Contacts of the strand formed by residues 274 - 278 (chain B) in PDB entry 2QU7
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 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B VAL* 3.7 25.8 - - + +
176B SER* 3.3 28.5 - - - +
178B CYS* 4.6 0.4 - - + -
245B LYS 2.8 18.5 + - - +
246B GLY* 3.5 6.4 - - - -
247B ILE 3.0 22.6 + - - -
269B ILE* 4.6 0.9 - - - -
270B LYS* 4.3 2.0 - - - -
273B VAL* 1.3 85.9 - - - +
275B ILE* 1.3 64.0 + - - +
332B SER 3.4 11.9 - - - +
333B CYS 3.4 19.5 - - - +
334B SER 3.6 31.2 - - - +
335B PHE* 3.7 21.8 - - + -
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Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL* 5.1 1.5 - - - +
247B ILE* 3.2 28.0 - - + +
249B ALA* 4.6 2.7 - - + -
255B LEU* 4.0 16.6 - - + -
258B ALA* 3.7 30.7 - - + -
259B LEU* 4.7 9.0 - - + -
262B ILE* 4.3 14.4 - - + -
269B ILE* 4.4 21.1 - - + -
273B VAL* 5.9 0.2 - - + -
274B ILE* 1.3 77.7 - - - +
276B VAL* 1.3 76.5 + - - +
277B GLY 4.3 0.2 - - - -
291B LEU* 4.7 3.4 - - + -
292B THR 4.1 1.0 - - - +
332B SER* 2.9 54.4 + - - +
333B CYS* 3.8 3.0 + - - +
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ALA* 3.7 32.3 - - + +
172B ARG* 4.4 6.5 - - + -
173B VAL* 3.5 26.9 - - + -
247B ILE 3.0 6.7 + - - +
248B VAL* 3.4 6.3 - - + +
249B ALA 2.9 25.1 + - - +
275B ILE* 1.3 82.4 - - - +
277B GLY* 1.3 74.3 + - - +
292B THR* 3.5 13.5 - - + +
293B VAL* 4.4 0.2 - - - -
294B ILE 4.5 0.2 - - - +
327B LEU* 4.1 15.7 - - + -
333B CYS* 4.0 17.9 - - + -
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Residues in contact with GLY 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA 3.3 11.0 - - - -
255B LEU* 4.2 20.2 - - - +
275B ILE 4.3 0.2 - - - -
276B VAL* 1.3 77.3 - - - +
278B PHE* 1.3 61.0 + - - -
292B THR 3.0 11.3 + - - -
293B VAL* 3.1 15.3 - - - +
294B ILE 2.8 26.0 + - - -
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Residues in contact with PHE 278 (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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165B ALA* 3.8 22.2 - - + -
166B ALA* 3.7 30.3 - - + -
169B ALA* 4.0 13.7 - - + -
196B ARG* 3.7 30.7 - - + -
248B VAL* 4.2 10.3 - - + -
249B ALA 3.2 17.1 + - - -
250B THR* 3.4 37.2 - - + +
251B ASN* 3.8 2.6 - - - +
252B HIS* 3.3 15.6 + - - -
255B LEU* 4.5 3.2 - - - +
277B GLY* 1.3 81.0 - - - -
279B ASP* 1.3 77.9 - - - +
293B VAL* 4.3 0.2 - - - -
294B ILE* 3.4 28.0 - - + -
296B GLN* 4.9 5.4 - - - -
325B THR* 5.9 0.2 - - + -
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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