Contacts of the strand formed by residues 169 - 174 (chain A) in PDB entry 4CEV
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A VAL* 3.5 13.2 - - + +
120A TRP* 5.0 2.9 - - + -
143A LEU* 4.1 25.6 - - + -
147A LEU* 4.2 10.1 - - + -
164A ILE* 4.0 25.6 - - + -
165A LYS 3.6 16.4 - - - +
166A PRO* 3.2 11.8 + - + +
167A GLU 3.4 0.6 - - - -
168A HIS* 1.3 81.1 - - - +
170A VAL* 1.3 74.5 + - - +
171A LEU* 4.6 1.6 - - + +
190A ILE* 3.8 18.4 - - + -
191A LYS* 3.4 26.8 + - - +
213A TYR* 4.6 2.1 + - - -
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL 2.9 9.2 + - - +
119A ILE* 3.4 6.0 - - + +
120A TRP 2.8 25.3 + - - -
169A VAL* 1.3 80.6 - - - +
171A LEU* 1.3 64.7 + - - +
172A ILE* 4.0 4.0 + - + -
191A LYS* 3.4 12.6 - - + +
193A TYR* 3.8 21.5 - - + -
210A THR* 3.4 36.3 - - + +
213A TYR* 3.8 27.1 - - + -
214A LEU* 3.9 18.4 - - + -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TRP* 3.4 41.7 - - + +
125A GLY* 4.1 14.1 - - - +
127A VAL* 5.6 0.2 - - + -
143A LEU* 3.8 14.8 - - + -
169A VAL* 4.7 0.4 - - + -
170A VAL* 1.3 72.8 - - - +
172A ILE* 1.3 61.3 + - - +
174A VAL* 3.9 12.3 - - + -
185A ILE* 3.7 33.9 - - + -
190A ILE* 4.2 14.8 - - + -
191A LYS 2.9 9.8 + - - +
192A ILE* 3.4 25.8 - - + -
193A TYR* 2.7 33.1 + - - +
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Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE* 4.1 20.4 - - + -
120A TRP 2.9 10.2 + - - +
121A TYR* 3.5 26.4 - - + -
122A ASP 2.9 28.6 + - - +
170A VAL* 4.1 10.1 - - + +
171A LEU* 1.3 80.3 - - - +
173A GLY* 1.3 64.9 + - - +
174A VAL* 3.4 2.4 - - - +
193A TYR* 3.5 11.4 - - + +
198A VAL* 4.9 3.1 - - + -
203A MET* 4.5 14.6 - - + -
206A VAL* 4.2 14.6 - - + -
207A MET* 3.9 22.7 - - - -
210A THR* 3.7 22.2 - - + +
246A LEU* 4.6 1.1 - - + +
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Residues in contact with GLY 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASP 3.0 12.6 - - - +
123A ALA* 3.6 1.6 - - - -
172A ILE* 1.3 73.5 - - - +
174A VAL* 1.3 65.3 + - - +
175A ARG* 3.4 24.3 + - - -
193A TYR 2.9 10.3 + - - -
195A MET* 3.8 16.2 - - - +
198A VAL* 4.5 2.8 - - - +
246A LEU* 3.9 22.0 - - - -
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TRP 5.3 0.2 - - - +
122A ASP 3.4 13.0 - - - +
123A ALA 3.6 9.6 - - - +
124A HIS 3.9 13.0 - - - +
171A LEU* 3.9 32.1 - - + -
172A ILE 4.5 3.4 - - - +
173A GLY* 1.3 75.8 - - - +
175A ARG* 1.3 62.5 + - - +
176A SER 4.1 1.1 - - - +
177A LEU* 3.5 41.3 - - + -
192A ILE* 3.9 15.3 - - + -
193A TYR 3.6 2.8 + - - +
194A THR* 3.0 16.2 - - + -
195A MET 3.0 23.0 + - - -
298C LEU 5.2 0.4 - - - +
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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