Contacts of the strand formed by residues 170 - 174 (chain X) in PDB entry 2QW0
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 170 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96X LEU* 5.9 0.2 - - - +
158X ILE* 3.5 15.5 - - + -
159X PHE 3.8 2.0 - - - -
160X TYR* 3.2 31.6 - - + +
168X PRO 4.1 0.2 + - - -
169X LYS* 1.3 70.7 - - - +
171X ALA* 1.3 62.6 + - - +
172X ILE* 3.5 0.5 + - - +
365X TYR* 3.2 3.6 - - - -
366X LEU* 2.7 52.3 + - + +
368X GLN* 4.2 5.8 - - - +
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Residues in contact with ALA 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158X ILE* 3.5 4.8 - - - -
159X PHE 2.8 37.9 + - - +
161X THR* 4.8 1.6 - - + -
169X LYS 3.5 2.9 + - - +
170X ALA* 1.3 70.2 - - - +
172X ILE* 1.3 62.5 + - - +
173X ILE* 3.6 5.2 + - + +
307X THR* 3.8 21.5 - - + -
308X GLU* 4.8 2.5 - - + -
362X PHE* 4.0 20.0 - - + -
364X GLY 3.8 4.7 - - - -
365X TYR* 4.0 14.8 - - + -
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Residues in contact with ILE 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155X PRO* 3.7 37.0 - - + -
157X PHE 3.9 5.4 - - - +
158X ILE* 4.5 13.2 - - + -
170X ALA 4.1 1.1 - - - +
171X ALA* 1.3 71.5 - - - +
173X ILE* 1.3 62.0 + - - +
174X PRO* 3.5 1.0 - - - +
362X PHE* 3.3 4.9 - - - +
363X VAL* 2.9 49.3 + - + -
364X GLY* 2.9 21.8 + - - +
365X TYR 4.6 0.7 - - - -
366X LEU* 3.9 44.6 - - + +
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Residues in contact with ILE 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X ALA* 2.9 24.0 + - - +
157X PHE* 2.8 31.0 + - + +
159X PHE* 3.8 23.1 - - + -
171X ALA* 3.9 11.2 - - + +
172X ILE* 1.3 77.9 - - - +
174X PRO* 1.4 67.5 - - + +
177X ALA* 3.8 23.3 - - + -
178X ALA 5.3 0.2 - - - +
181X ARG* 3.7 31.2 - - - +
212X PHE* 3.9 22.2 - - + -
307X THR* 4.0 9.2 - - + +
362X PHE* 3.9 13.5 - - + -
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Residues in contact with PRO 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152X PRO 3.6 13.7 - - - +
153X ALA* 3.8 12.6 - - - +
154X GLN 3.1 13.7 - - - +
155X PRO* 4.3 1.1 - - + -
156X ALA* 3.8 1.8 - - - +
172X ILE* 3.5 9.8 - - - +
173X ILE* 1.4 95.0 - - + +
175X GLN* 1.3 66.2 + - - +
176X ARG* 4.6 5.2 - - + +
177X ALA* 3.1 25.9 + - + +
178X ALA* 4.3 1.0 + - - +
359X ASP 4.6 3.8 - - - +
361X ALA 3.4 26.5 - - - +
363X VAL* 3.8 19.1 - - + -
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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