Contacts of the strand formed by residues 270 - 276 (chain A) 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 VAL 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A SER* 4.5 5.9 + - - -
221A ALA* 3.6 3.8 - - + +
222A ARG* 3.6 31.4 - - + +
225A LYS* 4.1 9.5 - - + +
227A SER* 2.9 39.7 - - - +
229A ILE* 3.5 37.9 - - + +
263A VAL* 4.1 24.8 - - + +
269A GLY* 1.3 84.5 + - - +
271A LEU* 1.3 61.9 + - - +
272A VAL* 4.2 1.9 + - - +
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Residues in contact with LEU 271 (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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148A ALA 5.9 0.2 - - - +
149A VAL* 3.8 39.7 - - + +
153A VAL* 4.9 12.3 - - + -
166A THR 5.4 2.7 - - - +
167A SER* 4.2 24.0 - - - +
168A GLY 5.3 0.7 - - - +
169A ILE* 4.5 4.5 - - + -
227A SER 3.3 5.6 + - - +
228A ILE* 3.6 19.4 - - + -
229A ILE 3.1 22.4 + - - -
270A VAL* 1.3 74.2 - - - +
272A VAL* 1.3 63.7 + - - +
273A LEU* 3.7 31.9 + - + -
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Residues in contact with VAL 272 (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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167A SER* 5.1 0.6 - - - -
168A GLY* 3.1 8.8 + - - +
169A ILE 2.9 24.8 + - - +
218A PHE* 3.6 34.3 - - + -
229A ILE* 3.4 18.6 - - + +
231A ILE* 4.2 16.4 - - + -
260A MET* 3.4 34.3 - - + -
263A VAL* 5.6 3.1 - - + -
270A VAL 5.1 2.9 - - - +
271A LEU* 1.3 78.6 - - - +
273A LEU* 1.3 67.1 + - - +
290A PHE* 3.8 13.0 - - + -
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Residues in contact with LEU 273 (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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145A LEU* 5.1 3.1 - - + -
149A VAL* 4.7 2.2 - - + -
169A ILE* 3.3 38.8 - - + +
171A LEU* 4.9 9.0 - - + -
183A ALA* 3.6 31.9 - - + -
186A VAL* 4.3 19.3 - - + -
228A ILE* 3.8 22.0 - - + -
229A ILE 2.9 9.4 + - - +
230A PHE* 3.3 15.7 - - + -
231A ILE 3.0 23.4 + - - -
271A LEU* 3.7 21.0 + - + -
272A VAL* 1.3 75.5 - - - +
274A GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 274 (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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169A ILE 2.8 8.5 + - - -
170A LEU* 3.3 8.9 - - - +
171A LEU* 2.6 35.4 + - - +
230A PHE* 4.7 0.9 - - - -
231A ILE* 3.3 11.9 - - - -
234A VAL* 3.8 8.1 - - - -
273A LEU* 1.3 75.0 - - - +
275A ALA* 1.3 55.0 + - - -
290A PHE* 3.5 17.1 - - - -
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Residues in contact with ALA 275 (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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170A LEU* 4.6 0.7 - - - -
171A LEU* 3.0 13.0 - - + +
179A LYS* 3.8 17.5 - - + -
230A PHE* 3.6 29.6 - - + -
231A ILE 3.1 7.3 + - - -
232A ASP* 3.8 10.3 - - - +
233A GLN 2.8 26.9 + - - -
234A VAL* 3.1 11.7 + - - +
274A GLY* 1.3 74.4 - - - +
276A THR* 1.3 58.6 + - - +
800A ADP 4.4 1.3 - - - +
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Residues in contact with THR 276 (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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170A LEU* 4.3 9.2 - - + -
171A LEU 2.8 9.4 + - - +
172A TYR* 3.1 20.1 - - + -
173A GLY 3.1 19.9 + - - -
179A LYS* 3.2 4.6 - - - +
232A ASP* 5.3 0.2 - - - -
233A GLN* 4.7 2.7 - - - +
234A VAL* 4.1 11.4 - - - -
235A ASP* 2.6 38.6 + - - +
275A ALA* 1.3 77.9 - - - +
277A ASN* 1.3 62.7 + - - +
278A ILE 3.3 2.9 + - - -
279A PRO* 3.5 26.2 - - + -
282A LEU* 4.9 3.1 - - + -
800A ADP 5.0 0.6 + - - -
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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