Contacts of the strand formed by residues 177 - 180 (chain R) in PDB entry 3EPD
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 177 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147R ASN* 4.3 0.9 - - - +
166R CYS* 4.5 8.5 - - - +
168R SER* 4.0 15.7 - - - -
175R ALA 2.9 10.8 + - - +
176R GLN* 1.3 71.2 - - - +
178R THR* 1.3 63.3 + - - +
191R GLN* 3.8 20.0 - - + +
203R THR* 3.1 32.5 - - + +
204R SER 4.1 0.9 - - - +
205R LEU* 3.3 47.9 - - + +
221R CYS* 4.8 1.3 - - - -
222R LYS 4.0 3.1 - - - -
223R VAL* 3.8 32.8 - - + +
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Residues in contact with THR 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176R GLN* 4.0 12.8 - - + +
177R ILE* 1.3 78.8 - - - +
179R TRP* 1.3 63.3 + - - +
180R HIS* 3.6 9.5 + - - -
205R LEU* 4.0 1.3 - - - -
220R THR 3.8 0.5 - - - +
221R CYS* 3.5 3.7 - - - -
222R LYS* 2.7 67.1 + - - +
224R GLU* 5.0 5.5 + - - +
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Residues in contact with TRP 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149R ALA* 5.3 3.1 - - + -
164R ALA* 3.8 25.8 + - + -
165R ARG 3.9 3.4 - - - -
166R CYS* 3.4 27.6 - - + +
178R THR* 1.3 69.6 - - - +
180R HIS* 1.3 61.3 + - - +
186R MET* 3.5 19.2 - - + +
189R THR* 4.0 16.0 + - - +
205R LEU* 2.9 61.4 + - + +
206R TRP* 3.7 4.6 - - - +
207R ILE* 3.6 30.7 - - + -
219R VAL* 3.4 35.9 - - + -
220R THR 3.8 2.0 - - - -
221R CYS* 3.5 31.6 - - + -
234R LEU 4.7 1.1 - - - -
236R VAL* 4.0 15.9 - - + -
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Residues in contact with HIS 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178R THR* 3.6 11.2 + - - -
179R TRP* 1.3 73.9 - - - +
181R SER* 1.3 70.1 + - - +
186R MET* 3.7 22.0 - - - -
207R ILE* 6.0 0.2 - - - -
219R VAL* 3.5 7.3 - - - +
220R THR* 2.8 60.0 + - + +
222R LYS* 4.4 20.4 - - + +
233R LEU* 5.0 5.7 - - + +
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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