Contacts of the strand formed by residues 169 - 174 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E VAL* 3.4 15.7 - - + +
120E TRP* 5.0 1.3 - - + -
143E LEU* 4.2 26.0 - - + -
147E LEU* 4.2 9.9 - - + -
164E ILE* 3.9 26.7 - - + -
165E LYS 3.7 12.6 - - - +
166E PRO* 3.2 11.8 + - + +
167E GLU 3.4 0.4 - - - -
168E HIS* 1.3 83.0 - - - +
170E VAL* 1.3 74.3 + - - +
171E LEU* 4.6 1.8 - - + +
190E ILE* 3.8 18.6 - - + -
191E LYS* 3.4 25.3 + - - +
213E TYR* 4.5 2.8 - - - -
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Residues in contact with VAL 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E VAL 2.9 9.4 + - - +
119E ILE* 3.5 5.6 - - + +
120E TRP* 2.9 25.5 + - - +
169E VAL* 1.3 81.4 - - - +
171E LEU* 1.3 61.4 + - - +
172E ILE* 4.0 4.6 + - + -
191E LYS* 3.4 26.0 - - + +
193E TYR* 3.8 20.9 - - + -
210E THR* 3.2 37.2 - - + +
213E TYR* 3.8 17.0 - - + -
214E LEU* 4.0 16.6 - - + -
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Residues in contact with LEU 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E TRP* 3.4 41.3 - - + +
125E GLY* 4.0 13.9 - - - +
127E VAL* 5.6 0.4 - - + -
143E LEU* 3.8 17.0 - - + -
169E VAL* 4.8 0.2 - - + -
170E VAL* 1.3 74.5 - - - +
172E ILE* 1.3 61.6 + - - +
174E VAL* 3.8 16.6 - - + -
185E ILE* 3.6 34.5 - - + -
190E ILE* 4.3 12.3 - - + -
191E LYS 2.9 11.0 + - - +
192E ILE* 3.5 18.2 - - + -
193E TYR* 2.8 32.0 + - - +
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Residues in contact with ILE 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E ILE* 4.0 23.1 - - + -
120E TRP 2.9 9.3 + - - +
121E TYR* 3.5 28.1 - - + -
122E ASP 3.0 28.1 + - - +
170E VAL* 4.2 9.6 - - + -
171E LEU* 1.3 79.2 - - - +
173E GLY* 1.3 65.2 + - - +
174E VAL 3.4 2.2 - - - -
193E TYR* 3.5 4.3 - - + +
198E VAL* 4.7 3.8 - - + -
203E MET* 4.5 15.0 - - + -
206E VAL* 4.2 21.3 - - + -
207E MET* 3.7 27.8 - - - -
210E THR* 3.8 17.0 - - + +
246E LEU* 4.5 1.0 - - + +
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Residues in contact with GLY 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E ASP 3.0 12.0 - - - +
123E ALA* 3.7 1.4 - - - -
172E ILE* 1.3 75.5 - - - +
174E VAL* 1.3 66.1 + - - +
175E ARG* 3.5 22.9 + - - -
193E TYR 2.9 10.5 + - - -
195E MET* 3.7 16.5 - - - +
198E VAL* 4.5 2.1 - - - +
246E LEU* 3.9 21.8 - - - -
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Residues in contact with VAL 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D LEU* 3.7 0.8 - - - +
122E ASP 3.4 12.8 - - - +
123E ALA 3.5 8.3 - - - +
124E HIS 3.8 13.9 - - - +
171E LEU* 3.8 32.3 - - + -
172E ILE 4.5 3.6 - - - +
173E GLY* 1.3 76.6 - - - +
175E ARG* 1.3 62.7 - - - +
176E SER 4.1 0.9 - - - +
177E LEU* 3.5 40.4 - - + -
192E ILE* 4.0 16.2 - - + -
193E TYR 3.6 2.8 + - - -
194E THR* 3.1 16.0 - - + -
195E MET 3.0 23.9 + - - -
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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