Contacts of the helix formed by residues 169 - 181 (chain B) in PDB entry 2WK6
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 SER 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B ILE* 4.2 1.0 + - - +
168B GLN* 1.3 79.4 - - - +
170B PRO* 1.3 76.3 - - - +
171B GLU* 2.9 23.7 + - - +
172B GLN* 3.0 26.5 + - - +
173B MET* 3.0 17.4 + - - +
190B GLN* 3.4 25.1 + - - -
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Residues in contact with PRO 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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100B GLN* 3.9 27.4 - - + +
101B GLN 6.0 0.7 - - - +
102B LEU* 3.7 32.4 - - + +
103B GLU 6.0 0.7 - - - +
104B TRP* 4.8 1.7 - - - -
168B GLN 4.6 0.7 - - - +
169B SER* 1.3 87.2 - - - +
171B GLU* 1.3 74.2 + - + +
173B MET* 3.0 16.2 + - + +
174B GLN* 3.1 12.7 + - - +
190B GLN* 3.7 20.2 - - + +
191B LEU* 4.1 12.3 - - + -
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Residues in contact with GLU 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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100B GLN* 5.4 2.9 + - - +
169B SER* 2.9 19.5 + - - +
170B PRO* 1.3 94.7 - - + +
172B GLN* 1.3 64.0 + - + +
174B GLN* 2.9 21.5 + - - +
175B VAL* 3.1 16.4 + - + +
190B GLN* 4.6 3.8 + - - -
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Residues in contact with GLN 172 (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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165B ASN* 6.0 1.6 - - - +
167B ILE 4.2 3.7 + - - +
168B GLN* 2.8 35.2 + - + +
169B SER* 3.0 38.1 + - - +
171B GLU* 1.3 77.7 - - + +
173B MET* 1.3 58.3 + - - +
175B VAL* 3.2 9.3 + - - +
176B LEU* 2.8 38.1 + - + +
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Residues in contact with MET 173 (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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102B LEU* 3.8 21.3 - - + -
104B TRP* 3.8 10.1 - - + -
141B PRO* 3.9 6.5 - - + +
143B ILE* 3.4 32.3 - - + -
168B GLN* 4.0 16.4 - - + +
169B SER 3.0 15.0 + - - +
170B PRO* 3.0 12.0 + - - +
172B GLN* 1.3 78.3 - - - +
174B GLN* 1.3 59.3 + - - +
176B LEU* 3.4 9.3 + - - +
177B LEU* 3.1 28.9 + - - +
183B CYS* 3.9 19.1 - - - -
185B VAL* 3.6 16.4 - - + -
191B LEU* 3.4 26.9 - - - -
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Residues in contact with GLN 174 (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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103B GLU 3.5 16.3 - - - +
104B TRP* 3.3 14.3 - - + -
105B PRO* 3.9 22.1 - - - +
108B TRP* 3.6 21.9 - - + -
170B PRO 3.1 8.9 + - - +
171B GLU* 2.9 14.5 + - - +
173B MET* 1.3 74.9 - - - +
175B VAL* 1.3 66.6 + - + +
177B LEU 3.3 1.7 + - - -
178B ASP* 2.9 24.5 + - + +
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Residues in contact with VAL 175 (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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171B GLU* 3.1 12.2 + - + +
172B GLN* 3.5 12.1 - - - +
174B GLN* 1.3 77.1 - - + +
176B LEU* 1.3 71.5 + - + +
178B ASP* 3.2 8.4 + - - +
179B GLN* 2.9 35.1 + - + +
349B ALA* 6.2 0.9 - - + -
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Residues in contact with LEU 176 (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* 3.9 20.4 - - + +
172B GLN* 2.8 26.9 + - + +
173B MET* 3.6 7.4 - - - +
174B GLN 3.2 0.2 - - - -
175B VAL* 1.3 83.6 - - + +
177B LEU* 1.3 52.9 + - - +
179B GLN* 5.1 0.4 - - - -
180B ALA* 2.7 38.0 + - + +
181B GLY 3.4 2.1 + - - -
182B CYS 4.1 4.7 - - - +
183B CYS* 3.4 29.2 - - + -
346B MET* 5.4 0.9 - - + +
349B ALA* 3.5 41.3 - - + +
350B GLN* 3.3 29.8 - - + -
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Residues in contact with LEU 177 (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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104B TRP* 3.4 36.1 - - + -
108B TRP* 3.9 7.0 - - + -
112B LEU* 4.0 16.8 - - + -
139B LYS* 3.3 23.2 + - + -
140B VAL 3.6 24.2 - - - +
141B PRO* 3.7 14.6 - - + -
173B MET 3.1 18.2 + - - +
174B GLN 3.8 3.4 - - - +
176B LEU* 1.3 74.8 - - - +
178B ASP* 1.3 60.6 + - - +
181B GLY* 2.7 49.2 + - - +
182B CYS* 3.6 7.4 - - - -
183B CYS* 4.4 2.7 - - - -
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Residues in contact with ASP 178 (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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108B TRP* 3.8 22.1 - - + -
139B LYS* 4.7 1.6 - - - +
174B GLN* 2.9 18.5 + - + +
175B VAL* 3.4 9.4 - - - +
177B LEU* 1.3 79.1 - - - +
179B GLN* 1.3 74.1 + - - +
181B GLY 5.1 0.2 + - - -
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Residues in contact with GLN 179 (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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175B VAL* 2.9 30.3 + - + +
176B LEU* 4.3 1.8 - - - +
178B ASP* 1.3 96.0 + - - +
180B ALA* 1.3 59.6 + - + +
181B GLY 3.9 0.2 - - - -
342B ARG* 6.2 0.2 - - - -
345B ARG* 3.6 24.1 + - - +
349B ALA* 5.5 7.9 - - + -
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Residues in contact with ALA 180 (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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176B LEU 2.7 17.1 + - - +
179B GLN* 1.3 76.4 - - + +
181B GLY* 1.3 56.7 + - - +
182B CYS* 3.1 13.4 + - - +
342B ARG* 2.9 38.1 + - - +
345B ARG* 3.6 31.0 - - + +
346B MET* 3.8 18.6 - - + +
349B ALA* 5.1 2.9 - - + -
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Residues in contact with GLY 181 (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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134B ALA* 3.6 8.2 - - - +
138B CYS 3.3 11.5 - - - +
139B LYS* 3.3 11.5 - - - -
140B VAL 2.8 23.7 + - - -
176B LEU 3.4 1.4 + - - -
177B LEU* 2.7 33.4 + - - -
180B ALA* 1.3 70.4 - - - +
182B CYS* 1.3 59.0 + - - +
342B ARG* 4.4 8.2 - - - +
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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