Contacts of the strand formed by residues 257 - 262 (chain A) in PDB entry 2QMQ
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 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 3.2 14.8 - - + +
168A LEU* 4.0 11.9 - - + -
253A LEU* 3.9 26.5 - - + -
255A CYS* 3.6 15.7 - - - +
256A PRO* 1.3 79.8 - - - +
258A MET* 1.3 63.5 + - - +
259A LEU* 3.7 31.6 - - + -
278A LEU* 3.9 18.4 - - + -
282A GLN 3.0 6.1 + - - +
283A THR* 3.2 9.7 - - - +
284A SER* 2.9 26.0 + - - +
310A PHE* 3.9 4.3 - - - -
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Residues in contact with MET 258 (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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166A LEU 2.9 10.3 + - - +
167A VAL* 3.4 35.1 - - + +
168A LEU 2.9 25.3 + - - +
257A VAL* 1.3 74.3 - - - +
259A LEU* 1.3 62.5 + - - +
260A VAL* 4.4 2.7 - - + -
284A SER* 3.3 21.1 - - - +
286A LEU* 4.0 17.3 - - + -
303A LEU* 4.3 7.2 - - + -
306A ALA* 3.6 48.7 - - + +
307A PHE* 4.2 11.7 - - + +
310A PHE* 3.8 19.4 - - + -
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Residues in contact with LEU 259 (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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168A LEU* 3.5 9.2 - - + -
171A ILE* 3.7 28.9 - - + -
245A PHE* 5.9 0.2 - - + -
257A VAL* 3.7 22.0 - - + -
258A MET* 1.3 74.1 - - - +
260A VAL* 1.3 63.8 + - - +
271A VAL* 3.7 9.9 - - + +
274A CYS* 4.1 6.3 - - + -
275A ASN* 3.5 44.9 - - + +
278A LEU* 4.2 6.7 - - + -
283A THR* 3.9 15.3 - - + -
284A SER 2.8 11.8 + - - +
285A PHE* 3.4 15.4 - - + -
286A LEU* 2.9 25.8 + - - +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A VAL* 4.4 6.5 - - + -
168A LEU 3.0 6.1 + - - +
169A ILE* 3.4 22.6 - - + -
170A ASN* 3.0 27.2 + - - +
258A MET* 4.2 17.0 - - + +
259A LEU* 1.3 81.2 - - - +
261A VAL* 1.3 65.6 + - - +
271A VAL* 4.2 3.7 - - - +
286A LEU* 3.4 10.1 - - + +
288A MET* 3.8 28.5 - - - -
295A PRO* 4.2 14.4 - - + -
303A LEU* 3.9 25.8 - - + -
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASN* 3.6 20.0 - - - +
260A VAL* 1.3 77.4 - - - +
262A GLY* 1.3 71.3 + - - +
265A ALA* 4.8 2.7 - - + -
267A HIS* 3.7 5.8 - - + +
268A GLU* 3.7 36.1 - - + +
271A VAL* 3.7 20.0 - - + -
285A PHE* 3.8 25.8 - - + -
286A LEU 3.1 5.3 + - - +
287A LYS* 3.3 9.6 - - + -
288A MET* 2.8 25.7 + - - +
291A SER* 4.4 1.8 - - - -
295A PRO* 4.4 4.9 - - - -
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Residues in contact with GLY 262 (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 ASN* 4.6 1.0 + - - -
261A VAL* 1.3 80.2 - - - +
263A ASP* 1.3 68.6 + - - -
264A GLN 3.4 0.7 + - - -
265A ALA* 3.2 17.6 + - - +
268A GLU* 3.8 12.0 - - - +
288A MET 3.6 0.9 - - - -
291A SER* 3.1 25.8 + - - -
292A GLY 3.5 15.3 + - - -
295A PRO* 4.1 3.6 - - - +
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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