Contacts of the helix formed by residues 179 - 189 (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 PRO 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B VAL* 5.8 4.9 - - + -
144B CYS* 6.5 0.2 - - + -
178B ILE* 1.3 93.6 - - + +
180B PHE* 1.3 64.7 + - - +
181B ASN* 4.0 18.6 - - - +
182B ILE* 3.2 26.8 + - + +
183B ALA* 3.0 18.6 + - - +
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Residues in contact with PHE 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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178B ILE 3.5 2.2 + - - -
179B PRO* 1.3 71.2 - - - +
181B ASN* 1.3 66.1 + - + +
183B ALA* 3.6 7.5 - - + +
184B GLN* 3.0 57.4 + - + +
273B ASP* 4.1 26.5 - - + -
276B LYS* 4.1 7.6 - - + -
277B ALA* 3.7 35.2 - - + -
280B ILE* 4.2 14.6 - - + -
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Residues in contact with ASN 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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179B PRO* 4.0 14.6 - - - +
180B PHE* 1.3 81.9 + - + +
182B ILE* 1.3 84.6 + - + +
184B GLN* 3.5 18.4 + - - +
185B MET* 3.2 33.7 + - + +
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Residues in contact with ILE 182 (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 VAL* 5.7 2.7 - - + -
137B ALA* 6.2 1.6 - - + -
138B CYS* 5.0 5.8 - - + +
144B CYS* 3.9 29.6 - - + -
178B ILE* 4.3 6.3 - - + -
179B PRO* 3.2 32.7 + - + +
181B ASN* 1.3 94.3 - - - +
183B ALA* 1.3 68.0 + - - +
184B GLN 3.2 0.2 - - - -
185B MET* 3.1 21.5 + - + +
186B LEU* 3.0 30.6 + - + +
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Residues in contact with ALA 183 (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 TYR* 3.7 28.1 - - + +
178B ILE* 3.7 17.6 - - + +
179B PRO 3.0 17.0 + - - +
180B PHE* 3.6 12.6 - - + +
182B ILE* 1.3 77.1 - - - +
184B GLN* 1.3 57.1 + - - +
186B LEU* 3.3 2.8 + - - +
187B ALA* 2.8 30.3 + - - +
280B ILE* 4.2 13.0 - - + -
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Residues in contact with GLN 184 (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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129B TRP* 3.7 19.0 - - + -
180B PHE* 3.0 40.1 + - + +
181B ASN* 3.5 20.1 + - - +
182B ILE 3.2 0.2 - - - -
183B ALA* 1.3 73.5 - - - +
185B MET* 1.3 64.7 + - + +
188B PHE* 3.0 51.6 + - + +
273B ASP* 4.4 3.1 + - - +
276B LYS* 3.3 30.3 + - - +
280B ILE* 4.0 10.5 - - + -
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Residues in contact with MET 185 (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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129B TRP* 3.7 43.7 - - + +
134B VAL* 3.7 25.0 - - + +
137B ALA* 6.4 1.8 - - + -
181B ASN* 3.2 30.3 + - + +
182B ILE* 3.1 25.0 + - + +
184B GLN* 1.3 78.3 - - - +
186B LEU* 1.3 60.2 + - - +
189B CYS* 3.1 27.9 + - - +
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Residues in contact with LEU 186 (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 VAL* 3.5 24.7 - - + -
138B CYS* 4.4 12.8 - - + -
144B CYS* 4.4 3.8 - - - -
148B LEU* 5.4 0.2 - - + -
174B PHE* 3.7 17.7 - - + -
175B TYR* 4.1 11.2 - - - +
178B ILE* 3.6 27.4 - - + -
182B ILE* 3.0 28.9 + - + +
183B ALA 3.7 3.8 - - - +
185B MET* 1.3 74.5 - - - +
187B ALA* 1.3 64.8 + - - +
188B PHE 3.3 0.5 + - - -
189B CYS* 3.5 9.4 - - - -
205B LEU* 3.9 33.8 - - + +
206B HIS* 2.8 26.0 + - + +
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Residues in contact with ALA 187 (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 TYR* 3.9 14.1 - - + +
183B ALA 2.8 17.3 + - - +
184B GLN 3.4 3.8 + - - +
186B LEU* 1.3 77.2 - - - +
188B PHE* 1.3 70.7 + - + +
206B HIS* 4.0 6.2 + - - -
279B TYR* 4.5 6.7 + - + -
280B ILE* 3.8 25.1 - - + -
283B LEU* 4.4 10.9 - - + +
313B ARG* 2.8 21.1 + - - -
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Residues in contact with PHE 188 (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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129B TRP* 3.9 20.7 - + + +
184B GLN* 3.0 38.5 + - + +
185B MET 4.1 0.4 - - - -
187B ALA* 1.3 83.5 - - + +
189B CYS* 1.3 69.1 + - - +
190B ASP* 3.6 4.7 + - - +
276B LYS* 3.9 33.4 - - + +
279B TYR* 3.5 34.3 - + - -
280B ILE* 4.2 3.4 - - + -
313B ARG* 3.4 16.5 + - + +
317B PHE* 3.2 53.4 - + + -
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Residues in contact with CYS 189 (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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129B TRP* 3.5 14.6 - - - +
131B CYS* 2.1 57.2 - - - +
134B VAL* 4.1 7.6 - - + -
185B MET 3.1 18.7 + - - +
186B LEU* 3.5 15.7 - - - -
187B ALA 3.6 0.6 - - - -
188B PHE* 1.3 76.5 - - - +
190B ASP* 1.3 58.4 + - - +
205B LEU* 4.4 11.2 - - - -
206B HIS* 3.8 9.8 - - - -
313B ARG* 3.1 22.9 + - - -
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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