Contacts of the strand formed by residues 175 - 179 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER* 4.1 5.6 - - - -
167A MET* 3.4 33.9 - - + -
168A GLU 2.9 22.7 - - - -
169A LEU* 3.4 38.1 - - + -
174A THR* 1.3 76.6 - - - +
176A GLU* 1.3 63.5 + - - +
236A LEU* 4.3 15.7 - - + -
238A ARG* 4.0 24.9 - - + -
239A ARG 2.9 8.4 + - - +
240A VAL* 3.0 33.2 - - + -
241A THR* 2.8 25.2 + - - -
339A PHE* 4.6 3.6 - + - -
350A TRP* 4.1 29.4 - + - -
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLN 3.4 1.2 - - - +
167A MET* 4.7 2.7 - - - -
168A GLU* 2.9 36.5 + - + +
170A MET* 3.7 38.4 - - + +
174A THR* 4.9 2.7 + - - +
175A PHE* 1.3 80.3 - - - +
177A TRP* 1.3 60.6 + - - +
178A HIS* 3.1 33.0 + - + +
241A THR* 3.2 23.8 + - - +
243A VAL* 4.7 6.4 - - + +
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Residues in contact with TRP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A PHE* 3.6 28.0 - + - -
164A LEU 2.8 23.4 + - - -
165A PHE* 3.7 26.9 - + - +
166A GLN 3.2 24.5 - - - +
167A MET* 4.2 9.2 - - - -
176A GLU* 1.3 73.6 - - - +
178A HIS* 1.3 61.9 + - - +
179A ALA* 3.8 15.6 - - + +
181A PHE* 4.0 11.9 - + - -
187A LEU* 5.0 0.2 - - + -
189A TRP* 4.0 15.9 - + - -
225A PRO* 3.6 28.0 - - + -
228A VAL* 4.1 9.4 - - + -
229A CYS* 3.9 22.6 - - - -
241A THR 3.0 8.1 + - - -
242A TYR* 3.1 31.7 - + - -
243A VAL 2.8 29.1 + - - -
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 4.2 8.8 - - - +
166A GLN* 4.3 2.7 + - - +
168A GLU* 5.2 8.0 + - - -
170A MET* 6.1 0.2 - - + -
176A GLU* 3.1 29.8 + - + +
177A TRP* 1.3 86.3 + - - +
179A ALA* 1.3 62.8 + - - +
243A VAL* 3.0 46.9 - - + +
245A VAL* 3.9 14.1 - - + +
248A VAL* 6.0 0.3 - - - -
249A GLU* 2.9 43.6 + - - +
251A LYS* 5.9 0.2 + - - -
247G LYS* 5.2 6.7 - - - -
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.9 7.9 - - + -
177A TRP* 3.8 19.3 - - + +
178A HIS* 1.3 76.1 - - - +
180A PRO* 1.3 72.9 - - + +
181A PHE* 3.1 19.3 - - + -
242A TYR* 2.9 24.8 + - - +
243A VAL 3.2 4.8 + - - -
244A GLN* 3.3 2.9 - - - -
245A VAL* 3.0 23.7 + - - +
248A VAL* 6.1 0.2 - - - +
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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