Contacts of the strand formed by residues 169 - 172 (chain C) in PDB entry 2QPA
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 169 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LEU* 5.6 2.5 - - + -
148C ALA* 4.3 18.2 - - + +
149C VAL* 3.4 33.4 - - + -
166C THR* 4.8 10.3 - - - +
168C GLY* 1.3 75.9 - - - +
170C LEU* 1.3 64.8 - - - +
171C LEU* 5.4 1.3 - - + -
271C LEU* 4.1 11.2 - - + -
272C VAL 2.6 13.7 + - - +
273C LEU* 3.7 14.4 - - + -
274C GLY 2.9 27.4 + - - +
290C PHE* 3.0 8.4 - - - -
292C ARG* 3.5 22.2 - - + +
294C ILE* 3.7 31.0 - - + -
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C ILE* 1.3 81.2 - - - +
171C LEU* 1.3 58.5 + - - +
172C TYR* 4.2 17.0 - - + +
234C VAL* 3.9 18.2 - - + -
274C GLY 3.5 21.5 - - - +
275C ALA* 4.1 3.6 - - - +
276C THR* 4.3 10.5 - - + -
279C PRO* 5.3 0.2 - - + -
282C LEU* 4.3 19.5 - - + -
287C ARG* 5.8 1.1 - - + -
290C PHE* 3.3 19.3 - - + -
292C ARG 3.1 4.8 + - - -
293C ARG* 3.9 26.9 - - + +
294C ILE* 2.5 35.9 + - - +
428C PHE* 4.2 19.5 - - + -
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C LEU* 4.4 13.2 - - + -
169C ILE* 4.1 1.1 + - + -
170C LEU* 1.3 71.4 - - - +
172C TYR* 1.3 58.6 + - - +
179C LYS* 3.3 30.0 - - + +
182C LEU* 3.6 28.3 - - + -
183C ALA* 4.4 1.6 - - + -
230C PHE* 5.1 0.2 - - + -
273C LEU* 4.0 27.1 - - + -
274C GLY 2.6 15.9 + - - +
275C ALA* 3.2 27.5 - - + +
276C THR 3.2 3.2 + - - -
294C ILE* 3.4 19.5 - - + -
296C ILE* 3.6 30.1 - - + -
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Residues in contact with TYR 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LEU* 4.0 8.5 - - + -
171C LEU* 1.3 76.2 - - - +
173C GLY* 1.3 53.0 + - - +
179C LYS* 3.8 3.4 - - - -
276C THR* 3.2 18.2 - - + -
279C PRO* 3.2 33.9 - - + -
293C ARG* 4.0 12.1 + - + -
294C ILE* 2.9 38.5 + - - -
295C TYR* 3.0 32.1 + + + +
296C ILE* 2.7 29.8 + - - -
425C GLN* 3.8 7.6 - - - -
428C PHE* 3.3 29.4 - + - -
429C THR* 2.8 39.3 + - - +
432C PHE* 5.1 4.0 - - + +
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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