Contacts of the strand formed by residues 176 - 179 (chain A) in PDB entry 2QPS
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 ALA 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A HIS* 5.3 0.7 - - + -
84A GLN* 5.2 0.2 - - - +
85A ALA 3.2 3.5 + - - +
86A ILE* 3.4 11.6 - - + -
87A ALA* 3.0 21.3 + - - +
175A ASP* 1.3 77.7 + - + +
177A TRP* 1.3 71.4 + - - +
199A PRO* 3.8 3.6 - - - -
200A SER* 3.1 19.5 - - - +
201A LEU* 2.8 42.4 - - + +
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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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86A ILE* 3.5 11.1 - - - +
87A ALA* 3.5 5.4 - - + -
89A ILE* 3.5 28.5 - - + -
165A LEU* 3.3 43.5 - - + +
168A LEU* 3.9 21.1 - - + -
169A LYS* 3.3 34.1 - - + -
174A PHE* 4.1 14.1 - - + -
175A ASP 5.6 0.2 - - - -
176A ALA* 1.3 96.1 - - - +
178A ARG* 1.3 59.6 + - - +
179A LEU* 4.0 16.2 - - + -
193A TYR* 4.9 2.0 + - + -
194A ILE* 5.2 6.3 - - + -
197A THR* 2.9 22.8 + - - +
199A PRO* 3.6 28.8 - - + +
201A LEU* 3.0 5.4 + - - +
202A ALA* 3.1 12.3 - - + -
203A VAL* 3.1 21.3 + - - +
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Residues in contact with ARG 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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39A TRP* 3.2 41.1 - - + +
52A TYR* 3.8 5.7 + - - -
86A ILE* 4.0 9.6 - - + -
87A ALA 2.9 13.6 + - - +
88A ASP* 2.7 37.5 + - - -
89A ILE 2.8 25.2 + - - -
177A TRP* 1.3 73.2 - - - +
179A LEU* 1.3 61.5 + - - +
180A ASP* 3.1 28.9 + - - +
203A VAL* 3.3 16.6 - - + +
205A GLU* 3.4 38.8 + - - +
246A PHE* 3.9 18.2 - - + -
289A ASN* 5.6 3.2 - - - +
290A HIS* 3.6 17.6 + - - -
291A ASP* 4.3 0.4 + - - -
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Residues in contact with LEU 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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89A ILE* 3.8 26.0 - - + -
91A ILE* 5.1 2.5 - - + -
177A TRP* 4.2 19.3 - - + -
178A ARG* 1.3 70.6 - - - +
180A ASP* 1.3 65.3 + - - +
181A PHE 3.6 0.3 + - - -
182A ALA* 3.8 6.2 + - + -
185A TYR* 3.8 24.5 - - + +
190A ALA* 4.1 23.3 - - + -
193A TYR* 5.9 5.4 - - + -
194A ILE* 4.3 21.1 - - + -
202A ALA* 4.9 6.1 - - + -
203A VAL 3.0 10.6 + - - +
204A ALA* 4.0 23.1 - - + -
205A GLU* 3.0 24.2 + - - +
232A TRP* 4.4 1.6 - - + -
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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