Contacts of the strand formed by residues 196 - 204 (chain C) in PDB entry 3HB8
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 HIS 196 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C GLU* 5.7 2.8 + - - -
91C PHE* 5.8 5.8 - + - -
135C TYR* 3.0 41.7 + + + +
181C ALA* 3.9 7.8 - - - +
194C PRO* 4.1 3.2 - - - +
195C CYS* 1.3 83.6 - - + +
197C ALA* 1.3 67.5 + - - +
198C LEU* 3.5 2.9 + - - -
212C LEU* 3.7 13.2 - - + +
213C TYR 3.9 5.6 - - - -
214C GLN* 3.6 15.2 + - - +
226C ASN* 2.9 38.1 + - + -
229C SER* 6.1 2.0 - - - -
230C TYR* 3.4 37.6 + + - +
365C UMP 3.9 10.4 + - - -
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Residues in contact with ALA 197 (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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180C CYS* 3.8 1.3 - - - -
181C ALA* 2.9 26.0 + - - +
182C TRP* 3.3 36.0 + - + +
194C PRO* 4.5 0.9 + - - +
195C CYS 3.5 4.6 + - - -
196C HIS* 1.3 71.7 - - - +
198C LEU* 1.3 67.8 + - + +
213C TYR* 3.1 32.2 + - + +
215C ARG* 5.0 7.2 - - + +
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Residues in contact with LEU 198 (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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178C ILE* 3.8 26.2 - - + -
179C MET 3.2 15.3 - - - +
180C CYS* 3.8 21.5 - - + -
181C ALA* 4.6 0.4 - - - +
196C HIS* 3.5 1.7 - - - -
197C ALA* 1.3 85.5 - - + +
199C CYS* 1.3 71.6 + - - +
200C GLN* 4.6 5.2 - - + +
212C LEU* 3.5 5.8 - - - +
213C TYR* 2.9 38.2 + - + +
230C TYR* 6.1 0.2 - - - -
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Residues in contact with CYS 199 (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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177C ILE 4.1 0.2 - - - +
178C ILE* 3.5 4.7 - - - +
179C MET* 3.0 57.7 + - - +
198C LEU* 1.3 83.0 - - - +
200C GLN* 1.3 60.0 + - - +
201C PHE* 4.0 21.9 - - - -
210C CYS* 4.4 6.1 - - - -
211C GLN 3.0 15.0 - - - +
212C LEU* 4.0 6.7 - - + -
230C TYR* 4.0 28.0 - - + -
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Residues in contact with GLN 200 (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 ARG* 3.2 29.3 - - - +
177C ILE 3.4 10.5 - - - +
178C ILE* 4.1 18.7 - - + +
198C LEU* 4.6 5.6 - - + +
199C CYS* 1.3 75.2 - - - +
201C PHE* 1.3 77.7 + - - +
202C TYR* 5.6 2.1 - - + +
210C CYS* 3.3 5.9 - - - -
211C GLN* 2.7 52.7 + - + +
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Residues in contact with PHE 201 (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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164C VAL* 3.3 37.7 - - + -
168C ILE* 4.4 3.4 - - + -
174C ASP 4.7 2.9 - - - +
175C ARG* 5.5 1.2 - - - -
177C ILE* 2.8 46.2 + - + +
179C MET* 4.9 4.5 - - + -
199C CYS* 4.0 16.6 - - - -
200C GLN* 1.3 83.5 - - - +
202C TYR* 1.3 61.1 + - - +
208C LEU* 4.3 17.7 - - + -
209C SER 3.5 14.4 - - - +
210C CYS* 3.2 32.5 - - + -
233C LEU* 3.9 17.3 - - + -
234C THR* 4.2 9.9 - - - -
237C ILE* 3.5 23.8 - - + -
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Residues in contact with TYR 202 (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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173C ASP 6.1 0.9 - - - -
174C ASP 5.8 0.7 - - - -
175C ARG* 6.1 6.7 - - + -
177C ILE* 5.3 0.2 - - - -
200C GLN* 5.6 2.7 - - + +
201C PHE* 1.3 75.6 - - - +
203C VAL* 1.3 68.5 + - - +
204C VAL* 3.5 43.8 - - + +
207C GLU 3.6 0.7 - - - +
208C LEU* 3.5 4.5 - - - +
209C SER* 2.7 56.4 + - - +
210C CYS* 5.9 0.2 - - - -
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Residues in contact with VAL 203 (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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168C ILE* 4.0 21.3 - - + -
172C PRO* 3.1 49.2 + - + +
173C ASP* 4.1 10.9 - - - +
174C ASP 5.8 0.2 + - - -
177C ILE* 4.5 5.1 - - + +
202C TYR* 1.3 85.8 - - - +
204C VAL* 1.3 65.6 + - - +
206C SER 5.1 2.7 - - - +
207C GLU 3.4 6.5 - - - +
208C LEU* 3.6 21.8 - - + -
243C LEU* 3.8 24.9 - - + -
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Residues in contact with VAL 204 (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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202C TYR* 3.5 36.5 - - + +
203C VAL* 1.3 76.3 - - - +
205C ASN* 1.3 89.8 + - + +
206C SER 3.3 1.8 - - - -
207C GLU* 2.9 27.5 + - + +
209C SER* 5.7 2.0 - - - +
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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