + +
120B TRP* 4.9 1.6 - - + -
143B LEU* 4.1 28.7 - - + -
147B LEU* 4.1 11.7 - - + -
164B ILE* 4.0 20.0 - - + -
165B LYS 3.6 16.2 - - - +
166B PRO* 3.2 11.2 + - + +
167B GLU 3.4 0.6 - - - -
168B HIS* 1.3 80.9 - - - +
170B VAL* 1.3 75.9 + - - +
171B LEU* 4.7 1.6 - - + +
190B ILE* 3.8 19.3 - - + -
191B LYS* 3.5 22.7 + - - +
213B TYR* 4.6 2.3 - - - -
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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
----------------------------------------------------------
118B VAL 2.9 9.6 + - - +
119B ILE* 3.4 6.0 - - + +
120B TRP 2.9 24.6 + - - +
169B VAL* 1.3 81.4 - - - +
171B LEU* 1.3 65.0 + - - +
172B ILE* 3.9 4.0 + - + -
191B LYS* 3.3 13.7 - - + +
193B TYR* 3.9 20.9 - - + -
210B THR* 3.4 37.2 - - + +
213B TYR* 3.8 26.9 - - + -
214B LEU* 4.0 16.6 - - + -
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Residues in contact with LEU 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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120B TRP* 3.4 41.7 - - + +
124B HIS 4.2 1.3 - - - +
125B GLY* 4.1 7.6 - - - +
143B LEU* 3.9 15.0 - - + -
169B VAL* 4.7 0.4 - - + -
170B VAL* 1.3 74.5 - - - +
172B ILE* 1.3 60.4 + - - +
174B VAL* 3.9 14.1 - - + -
185B ILE* 3.7 31.6 - - + -
190B ILE* 4.1 21.5 - - + -
191B LYS 2.8 7.2 + - - +
192B ILE* 3.5 24.0 - - + -
193B TYR* 2.8 32.1 + - - +
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Residues in contact with ILE 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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119B ILE* 3.9 21.5 - - + -
120B TRP 2.9 10.8 + - - +
121B TYR* 3.4 30.0 - - + -
122B ASP 2.9 27.4 + - - -
170B VAL* 4.1 11.2 - - + +
171B LEU* 1.3 80.1 - - - +
173B GLY* 1.3 64.5 + - - +
174B VAL* 3.4 2.0 - - - +
193B TYR* 3.6 9.2 - - + +
198B VAL* 4.8 2.7 - - + -
203B MET* 4.4 12.8 - - + -
206B VAL* 4.2 16.6 - - + -
207B MET* 3.8 25.1 - - - -
210B THR* 3.8 21.1 - - + +
246B LEU* 4.3 0.2 - - - +
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Residues in contact with GLY 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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122B ASP 2.9 9.1 - - - +
172B ILE* 1.3 75.5 - - - +
174B VAL* 1.3 65.1 + - - +
175B ARG* 3.1 26.3 + - - -
193B TYR 3.0 11.1 + - - -
195B MET* 3.7 16.2 - - - +
198B VAL* 4.5 1.9 - - - +
246B LEU* 3.7 22.0 - - - -
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Residues in contact with VAL 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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298A LEU* 3.8 0.8 - - - +
122B ASP 2.9 13.0 + - - +
123B ALA 3.4 8.5 - - - +
124B HIS 3.8 15.0 - - - +
171B LEU* 3.9 32.1 - - + -
172B ILE 4.6 2.7 - - - +
173B GLY* 1.3 76.3 - - - +
175B ARG* 1.3 61.5 + - - +
176B SER 4.1 1.3 - - - +
177B LEU* 3.5 40.8 - - + -
192B ILE* 4.1 16.6 - - + -
193B TYR 3.7 2.2 + - - -
194B THR* 3.1 14.5 - - + -
195B MET 3.1 23.0 + - - -
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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