Contacts of the strand formed by residues 169 - 174 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F VAL* 3.4 17.7 - - + +
120F TRP* 5.0 1.3 - - + -
143F LEU* 4.1 27.8 - - + -
147F LEU* 4.2 10.8 - - + -
164F ILE* 3.9 21.8 - - + -
165F LYS 3.7 13.5 - - - +
166F PRO* 3.2 10.7 + - + +
167F GLU 3.4 0.6 - - - -
168F HIS* 1.3 82.3 - - - +
170F VAL* 1.3 72.3 + - - +
171F LEU* 4.7 1.6 - - + +
190F ILE* 3.7 18.2 - - + -
191F LYS* 3.3 27.8 + - - +
213F TYR* 4.5 1.6 - - - -
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Residues in contact with VAL 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F VAL 3.0 8.7 + - - +
119F ILE* 3.4 6.1 - - + +
120F TRP* 2.8 24.9 + - - +
169F VAL* 1.3 80.3 - - - +
171F LEU* 1.3 65.5 + - - +
172F ILE* 4.0 3.8 + - + -
191F LYS* 3.2 13.2 - - + +
193F TYR* 3.8 22.9 - - + -
210F THR* 3.4 37.2 - - + +
213F TYR* 3.7 28.0 - - + -
214F LEU* 3.9 16.6 - - + -
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Residues in contact with LEU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F TRP* 3.4 41.7 - - + +
124F HIS 4.1 2.0 - - - +
125F GLY* 4.1 9.4 - - - +
127F VAL* 5.4 0.2 - - + -
143F LEU* 4.0 15.5 - - + -
169F VAL* 4.8 0.7 - - + -
170F VAL* 1.3 74.1 - - - +
172F ILE* 1.3 64.6 + - - +
174F VAL* 3.8 21.3 - - + -
185F ILE* 3.6 33.2 - - + -
190F ILE* 4.1 19.5 - - + -
191F LYS 2.8 7.7 + - - +
192F ILE* 3.5 16.2 - - + -
193F TYR* 2.8 28.1 + - - +
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Residues in contact with ILE 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F ILE* 3.9 24.0 - - + -
120F TRP 2.9 11.3 + - - +
121F TYR* 3.5 26.8 - - + -
122F ASP 3.0 27.1 + - - +
170F VAL* 4.0 9.4 - - + -
171F LEU* 1.3 79.4 - - - +
173F GLY* 1.3 65.3 + - - +
174F VAL 3.4 2.0 - - - -
193F TYR* 3.6 9.2 - - + +
198F VAL* 4.8 3.6 - - + -
203F MET* 4.6 9.0 - - + -
206F VAL* 4.2 15.9 - - + -
207F MET* 3.9 21.8 - - - -
210F THR* 3.7 23.8 - - + +
246F LEU* 4.4 5.9 - - + +
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Residues in contact with GLY 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F ASP 2.9 12.3 - - - +
172F ILE* 1.3 74.6 - - - +
174F VAL* 1.3 65.3 + - - +
175F ARG* 3.1 23.2 + - - -
193F TYR 2.9 11.0 + - - -
195F MET* 3.8 16.5 - - - +
198F VAL* 4.5 2.6 - - - +
246F LEU* 3.8 22.2 - - - -
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Residues in contact with VAL 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E LEU* 3.7 1.1 - - - +
122F ASP 3.4 11.9 - - - +
123F ALA 3.6 9.4 - - - +
124F HIS 4.0 14.4 - - - +
171F LEU* 3.8 32.8 - - + -
172F ILE 4.6 3.1 - - - +
173F GLY* 1.3 76.4 - - - +
175F ARG* 1.3 63.3 + - - +
176F SER 4.1 1.1 - - - +
177F LEU* 3.5 40.2 - - + -
192F ILE* 3.9 17.7 - - + -
193F TYR 3.6 2.8 + - - -
194F THR* 3.1 13.0 - - + -
195F MET 3.0 23.6 + - - -
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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