Contacts of the helix formed by residues 164 - 180 (chain B) in PDB entry 4WGK
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 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B MET 3.7 2.4 + - - -
163B VAL* 1.3 75.3 - - - +
165B GLN* 1.3 65.7 + - - +
166B ARG 3.8 2.8 + - - -
167B LEU* 3.2 24.0 + - - +
168B ARG* 3.0 19.8 + - - +
202B TYR* 2.7 26.1 + - - -
203B PHE* 3.5 37.0 - - - -
204B GLN 5.4 0.4 - - - -
574B ASN 3.2 8.3 - - - +
575B VAL* 4.5 1.1 - - - +
576B TYR 4.7 2.0 - - - +
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Residues in contact with GLN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 1.3 72.3 - - - +
166B ARG* 1.3 62.8 + - - +
168B ARG* 3.3 4.9 + - - +
169B LEU* 3.0 44.7 + - + +
204B GLN* 3.6 23.3 - - + +
205B TYR* 3.8 22.4 + - + +
429B TRP* 5.1 0.6 + - - -
521B ILE 3.2 25.5 + - - -
523B ASP* 3.2 22.8 + - - +
574B ASN 3.5 8.2 + - - +
575B VAL* 3.9 21.5 - - + +
631B PRO* 3.4 28.3 - - + +
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Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 3.3 5.5 + - - +
165B GLN* 1.3 79.2 - - - +
167B LEU* 1.3 62.6 + - - +
170B GLU* 3.2 24.3 + - - +
202B TYR 4.5 1.3 - - - +
203B PHE 4.4 0.4 - - - -
204B GLN* 3.4 56.1 + - + +
215B PHE* 4.1 24.3 - - - -
220B PHE* 4.0 11.0 - - + -
633B PHE* 3.5 41.8 - - + -
634B PHE 2.4 30.7 + - - -
635B LYS* 4.4 8.5 + - - +
637B LEU* 3.5 27.1 - - - +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE* 5.1 0.9 - - + -
160B ILE* 4.1 24.7 - - + -
163B VAL* 4.4 13.7 - - + -
164B SER* 3.2 33.2 + - - +
166B ARG* 1.3 78.4 - - - +
168B ARG* 1.3 62.5 + - - +
170B GLU* 3.7 1.7 - - - +
171B VAL* 3.0 29.3 + - + +
190B LEU* 5.7 0.9 - - + -
202B TYR* 4.7 2.9 - - + +
220B PHE* 3.7 26.6 - - + -
223B MET* 4.1 19.3 - - + -
224B VAL* 3.9 19.5 - - + -
227B ILE* 4.0 25.8 - - + -
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Residues in contact with ARG 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B VAL* 4.5 1.7 - - + +
164B SER 3.0 7.1 + - - +
165B GLN* 3.3 5.4 + - - +
167B LEU* 1.3 76.6 - - - +
169B LEU* 1.3 63.2 + - + +
171B VAL* 3.3 1.4 + - - +
172B LEU* 2.9 50.7 + - + +
185B ARG* 2.5 45.3 + - - +
188B VAL 2.9 23.8 + - - -
190B LEU* 3.8 25.3 - - + +
427B HIS* 3.7 13.3 + - - -
429B TRP* 5.8 0.2 - - - +
523B ASP* 4.0 15.0 + - - -
525B GLN* 4.1 0.6 + - - -
574B ASN* 2.9 61.9 + - - +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLN* 3.0 36.8 + - + +
168B ARG* 1.3 80.5 - - + +
170B GLU* 1.3 58.0 + - - +
172B LEU* 3.9 13.2 - - + +
173B ASN* 3.0 31.4 + - - +
204B GLN* 5.0 0.2 - - - +
429B TRP* 5.0 11.2 - - + +
630B GLU* 6.5 0.4 - - + -
631B PRO* 4.4 26.2 - - + +
632B PRO 3.8 22.9 - - - +
633B PHE* 3.9 25.6 - - + -
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Residues in contact with GLU 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 ARG 3.2 17.1 + - - +
167B LEU 3.7 3.6 - - - +
169B LEU* 1.3 78.9 - - - +
171B VAL* 1.3 62.0 + - - +
173B ASN* 3.3 8.7 + - - +
174B ARG* 3.2 48.4 + - - +
220B PHE* 3.9 27.0 - - + -
221B GLN* 5.5 6.8 + - - +
224B VAL* 4.0 16.8 - - + -
633B PHE* 3.6 21.6 - - + -
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU 3.0 22.6 + - - +
168B ARG 3.6 3.4 - - - +
170B GLU* 1.3 76.3 - - - +
172B LEU* 1.3 59.0 + - + +
174B ARG* 3.3 1.8 + - - -
175B LEU* 2.9 41.2 + - + +
190B LEU* 4.1 17.7 - - + -
224B VAL* 4.3 22.2 - - + +
227B ILE* 4.1 42.4 - - + -
228B LEU* 3.7 21.5 - - + +
231B ILE* 4.8 0.7 - - + -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG* 2.9 61.2 + - + +
169B LEU* 3.9 13.5 - - + +
171B VAL* 1.3 75.0 - - + +
173B ASN* 1.3 63.5 + - - +
175B LEU* 3.4 13.5 + - + +
176B GLN* 3.0 22.9 + - - +
183B TYR 4.8 3.1 - - - +
184B ARG* 3.7 28.5 - - - +
185B ARG* 3.9 14.8 - - + +
188B VAL* 4.1 20.9 - - + -
190B LEU* 5.5 0.9 - - + -
429B TRP* 6.4 0.7 - - + -
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Residues in contact with ASN 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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169B LEU 3.0 19.3 + - - +
170B GLU* 3.6 12.5 + - - +
171B VAL 3.2 0.2 - - - -
172B LEU* 1.3 77.2 - - - +
174B ARG* 1.3 58.4 + - + +
176B GLN* 3.3 17.9 + - - +
177B SER* 3.1 30.4 + - - -
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLU* 3.2 32.9 + - - +
171B VAL 3.8 0.9 - - - +
173B ASN* 1.3 75.0 - - + +
175B LEU* 1.3 64.1 + - - +
177B SER* 3.4 10.1 + - - -
178B LYS* 3.1 23.9 + - - +
221B GLN* 4.2 12.1 + - - -
224B VAL* 3.6 24.8 - - - +
225B THR* 3.9 21.4 - - - +
228B LEU* 3.3 32.6 - - + +
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Residues in contact with LEU 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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154B VAL* 6.4 0.2 - - + -
171B VAL* 2.9 34.9 + - + +
172B LEU* 3.6 21.1 - - + +
174B ARG* 1.3 77.0 - - - +
176B GLN* 1.3 52.0 + - - +
178B LYS* 4.9 0.2 - - - -
179B TYR* 2.7 67.5 + - + +
180B GLY 4.4 0.6 - - - +
183B TYR* 4.2 28.0 - - + +
188B VAL* 4.5 7.6 - - + -
228B LEU* 3.7 18.8 - - + -
231B ILE* 4.0 28.7 - - + -
232B ASP* 5.2 0.9 - - - +
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Residues in contact with GLN 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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172B LEU 3.0 13.6 + - - +
173B ASN* 3.4 20.5 - - - +
175B LEU* 1.3 75.1 - - - +
177B SER* 1.3 62.0 + - - +
180B GLY* 2.7 49.1 + - - +
183B TYR 4.9 2.4 + - - +
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Residues in contact with SER 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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173B ASN* 3.1 20.2 + - - -
174B ARG* 3.5 12.7 - - - -
176B GLN* 1.3 78.7 + - - +
178B LYS* 1.3 58.1 + - - +
180B GLY 4.8 0.3 + - - -
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Residues in contact with LYS 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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329A GLU* 5.6 3.4 - - - -
406A GLN* 5.8 1.4 + - - -
409A LYS* 3.8 25.3 + - - +
174B ARG 3.1 14.7 + - - +
177B SER* 1.3 81.5 - - - +
179B TYR* 1.3 94.2 + - + +
180B GLY 3.7 0.2 - - - -
232B ASP* 3.5 24.7 + - - +
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Residues in contact with TYR 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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409A LYS* 5.9 2.7 - - - -
175B LEU* 2.7 41.4 + - + +
178B LYS* 1.3 102.0 - - + +
180B GLY* 1.3 61.1 + - - +
181B SER 3.3 3.3 + - - -
182B LEU* 3.3 21.9 + - + +
183B TYR* 3.7 30.3 - + + +
231B ILE* 4.7 1.8 - - + -
232B ASP* 2.3 47.7 + - - +
235B HIS* 3.5 47.1 - + + -
236B THR* 5.4 1.0 - - - +
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Residues in contact with GLY 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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175B LEU 4.4 0.3 - - - +
176B GLN* 2.7 46.3 + - - +
177B SER 4.6 0.4 + - - -
178B LYS 3.7 1.0 - - - -
179B TYR* 1.3 75.9 - - - +
181B SER* 1.3 59.3 + - - -
182B LEU 3.3 1.2 + - - -
183B TYR 4.5 6.6 - - - +
184B ARG* 5.2 0.7 - - - +
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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