Contacts of the helix formed by residues 176 - 182 (chain C) in PDB entry 4YCV
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 ASN 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167C TYR* 5.1 6.1 + - - -
170C HIS* 4.1 0.2 - - - -
172C HIS* 5.2 0.4 - - - -
175C GLY* 1.3 72.1 - - - -
177C PHE* 1.3 76.3 + - - +
178C ALA* 3.9 10.2 + - - +
179C GLU* 3.8 28.8 - - + +
180C CYS* 3.0 26.2 + - - +
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Residues in contact with PHE 177 (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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147C GLN 3.3 27.1 - - - -
148C LYS 4.0 8.5 - - - -
150C ARG* 3.8 34.3 - - + -
165C ALA* 3.8 16.4 - - + -
166C ASN 4.1 10.5 - - - -
167C TYR* 3.6 29.1 - + + -
170C HIS* 3.3 46.1 - + + +
172C HIS* 5.6 0.2 - - + -
175C GLY 3.5 2.8 + - - -
176C ASN* 1.3 77.7 + - - +
178C ALA* 1.3 79.6 + - + +
181C TYR* 3.0 51.6 + + - -
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Residues in contact with ALA 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLN* 5.7 5.8 - - - +
150C ARG* 4.0 19.5 - - - +
176C ASN* 3.6 11.0 + - - +
177C PHE* 1.3 87.3 - - + +
179C GLU* 1.3 64.3 + - - +
181C TYR* 3.7 0.6 - - - -
182C ASP* 2.8 34.6 + - - +
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Residues in contact with GLU 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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176C ASN* 3.6 30.8 + - + +
177C PHE 3.3 0.4 - - - -
178C ALA* 1.3 80.3 - - - +
180C CYS* 1.3 63.2 + - - +
182C ASP* 3.5 11.9 + - - +
183C LYS* 3.8 8.8 + - - +
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Residues in contact with CYS 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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94C GLN* 6.2 2.5 - - - -
170C HIS* 5.9 2.2 - - + +
174C LYS* 5.1 4.5 - - - -
175C GLY* 4.4 18.4 - - - +
176C ASN 3.0 19.3 + - - +
177C PHE* 3.9 2.2 - - - +
179C GLU* 1.3 78.5 - - - +
181C TYR* 1.3 70.7 + - + +
183C LYS* 3.5 18.8 + - - +
184C ILE* 4.2 7.1 + - - +
211C THR 5.5 8.1 - - - +
213C LEU* 6.0 0.3 - - - +
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Residues in contact with TYR 181 (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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150C ARG* 4.2 23.6 + - + +
152C PHE* 3.9 22.3 - + - -
163C VAL* 5.9 1.1 - - + -
165C ALA* 3.5 25.8 - - + +
170C HIS* 4.5 16.2 - + - -
177C PHE* 3.0 49.7 + + + +
178C ALA 4.1 1.8 - - - +
180C CYS* 1.3 80.6 - - + +
182C ASP* 1.3 65.1 + - - +
183C LYS 3.1 2.5 + - - -
184C ILE* 3.4 37.0 + - + +
208C PRO* 3.4 19.4 + - + +
210C GLU* 4.2 2.8 - - - -
211C THR* 2.9 40.6 + - - -
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Residues in contact with ASP 182 (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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145C SER* 5.1 1.8 + - - -
150C ARG* 2.4 41.7 + - - +
178C ALA* 2.8 24.2 + - - +
179C GLU* 3.9 7.6 - - - +
180C CYS 3.3 0.8 - - - -
181C TYR* 1.3 77.7 - - - +
183C LYS* 1.3 62.1 + - - +
184C ILE 3.3 6.4 + - - +
185C ARG* 4.3 14.2 + - - -
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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