Contacts of the strand formed by residues 175 - 185 (chain C) in PDB entry 6H2V
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 LYS 175 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 1.4 75.7 - - - +
176C ILE* 1.3 59.6 + - - +
206C ARG 4.4 0.4 - - - -
207C PHE* 3.2 6.9 - - - -
208C SER* 2.8 51.4 + - - +
209C PHE 3.3 29.7 + - - +
210C HIS* 3.7 20.8 - - + +
211C HIS* 4.1 8.1 + - - -
303C SO4 4.5 7.3 + - - -
304C SO4 3.1 37.8 + - - +
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Residues in contact with ILE 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C VAL* 3.8 26.9 - - + +
166C GLN* 4.0 28.0 - - + +
169C ALA* 3.7 22.0 - - + -
174C ILE 4.0 1.8 + - - +
175C LYS* 1.3 74.3 - - - +
177C ASP* 1.3 65.4 + - - +
178C ILE* 4.1 9.6 - - + -
205C ILE* 3.4 20.6 - - + -
206C ARG 3.6 3.1 - - - -
207C PHE* 3.7 22.9 - - + -
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Residues in contact with ASP 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C TYR* 3.2 25.8 + - - -
176C ILE* 1.3 79.1 - - - +
178C ILE* 1.4 68.6 + - - +
179C ILE* 3.2 11.8 + - - +
205C ILE* 3.6 3.4 - - - +
206C ARG* 2.9 46.8 + - + +
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Residues in contact with ILE 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ARG* 3.8 33.9 - - + +
166C GLN* 3.9 20.6 - - - +
176C ILE* 4.1 18.8 - - + -
177C ASP* 1.4 75.5 + - - +
179C ILE* 1.3 64.4 + - - +
180C ALA 4.0 9.2 - - - +
181C GLU* 4.4 13.0 - - - +
203C ASP* 3.8 33.0 - - + +
204C LEU 3.8 2.9 - - - +
205C ILE* 3.9 18.2 - - + +
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Residues in contact with ILE 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C THR* 3.8 24.2 - - + -
46C THR* 6.1 0.4 - - + -
47C TYR* 3.7 22.9 - - + +
154C TYR* 3.8 22.2 - - + -
177C ASP* 3.5 16.4 - - - +
178C ILE* 1.3 73.6 - - - +
180C ALA* 1.3 58.3 + - + +
181C GLU* 5.9 0.2 - - - -
204C LEU* 2.8 30.6 + - + +
205C ILE 3.9 3.6 - - - -
206C ARG* 3.5 32.5 - - + +
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Residues in contact with ALA 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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38C CYS* 4.9 7.4 - - - -
178C ILE* 3.6 5.9 - - - +
179C ILE* 1.3 79.2 - - + +
181C GLU* 1.3 64.4 + - - +
182C LEU* 3.8 26.5 - - + -
203C ASP* 3.5 4.0 - - - -
204C LEU* 2.9 38.2 + - + +
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Residues in contact with GLU 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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159C SER* 4.8 4.0 - - - +
162C ARG* 3.1 34.4 + - - +
178C ILE* 4.4 9.9 - - + +
180C ALA* 1.3 73.6 - - - +
182C LEU* 1.3 63.0 + - - +
183C ARG* 2.9 29.7 + - - +
202C VAL 3.9 3.4 - - - -
203C ASP* 3.7 10.5 - - - +
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Residues in contact with LEU 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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34C HIS* 4.6 17.5 - - + +
35C ILE* 3.6 33.4 - - + +
38C CYS* 4.1 27.1 - - + -
39C MET* 5.8 0.4 - - + -
156C LEU* 4.6 8.7 - - + -
159C SER* 4.9 0.2 + - - -
180C ALA* 3.8 22.4 - - + -
181C GLU* 1.3 77.4 - - - +
183C ARG* 1.4 71.5 + - - +
201C GLU* 3.9 0.9 - - - -
202C VAL* 2.9 41.2 + - + +
204C LEU* 4.2 18.4 - - + -
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Residues in contact with ARG 183 (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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34C HIS* 5.8 1.7 - - - -
35C ILE* 3.6 9.7 - - - +
181C GLU* 2.9 42.4 + - - +
182C LEU* 1.4 82.9 - - - +
184C TYR* 1.4 67.9 + - - +
199C ASP* 4.4 8.5 - - - +
200C ILE 3.3 11.9 - - - +
201C GLU* 3.3 39.4 + - - +
302C PG0 5.2 3.8 - - - +
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Residues in contact with TYR 184 (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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29C TYR* 2.7 39.5 + + - -
32C ARG* 3.8 24.9 - - + -
35C ILE* 3.8 32.3 - - + -
126C ASN* 3.5 14.3 + - - -
129C PHE* 4.0 11.6 - - - -
156C LEU* 5.1 0.9 - - + -
183C ARG* 1.4 74.8 - - - +
185C ASP* 1.3 72.7 + - - +
199C ASP* 3.5 8.7 + - - +
200C ILE* 2.9 59.3 + - + +
202C VAL* 3.7 30.3 - - + +
302C PG0 4.9 4.5 - - - -
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Residues in contact with ASP 185 (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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133A ASN* 3.4 26.3 + - - +
32C ARG* 3.0 30.6 + - - +
184C TYR* 1.3 78.3 - - - +
186C LEU* 1.3 61.6 + - - +
198C VAL 3.5 14.0 - - - +
199C ASP* 3.2 19.2 - - - +
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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