Contacts of the strand formed by residues 176 - 181 (chain C) in PDB entry 5IHB
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 ILE 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C PRO 5.6 0.2 - - - +
175C PRO* 1.3 77.4 - - + +
177C PHE* 1.3 72.0 + - - +
178C SER* 5.4 4.0 - - - -
190C ARG* 4.6 1.6 - - - +
213C GLN 3.7 0.5 - - - +
214C VAL* 3.2 6.4 - - - +
215C LYS* 2.9 58.4 + - + +
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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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163C CYS* 3.5 25.4 - - - -
164C SER 4.7 0.4 - - - -
165C VAL* 4.3 9.9 - - + -
175C PRO* 3.7 15.3 - - + -
176C ILE* 1.3 83.3 - - - +
178C SER* 1.3 62.3 + - - +
179C TRP* 4.9 6.6 - - + +
190C ARG* 3.4 45.4 + - - +
193C HIS 3.7 28.0 - - - -
194C SER 3.9 1.1 - - - -
195C SER* 3.8 24.9 - - - +
212C CYS* 3.8 11.9 - - - -
213C GLN 3.3 3.4 - - - -
214C VAL* 3.6 25.8 - - + -
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Residues in contact with SER 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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176C ILE* 5.4 4.9 - - - -
177C PHE* 1.3 77.5 - - - +
179C TRP* 1.3 65.9 + - - +
180C LEU* 4.0 10.8 - - - +
211C THR 3.9 0.5 - - - +
212C CYS* 3.6 2.4 - - - -
213C GLN* 2.7 58.5 + - - +
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Residues in contact with TRP 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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147C ILE* 4.5 11.7 - - + -
161C LEU* 4.6 4.7 - - + -
162C THR 4.4 3.1 - - - -
163C CYS* 3.3 38.8 - - + -
177C PHE* 4.9 5.4 - - + +
178C SER* 1.3 82.3 + - - +
180C LEU* 1.3 65.3 + - - +
181C SER* 4.2 1.5 + - - +
187C LEU* 3.5 25.8 - - + +
195C SER* 2.9 37.3 + - - -
197C LEU* 3.5 51.9 - - + +
210C LEU* 4.1 20.6 - - + -
211C THR 3.4 18.2 - - - -
212C CYS* 4.2 13.2 - - + -
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Residues in contact with LEU 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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178C SER* 4.0 15.3 - - - +
179C TRP* 1.3 80.5 - - - +
181C SER* 1.3 62.1 + - - +
209C ASN 4.3 1.0 - - - +
210C LEU* 3.5 5.1 - - - +
211C THR* 3.0 44.8 + - + +
213C GLN* 3.8 37.7 - - + +
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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
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179C TRP* 4.2 2.1 + - - -
180C LEU* 1.3 75.7 - - - +
182C ALA* 1.3 58.7 + - - +
183C ALA* 3.1 26.9 + - - +
185C THR* 3.6 25.2 + - - +
197C LEU* 4.9 2.2 - - - -
199C ILE* 4.9 1.4 - - - +
209C ASN 4.3 8.2 + - - -
210C LEU* 3.5 21.0 - - - +
229C LEU* 5.4 1.2 - - - +
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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