Contacts of the helix formed by residues 163 - 176 (chain B) in PDB entry 5VZ4
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 ASP 163 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B ALA 4.2 4.2 + - - +
156B SER 5.1 0.4 + - - -
159B GLY* 4.0 9.4 - - - +
162B CYS* 1.3 73.2 - - - +
164B LEU* 1.3 58.4 + - - +
165B LYS* 3.5 10.6 + - - +
166B GLN* 3.2 41.5 + - + +
167B CYS* 3.0 24.9 + - - +
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Residues in contact with LEU 164 (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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162B CYS* 3.6 9.4 + - - +
163B ASP* 1.3 68.8 + - - +
165B LYS* 1.3 63.0 + - + +
167B CYS* 3.3 1.4 + - + +
168B GLN* 2.9 59.7 + - + +
210B CYS* 3.5 31.0 - - - +
211B ALA* 4.0 10.3 - - - -
214B MET* 4.1 22.9 - - + -
289B VAL* 5.3 2.9 - - + -
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Residues in contact with LYS 165 (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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163B ASP* 3.5 8.2 + - - +
164B LEU* 1.3 78.5 - - + +
166B GLN* 1.3 61.8 - - - +
168B GLN* 3.5 11.4 + - - +
169B ALA* 3.1 24.3 + - - +
172B ARG* 4.6 2.4 + - - -
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Residues in contact with GLN 166 (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 ALA* 3.7 32.5 - - + +
163B ASP* 3.2 35.8 + - + +
165B LYS* 1.3 74.9 - - - +
167B CYS* 1.3 66.6 + - - +
169B ALA* 3.4 5.9 + - - +
170B ALA* 3.0 22.7 + - - +
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Residues in contact with CYS 167 (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 ALA* 3.6 11.0 - - - +
155B CYS* 2.1 50.8 - - - -
163B ASP 3.0 6.5 + - - +
164B LEU* 3.3 6.9 + - + +
166B GLN* 1.3 75.6 - - - +
168B GLN* 1.3 58.7 + - - +
170B ALA* 3.2 2.9 + - - +
171B ILE* 2.9 43.8 + - - +
210B CYS* 3.4 30.5 - - - -
211B ALA* 3.8 13.5 - - - -
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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
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164B LEU* 2.9 50.3 + - + +
165B LYS* 3.8 9.0 - - - +
166B GLN 3.2 0.2 - - - -
167B CYS* 1.3 77.7 - - - +
169B ALA* 1.3 61.6 + - - +
171B ILE* 3.3 6.1 + - + -
172B ARG* 3.1 29.1 + - - +
211B ALA* 5.0 4.7 + - + -
284B GLY* 3.4 35.7 - - - +
285B THR* 3.4 29.2 + - - -
286B VAL* 3.7 7.7 + - - +
288B GLN* 5.4 0.7 - - - +
289B VAL* 4.4 8.9 - - - +
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Residues in contact with ALA 169 (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 LYS 3.1 17.0 + - - +
166B GLN* 3.8 6.1 - - - +
168B GLN* 1.3 75.2 - - - +
170B ALA* 1.3 58.7 + - - +
172B ARG* 3.3 26.5 + - - +
173B PHE* 2.9 29.2 + - - +
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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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150B SER* 4.2 5.3 - - - +
151B TYR* 4.1 16.3 - - - +
154B ALA* 3.3 33.7 - - + -
155B CYS* 5.2 0.2 - - - -
166B GLN 3.0 9.8 + - - +
167B CYS 3.6 3.1 - - - +
169B ALA* 1.3 77.9 - - - +
171B ILE* 1.3 56.6 + - - +
173B PHE* 3.8 6.4 - - - +
174B PHE* 2.9 28.6 + - - +
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Residues in contact with ILE 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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151B TYR* 3.7 23.6 - - + -
167B CYS* 2.9 34.3 + - - +
168B GLN* 3.7 8.7 - - - +
169B ALA 3.2 0.2 - - - -
170B ALA* 1.3 72.3 - - - +
172B ARG* 1.3 65.3 + - - +
174B PHE* 3.3 6.4 + - + +
175B TYR* 3.1 48.0 + - + -
207B SER* 3.5 23.1 - - - +
211B ALA* 3.8 11.4 - - + -
283B LEU* 4.1 2.7 - - + -
284B GLY* 3.8 17.5 - - - +
288B GLN* 3.8 15.9 - - - +
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Residues in contact with ARG 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 LYS* 4.6 2.4 + - - +
168B GLN* 3.1 20.4 + - - +
169B ALA* 3.3 36.7 + - - +
171B ILE* 1.3 76.9 - - - +
173B PHE* 1.3 62.4 + - - +
175B TYR* 3.4 4.7 + - - +
176B GLN* 3.2 44.1 + - - +
232B LEU* 3.8 41.0 - - - +
281B ASP 5.7 2.2 - - - +
283B LEU 3.7 15.0 - - - +
284B GLY 2.9 26.8 + - - +
285B THR* 4.6 3.2 - - + +
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Residues in contact with PHE 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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147B GLN* 3.6 26.7 - - - -
150B SER* 5.9 5.8 - - - -
169B ALA 2.9 16.5 + - - +
170B ALA* 3.8 7.6 - - - +
172B ARG* 1.3 75.8 - - - +
174B PHE* 1.3 64.7 + - - +
176B GLN* 3.3 8.5 + - - -
177B ASN* 2.9 55.9 + - - +
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Residues in contact with PHE 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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144B CYS* 4.3 5.6 - - - -
147B GLN* 3.3 33.7 - - + +
148B LEU* 3.5 38.4 - - + -
151B TYR* 4.2 22.7 - + + -
170B ALA 2.9 18.2 + - - +
171B ILE* 3.5 5.4 - - - +
173B PHE* 1.3 78.9 - - - +
175B TYR* 1.3 85.3 + + - +
177B ASN* 3.0 20.0 + - - -
178B ILE* 3.4 44.4 + - + +
186B LEU* 3.7 20.9 - - + -
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Residues in contact with TYR 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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151B TYR* 5.8 4.2 - + - -
171B ILE* 3.1 43.5 + - + +
172B ARG* 3.4 4.0 + - - +
173B PHE 3.3 0.2 - - - -
174B PHE* 1.3 98.6 - + - +
176B GLN* 1.3 60.5 + - + +
177B ASN 3.4 0.6 + - - -
178B ILE* 4.0 13.2 - - + +
183B ALA* 3.7 36.7 - - + +
186B LEU* 4.1 8.8 + - + +
187B ALA* 3.9 21.9 + - + -
205B LEU 4.9 4.0 + - - -
206B HIS* 4.8 8.3 - - - -
280B ILE* 3.7 32.6 - - + +
281B ASP* 5.7 1.5 - - - +
283B LEU* 3.7 28.8 - - + +
288B GLN* 6.2 0.2 - - - -
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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 ARG* 3.2 34.9 + - - +
173B PHE* 3.9 8.2 - - - +
174B PHE 3.3 0.2 - - - -
175B TYR* 1.3 77.7 - - + +
177B ASN* 1.3 69.1 + - - +
178B ILE 3.8 2.5 - - - -
232B LEU* 6.1 2.4 - - - +
236B HIS* 5.6 8.9 + - - -
281B ASP* 5.8 6.6 - - - +
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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