Contacts of the helix formed by residues 173 - 181 (chain C) in PDB entry 3VZC
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 PHE 173 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C TRP 4.1 0.6 + - - -
172C GLY* 1.3 70.4 - - - +
174C ILE* 1.3 61.3 + - + +
176C ASP* 3.1 3.7 + - - +
177C VAL* 2.9 36.4 + - + +
196C THR* 3.1 29.2 - - - -
199C ARG* 3.3 45.3 - - + +
200C LEU* 3.6 26.2 - - + -
203C LEU* 4.0 20.6 - - + -
204C ARG 5.9 0.2 - - - +
206C TYR* 3.4 11.5 - - + -
258C VAL* 2.8 23.2 + - + +
259C LEU* 4.1 13.6 - - + +
299C LEU* 4.5 8.7 - - + -
1001C UUL 3.2 28.0 - + - -
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Residues in contact with ILE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ALA* 3.8 18.8 - - + -
171C TRP 5.4 0.4 - - - +
172C GLY 3.3 0.8 - - - -
173C PHE* 1.3 74.4 - - - +
175C ALA* 1.3 63.2 + - - +
177C VAL* 3.2 3.1 + - - +
178C ASP* 3.0 27.5 + - - +
259C LEU* 4.0 25.2 - - + +
260C VAL 5.4 0.4 - - - +
261C LEU* 4.0 26.0 - - + -
268C LEU* 4.4 8.5 - - + -
1001C UUL 3.4 77.2 - - + +
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Residues in contact with ALA 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ALA* 3.6 21.0 - - - +
171C TRP* 3.8 4.7 - - - -
172C GLY 3.0 8.3 + - - +
174C ILE* 1.3 79.0 - - - +
176C ASP* 1.3 63.7 + - - +
178C ASP* 3.3 3.5 + - - +
179C LEU* 3.1 23.0 + - - +
337C VAL* 3.3 31.6 - - + +
338C PHE 4.1 1.1 - - - -
339C ALA* 3.8 20.8 - - - +
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Residues in contact with ASP 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C GLY* 2.9 10.3 + - - +
173C PHE 3.5 7.4 - - - +
175C ALA* 1.3 75.2 - - - +
177C VAL* 1.3 59.5 + - - +
179C LEU* 4.2 3.7 - - - +
180C GLU* 3.0 33.7 + - - +
199C ARG* 4.0 17.6 + - - +
204C ARG* 3.8 12.8 + - - -
206C TYR* 2.6 36.5 + - - +
337C VAL* 3.4 29.8 - - - +
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Residues in contact with VAL 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 2.9 43.5 + - + +
174C ILE 3.2 0.6 + - - +
176C ASP* 1.3 76.1 - - - +
178C ASP* 1.3 56.6 + - - +
180C GLU* 4.8 2.9 - - - -
181C SER* 2.8 35.3 + - - +
192C PHE* 3.9 14.1 - - + +
195C GLY* 3.7 29.4 - - - +
196C THR* 3.8 6.3 - - - +
199C ARG* 3.7 18.6 - - + -
1001C UUL 3.5 26.2 - - + -
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE* 3.0 16.9 + - - +
175C ALA 3.5 9.4 - - - +
176C ASP 3.2 0.2 - - - -
177C VAL* 1.3 79.3 - - - +
179C LEU* 1.3 61.1 + - - +
181C SER* 3.6 12.3 - - - +
191C ARG* 3.8 12.9 + - - +
192C PHE* 3.6 15.3 - - - -
339C ALA* 3.8 15.9 - - + +
342C GLY* 3.7 31.7 + - - +
1001C UUL 2.8 33.0 + - - -
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C ALA 3.1 14.8 + - - +
176C ASP* 4.2 3.1 - - - +
178C ASP* 1.3 75.2 - - - +
180C GLU* 1.3 65.1 + - - +
181C SER 3.2 8.8 - - - +
182C GLU* 5.0 1.7 - - - +
337C VAL* 4.8 9.4 - - + -
344C LEU* 3.8 50.0 - - + -
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Residues in contact with GLU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ASP 3.0 19.2 + - - +
177C VAL* 4.8 3.6 - - - +
179C LEU* 1.3 73.3 - - - +
181C SER* 1.3 65.8 + - - +
182C GLU* 3.5 18.9 + - - +
183C LYS* 4.2 10.8 + - - +
195C GLY* 4.7 6.5 - - - +
198C LEU* 3.3 36.5 - - - +
199C ARG* 4.6 21.2 + - + +
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Residues in contact with SER 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C VAL* 2.8 22.6 + - - +
178C ASP* 3.6 5.4 - - - +
179C LEU 3.2 11.7 - - - +
180C GLU* 1.3 74.2 - - - +
182C GLU* 1.3 65.5 + - - +
183C LYS* 4.2 7.0 - - - +
191C ARG* 2.6 71.1 + - - +
192C PHE* 3.9 3.9 + - - -
195C GLY* 4.6 0.6 - - - -
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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