Contacts of the strand formed by residues 253 - 260 (chain A) in PDB entry 2C0O
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 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A GLY* 3.0 27.6 + - - +
251A GLN 3.8 0.8 - - - -
252A PHE* 1.3 76.6 - - - +
254A GLU* 1.3 67.8 + - - +
269A LYS* 5.5 4.7 - - - -
270A THR 2.8 17.9 - - - -
271A MET* 4.2 1.8 - - - -
272A LYS* 3.9 7.6 - - - +
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Residues in contact with GLU 254 (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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246A LYS* 4.3 18.0 + - + -
248A GLY 3.4 11.7 - - - +
249A ALA* 4.2 13.5 - - + +
253A GLY* 1.3 79.9 - - - +
255A VAL* 1.3 65.6 + - - +
256A TRP* 2.9 31.6 + - - +
268A VAL 3.6 0.6 - - - +
269A LYS* 3.3 6.3 - - - +
270A THR* 3.0 38.8 + - - +
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Residues in contact with VAL 255 (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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246A LYS* 3.6 1.4 - - - -
247A LEU* 2.6 37.9 + - + -
248A GLY* 2.9 14.5 + - - +
254A GLU* 1.3 73.7 - - - +
256A TRP* 1.3 65.0 + - - +
267A ALA* 4.7 1.6 - - + -
268A VAL 3.3 4.9 - - - +
269A LYS* 3.3 38.4 - - + +
1506A L2G 3.7 57.0 - - + +
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Residues in contact with TRP 256 (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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243A LEU* 3.4 63.1 - - + +
244A GLU 4.3 2.7 - - - -
245A LYS* 3.2 13.0 - - - -
246A LYS* 3.4 46.6 - - + +
247A LEU* 4.0 4.7 - - - -
254A GLU* 2.9 40.1 + - + +
255A VAL* 1.3 80.4 - - - +
257A MET* 1.3 63.1 + - - +
267A ALA* 3.3 7.1 - - - +
268A VAL* 2.8 35.6 + - + +
270A THR* 4.4 3.9 + - + +
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Residues in contact with MET 257 (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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243A LEU 3.7 0.5 - - - -
244A GLU* 2.8 66.3 + - + +
245A LYS* 2.7 38.1 + - + +
247A LEU* 3.7 12.9 - - + +
256A TRP* 1.3 71.8 - - - +
258A ALA* 1.3 63.2 + - - +
259A THR* 5.0 0.2 - - - -
265A LYS* 3.9 29.4 - - + +
266A VAL 3.7 3.4 - - - -
314A PHE* 3.6 30.3 - - + -
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Residues in contact with ALA 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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241A LEU* 5.0 0.9 - - + -
242A LYS 3.2 15.9 - - - +
243A LEU* 3.5 17.3 - - + -
244A GLU* 4.0 0.4 - - - +
256A TRP 3.7 0.6 + - - +
257A MET* 1.3 82.1 - - - +
259A THR* 1.3 67.7 + - - +
265A LYS* 3.6 5.5 - - - +
266A VAL* 2.8 34.2 + - + +
268A VAL* 3.6 28.9 - - + -
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Residues in contact with THR 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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240A SER 3.7 0.5 - - - +
241A LEU* 3.2 12.2 - - - +
242A LYS* 3.0 37.1 + - + -
244A GLU* 2.9 31.9 + - - +
257A MET* 5.0 0.5 - - - -
258A ALA* 1.3 74.2 + - - +
260A TYR* 1.3 61.9 + - - +
261A ASN 4.0 0.4 - - - +
262A LYS* 3.5 42.8 - - - +
264A THR 3.3 10.2 + - - +
265A LYS* 5.1 2.9 - - - +
266A VAL* 4.7 0.9 - - - -
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Residues in contact with TYR 260 (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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72A HIS* 4.9 5.4 - + - -
229A TRP* 3.5 39.7 - + + -
230A GLU* 2.9 35.2 + - + -
233A ALA* 4.0 5.0 - - - +
236A ILE* 3.8 32.8 - - + +
237A PRO* 5.8 0.7 - - - +
240A SER* 3.5 32.3 - - - -
241A LEU* 4.0 8.7 - - + -
259A THR* 1.3 71.8 - - - +
261A ASN* 1.3 87.5 + - + +
262A LYS 3.3 0.7 - - - -
263A HIS 3.5 0.3 + - - -
264A THR* 2.8 44.5 + - - +
266A VAL* 4.5 5.1 - - + +
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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