Contacts of the strand formed by residues 177 - 181 (chain C) in PDB entry 3BQM
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 TYR 177 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C VAL* 4.5 2.2 - - + -
172C GLN 3.4 5.6 - - - +
173C PHE* 3.7 11.0 - - + -
174C SER 4.8 0.2 - - - -
175C THR 3.9 14.1 + - - -
176C SER* 1.3 97.8 + - - +
178C LYS* 1.3 63.0 + - - +
179C THR 4.3 0.2 - - - -
202C MET* 4.1 1.1 - - - -
207C ASN* 3.4 26.6 + - + +
210C GLY* 3.2 29.3 - - - -
211C ALA* 3.3 25.1 - - + -
214C TYR* 3.7 51.4 + + + -
244C ASP* 4.1 0.7 + - - -
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Residues in contact with LYS 178 (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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171C VAL* 3.2 4.2 - - - +
172C GLN* 2.9 36.9 + - - +
177C TYR* 1.3 74.8 - - - +
179C THR* 1.3 71.2 + - - +
180C GLU* 3.0 39.4 + - - +
198C HIS* 4.0 22.2 + - - +
199C VAL* 5.0 0.6 - - - +
200C LYS* 5.1 3.8 - - - +
202C MET* 3.6 19.5 - - + +
214C TYR* 4.5 0.4 - - - -
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Residues in contact with THR 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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170C ALA 3.7 5.4 - - - +
171C VAL* 4.2 7.4 - - + -
178C LYS* 1.3 78.2 - - - +
180C GLU* 1.3 62.0 + - - +
181C PHE* 3.7 27.7 - - - +
182C ASP* 3.9 15.7 - - + +
214C TYR* 2.6 35.0 + - - -
218C GLU 5.1 1.9 + - - -
219C VAL* 3.8 13.4 - - + +
224C LEU* 5.3 5.6 - - + +
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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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136C PHE* 4.0 14.1 - - + -
170C ALA 2.8 14.1 + - - +
172C GLN* 3.0 39.6 - - - +
178C LYS* 3.0 48.8 + - - +
179C THR* 1.3 72.5 - - - +
181C PHE* 1.3 62.6 + - - +
185C ASP* 5.0 0.2 - - - +
195C LEU 4.0 8.3 - - - +
196C LEU* 4.3 18.2 - - + -
198C HIS* 4.6 0.9 - - - +
199C VAL* 3.9 25.4 + - + +
200C LYS 4.6 0.5 + - - -
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Residues in contact with PHE 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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158C MET* 3.5 29.8 - - + -
168C PHE* 3.5 22.4 - - + -
169C ALA* 3.3 10.3 - - - +
170C ALA* 2.9 53.1 + - + +
179C THR* 3.7 7.4 - - - +
180C GLU* 1.3 78.6 - - - +
182C ASP* 1.3 70.6 + - - +
185C ASP* 3.6 19.1 - - + +
186C TYR* 4.1 4.3 - - + -
195C LEU* 3.7 49.4 - - + +
196C LEU* 3.6 24.7 - - + -
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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