Contacts of the helix formed by residues 142 - 147 (chain E) in PDB entry 2V8W
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 PHE 142 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E CYS* 3.7 35.9 - - + -
137E LEU* 4.4 4.5 - - + -
141E SER* 1.3 77.5 - - - +
143E ASP* 1.3 72.5 + - - +
144E ASP 3.5 0.2 + - - -
145E TYR* 3.0 17.3 + - - +
146E SER* 3.2 20.6 + - - +
149E VAL* 3.6 30.1 - - + -
165E ILE* 3.7 27.6 - - + -
178E HIS* 3.4 15.3 - - - +
179E ILE* 3.6 41.1 - - + -
182E VAL* 3.6 31.2 - - + -
183E TYR* 3.9 6.3 - - + -
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Residues in contact with ASP 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 2.9 44.4 + - - +
177A THR* 3.2 38.2 + - + +
216A VAL 5.8 0.2 - - - +
140E GLU* 3.6 9.0 + - - +
141E SER 3.3 3.8 - - - +
142E PHE* 1.3 77.9 - - - +
144E ASP* 1.3 66.6 + - - +
145E TYR* 3.1 1.5 + - + -
146E SER* 3.1 17.7 + - - -
178E HIS* 4.2 13.8 + - + -
51F ARG* 4.0 15.6 + - - +
53F ILE* 4.4 10.9 - - - +
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Residues in contact with ASP 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU* 5.4 2.3 - - - +
177A THR* 4.7 3.5 - - - +
178A HIS* 2.9 35.9 + - - +
181A ARG* 2.6 57.6 + - + +
143E ASP* 1.3 78.1 - - - +
145E TYR* 1.3 63.1 + - + +
146E SER 3.3 1.0 + - - -
147E ASP* 3.4 25.1 + - - +
51F ARG* 3.2 27.9 + - - +
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Residues in contact with TYR 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ARG* 3.2 46.6 + - + +
185A GLU* 4.2 9.4 + - - +
217A VAL* 4.6 6.1 - - + +
142E PHE* 3.2 11.4 - - - +
143E ASP* 3.0 1.2 - - + -
144E ASP* 1.3 76.9 - - + +
146E SER* 1.3 57.7 + - - +
147E ASP 3.2 2.2 - - - -
148E ASP* 2.9 31.3 + - - +
174E GLU* 3.2 30.0 - - + +
175E ALA* 3.5 27.8 - - + -
178E HIS* 3.4 44.9 - + + +
179E ILE* 3.5 19.9 - - + +
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Residues in contact with SER 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E LYS* 3.0 19.4 + - - -
140E GLU* 3.2 41.4 + - - +
141E SER 3.7 0.2 + - - -
142E PHE* 3.2 33.9 + - - +
143E ASP 3.1 13.0 + - - -
145E TYR* 1.3 76.7 - - - +
147E ASP* 1.3 58.4 + - - +
149E VAL* 3.1 19.3 + - - +
51F ARG* 4.7 2.5 - - - -
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Residues in contact with ASP 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E GLN* 5.6 0.9 + - - +
41E ASN* 5.8 0.2 - - - +
95E LYS* 3.8 13.5 + - - +
140E GLU* 4.9 1.9 - - - +
144E ASP 3.4 8.4 + - - +
146E SER* 1.3 77.1 - - - +
148E ASP* 1.3 63.6 + - - +
149E VAL 3.5 1.9 + - - +
168E THR* 4.7 4.7 - - - +
51F ARG* 2.8 46.8 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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