Contacts of the strand formed by residues 175 - 179 (chain H) in PDB entry 2VUU
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 PHE 175 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H SER* 4.4 6.1 - - - -
167H MET* 3.3 32.1 - - + -
168H GLU 3.2 20.2 - - - -
169H LEU* 3.1 37.9 - - + -
170H MET* 4.5 0.9 - - - -
174H THR* 1.3 76.4 + - - +
176H GLU* 1.3 64.6 + - - +
236H LEU* 4.0 25.8 - - + -
238H ARG* 4.0 23.3 - - + -
239H ARG 2.7 8.1 + - - +
240H VAL* 3.0 26.2 - - + -
241H THR* 2.9 21.7 + - - +
339H PHE* 4.8 3.6 - + - -
350H TRP* 4.2 31.0 - + - -
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Residues in contact with GLU 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H GLN 3.7 0.3 - - - +
167H MET* 4.6 2.2 - - - -
168H GLU* 3.1 27.5 + - - +
170H MET* 3.2 46.9 - - + +
174H THR* 4.9 0.7 + - - -
175H PHE* 1.3 77.9 - - - +
177H TRP* 1.3 59.9 + - - +
178H HIS* 2.7 33.4 + - + -
240H VAL* 4.3 1.8 - - - +
241H THR* 2.9 31.7 + - - +
243H VAL* 4.3 7.7 - - + +
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Residues in contact with TRP 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H PHE* 3.6 27.7 - + - -
164H LEU 2.9 22.7 + - - -
165H PHE* 3.9 11.0 - + - +
166H GLN 3.5 22.4 - - - +
167H MET* 3.6 19.3 - - - -
176H GLU* 1.3 73.2 - - - +
178H HIS* 1.3 69.6 + - - +
179H ALA* 3.7 3.8 - - + +
181H PHE* 4.0 23.1 - + - -
187H LEU* 5.3 0.2 - - + -
189H TRP* 4.1 14.1 - + - -
225H PRO* 3.4 40.6 - - + -
228H VAL* 3.9 13.0 - - + -
229H CYS* 3.7 15.0 - - - -
241H THR 3.1 5.7 + - - -
242H TYR* 3.1 35.5 - + - -
243H VAL 3.0 21.9 + - - -
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Residues in contact with HIS 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H LEU* 3.8 8.7 - - - +
166H GLN* 4.3 6.1 + - - -
168H GLU* 3.5 24.6 + - - +
170H MET* 5.2 0.2 - - + -
176H GLU* 2.7 43.9 + - + -
177H TRP* 1.3 82.0 - - - +
179H ALA* 1.3 65.0 + - - +
243H VAL* 3.2 39.6 - - + +
245H VAL* 3.7 11.1 - - + +
249H GLU* 3.3 34.0 + - - +
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Residues in contact with ALA 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H LEU* 3.7 15.0 - - + -
177H TRP* 3.7 18.2 - - + +
178H HIS* 1.3 77.5 - - - +
180H PRO* 1.3 72.1 - - + +
181H PHE* 3.1 12.5 + - + -
242H TYR* 2.6 27.6 + - - +
243H VAL 3.3 4.0 + - - -
244H GLN* 3.3 4.2 - - - -
245H VAL* 3.2 22.6 + - - +
248H VAL* 5.9 0.4 - - - +
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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