Contacts of the strand formed by residues 244 - 249 (chain A) in PDB entry 2COJ
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 GLN 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A TYR* 5.3 7.3 - - - -
194A PHE* 3.8 25.9 - - + -
202A VAL* 5.0 6.5 - - + -
203A SER 3.5 3.3 + - - +
204A LEU* 3.4 25.1 - - + -
205A TRP* 2.9 26.2 + - - +
234A GLN* 3.2 24.4 + - - +
237A ALA* 4.3 2.5 - - - -
242A CYS* 3.5 2.2 - - - +
243A GLN* 1.3 94.6 - - + +
245A VAL* 1.3 64.7 + - - +
258A VAL* 4.6 1.1 - - + -
259A GLY* 3.4 26.2 - - - -
260A THR* 3.9 6.9 + - - +
261A MET* 3.6 23.2 - - + +
420A GBN 5.3 1.0 + - - -
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Residues in contact with VAL 245 (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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204A LEU* 4.5 2.5 - - - -
205A TRP* 3.6 15.5 - - + +
207A ASN* 5.7 3.4 - - + +
210A TYR* 6.0 2.2 - - + -
233A ALA* 3.6 39.9 - - + +
234A GLN* 3.7 14.1 + - + +
237A ALA* 3.9 5.2 - - + -
244A GLN* 1.3 77.9 - - - +
246A LEU* 1.3 69.0 + - - +
247A TRP* 3.5 38.1 + - + +
259A GLY* 2.6 37.0 + - - -
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Residues in contact with LEU 246 (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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204A LEU* 3.9 27.8 - - + +
205A TRP 2.8 23.0 + - - +
206A ALA* 4.0 8.6 - - + -
207A ASN 4.5 3.1 + - - +
245A VAL* 1.3 76.2 - - - +
247A TRP* 1.3 61.4 + - - +
248A LEU* 3.5 21.7 + - + +
255A ILE* 4.1 9.0 - - + -
257A GLU 3.8 14.6 - - - +
258A VAL* 4.6 1.8 - - + -
259A GLY 4.8 0.2 - - - +
263A LEU* 3.9 24.0 - - + -
313A MET* 4.0 21.5 - - - -
316A LEU* 5.6 0.2 - - + -
328A MET* 5.7 1.8 - - - -
343A ILE* 3.8 34.5 - - + -
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Residues in contact with TRP 247 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A TYR* 3.7 32.5 - - + -
211A VAL 4.1 1.3 - - - -
212A ARG* 3.5 56.6 - - + +
229A SER 5.3 1.1 - - - -
230A SER* 3.3 36.3 - - - -
233A ALA* 4.0 16.2 - - + -
245A VAL* 3.6 30.0 + - + +
246A LEU* 1.3 70.4 - - - +
248A LEU* 1.3 61.9 + - - +
254A GLN 3.7 0.2 - - - +
255A ILE* 3.9 2.1 - - - -
256A THR* 3.1 42.7 + - - +
257A GLU* 3.2 11.9 + - + +
259A GLY* 3.2 36.5 + - - -
260A THR* 5.1 3.7 - - + +
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Residues in contact with LEU 248 (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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206A ALA* 4.0 17.0 - - + -
207A ASN 4.9 1.1 + - - -
208A PRO* 3.8 48.0 - - + +
210A TYR 4.0 15.7 + - - +
211A VAL* 4.3 13.2 - - - +
212A ARG 5.1 0.5 + - - -
246A LEU* 3.5 29.1 + - + +
247A TRP* 1.3 79.3 - - - +
249A TYR* 1.3 63.5 + - - +
253A HIS* 4.3 12.3 - - + +
254A GLN 3.3 12.8 - - - +
255A ILE* 4.1 12.8 - - + -
256A THR* 4.9 0.2 - - - -
313A MET* 4.2 9.6 - - + -
345A TYR* 4.0 15.0 - - + -
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Residues in contact with TYR 249 (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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211A VAL* 4.1 11.4 - - + -
213A ALA 3.5 25.4 - - - -
214A TRP* 3.7 36.0 - + - -
215A LYS* 3.0 50.6 + - + +
248A LEU* 1.3 75.3 - - - +
250A GLY* 1.3 74.9 + - - +
253A HIS* 4.5 0.6 - - - +
254A GLN* 3.0 50.7 + - + +
256A THR* 3.9 20.4 - - + -
284A ILE* 3.7 14.4 - - + -
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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