Contacts of the strand formed by residues 168 - 172 (chain B) 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 GLY 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B THR* 3.8 0.7 - - - -
167B SER* 1.3 80.3 - - - +
169B ILE* 1.3 61.9 + - - +
260B MET* 3.7 3.4 - - - -
272B VAL 4.1 1.1 - - - -
289B ARG 3.1 17.7 - - - -
290B PHE* 2.9 31.1 - - - -
291B GLU* 2.9 16.9 + - - +
292B ARG* 3.2 8.8 + - - +
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Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 4.2 7.4 - - + -
148B ALA* 4.2 16.8 - - + +
149B VAL* 3.3 34.1 - - + -
166B THR* 4.4 11.4 - - - +
167B SER 5.4 1.1 - - - -
168B GLY* 1.3 74.2 - - - +
170B LEU* 1.3 58.3 + - - +
171B LEU* 3.7 3.4 + - + +
271B LEU* 5.4 5.4 - - + -
272B VAL 3.3 10.1 + - - +
273B LEU* 3.4 27.8 - - + +
274B GLY 3.1 22.0 + - - +
290B PHE* 3.1 7.1 - - - -
292B ARG* 3.4 10.5 - - + +
294B ILE* 3.4 32.8 - - + -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ILE* 1.3 71.8 - - - +
171B LEU* 1.3 64.2 + - - +
172B TYR* 4.1 20.0 - - + -
234B VAL* 4.1 15.0 - - + -
274B GLY* 3.3 11.2 - - - +
276B THR* 3.2 29.6 - - + -
279B PRO* 5.0 0.2 - - + -
282B LEU* 4.1 20.2 - - + -
287B ARG* 5.7 1.6 - - + -
290B PHE* 3.6 19.2 - - + +
292B ARG 2.8 9.3 + - - -
293B ARG* 3.3 28.5 - - + +
294B ILE* 2.8 30.3 + - - +
428B PHE* 4.4 13.0 - - + -
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 4.1 24.2 - - + -
169B ILE* 4.4 6.5 - - + +
170B LEU* 1.3 74.3 - - - +
172B TYR* 1.3 59.4 + - - +
179B LYS* 3.3 42.9 - - + +
182B LEU* 4.7 13.5 - - + -
183B ALA* 4.5 17.5 - - + +
230B PHE* 4.7 2.9 - - + -
273B LEU* 4.9 7.2 - - + -
274B GLY 2.7 15.1 + - - +
275B ALA* 3.3 6.3 - - + -
276B THR 2.9 24.0 + - - -
294B ILE* 3.5 30.3 - - + -
296B ILE* 4.7 4.5 - - + -
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Residues in contact with TYR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LEU* 4.1 12.1 - - + -
171B LEU* 1.3 75.4 - - - +
173B GLY* 1.3 57.2 + - - +
179B LYS* 3.7 3.8 - - - -
276B THR* 3.1 14.4 - - + +
279B PRO* 3.1 35.4 - - + -
293B ARG* 3.6 22.8 + - + -
294B ILE 3.0 33.4 + - - -
295B TYR* 3.3 35.1 + + + +
296B ILE* 2.9 24.8 + - - +
425B GLN* 3.9 6.7 - - + -
428B PHE* 3.7 23.3 - + - -
429B THR* 3.2 37.9 + - - +
432B PHE* 5.1 3.5 - + - -
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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
------------------------------------------------------------
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