Contacts of the helix formed by residues 165 - 171 (chain B) in PDB entry 2W99
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 TYR 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA 5.1 0.4 - - - -
17B TYR* 3.5 44.3 + + + -
35B LYS* 3.7 17.2 - - - +
36B SER 2.3 33.0 + - - -
37B VAL* 3.1 34.4 - - + +
91B LEU* 4.3 7.2 - - + +
161B LEU* 2.9 49.8 + - + +
162B ALA 3.3 4.5 + - - +
163B ARG 3.1 0.4 - - - -
164B ILE* 1.3 81.4 - - + +
166B SER* 1.3 50.4 + - - +
167B TYR 2.7 6.9 + - - +
168B GLN* 2.5 58.9 + - + +
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ALA 3.3 10.1 + - - -
163B ARG* 3.0 21.0 + - - -
164B ILE 3.4 1.0 - - - -
165B TYR* 1.3 75.6 - - - +
167B TYR* 1.3 57.4 + - - +
168B GLN* 3.0 7.2 + - - +
169B MET* 3.8 15.2 + - - +
170B ALA 5.0 0.3 + - - -
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Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 6.4 0.4 - - - -
38B ARG* 3.2 33.4 - - + +
39B VAL* 4.1 2.0 - - + -
40B PRO* 3.7 38.0 - - + +
85B ARG* 3.8 19.6 + - - +
86B GLU* 3.1 36.3 + - + -
164B ILE 4.6 4.8 + - - +
165B TYR* 2.7 5.8 + - - +
166B SER* 1.3 73.8 - - - +
168B GLN* 1.3 61.2 + - - +
169B MET 3.5 0.2 - - - -
170B ALA* 3.5 28.5 - - + +
171B LEU 4.8 0.2 + - - -
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Residues in contact with GLN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA* 3.3 35.6 + - - +
17B TYR* 4.6 6.7 - - - -
37B VAL* 6.3 0.2 - - - +
162B ALA* 4.9 4.5 - - - +
165B TYR* 2.5 50.1 + - + +
166B SER* 4.6 2.4 - - - +
167B TYR* 1.3 69.2 - - - +
169B MET* 1.3 80.9 + - + +
170B ALA 2.8 4.7 - - - -
171B LEU* 2.5 39.6 + - - +
173B PRO* 3.4 11.4 + - + +
174B VAL* 5.5 3.8 - - - +
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Residues in contact with MET 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B SER* 3.8 10.2 + - - +
167B TYR 3.5 0.6 - - - -
168B GLN* 1.3 92.6 - - + +
170B ALA* 1.3 54.7 + - - +
171B LEU 3.0 5.2 - - - -
172B ALA* 3.3 29.8 + - - +
173B PRO* 3.9 24.5 - - - +
176B VAL* 6.1 4.3 - - + -
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Residues in contact with ALA 170 (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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166B SER 5.0 0.2 + - - -
167B TYR* 3.5 35.7 + - + +
168B GLN 2.7 4.0 + - - -
169B MET* 1.3 74.6 - - - +
171B LEU* 1.3 57.2 + - - +
172B ALA* 3.5 0.7 - - - -
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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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168B GLN* 2.5 13.1 + - - +
170B ALA* 1.3 78.9 - - - +
172B ALA* 1.3 63.7 + - - +
173B PRO* 3.0 27.7 - - + +
174B VAL* 5.0 5.2 - - + -
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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