Contacts of the strand formed by residues 263 - 272 (chain B) in PDB entry 2PY5
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 LEU 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257B GLN 4.1 2.7 - - - +
258B MET* 4.0 24.0 - - - +
261B ARG* 3.5 13.5 - - + +
262B LEU* 1.3 82.2 - - - +
264B PRO* 1.3 69.9 - - + +
265B TYR* 4.4 1.0 - - - -
283B LEU* 3.6 4.5 - - - -
355B ALA* 3.1 2.1 - - - -
356B THR* 2.9 36.9 + - - +
359B LEU* 5.0 1.1 - - + +
360B PHE* 3.9 27.1 - - + -
429B MET* 3.5 16.1 - - + +
432B PHE* 3.8 22.7 - - + -
433B ILE* 4.1 12.1 - - + +
436B TRP* 3.8 19.5 - - + -
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Residues in contact with PRO 264 (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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211B PHE* 4.3 0.3 - - - -
263B LEU* 1.3 90.6 - - + +
265B TYR* 1.3 64.3 + - - +
283B LEU* 3.5 6.9 - - + -
353B PHE* 3.8 30.7 - - + -
354B LYS 3.3 8.5 - - - +
426B TYR* 3.6 7.4 - - - -
428B PRO* 3.4 32.3 - - + +
429B MET* 3.5 20.2 - - - +
432B PHE* 3.6 29.8 - - + -
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Residues in contact with TYR 265 (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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209B LYS 5.6 0.2 - - - -
210B VAL* 3.5 38.8 - - + +
211B PHE* 4.4 0.9 - - + -
264B PRO* 1.3 76.7 - - - +
266B GLY* 1.3 67.3 + - - +
267B GLU 4.9 0.3 - - - +
353B PHE* 4.5 2.9 - - - -
354B LYS* 3.0 66.1 + - + +
355B ALA* 3.6 38.5 + - - -
356B THR* 4.0 19.3 - - + -
359B LEU* 4.2 5.4 - - + -
426B TYR* 3.1 13.9 + - - -
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Residues in contact with GLY 266 (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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209B LYS 4.7 3.8 - - - -
210B VAL 2.8 21.5 + - - -
212B PRO* 3.5 13.2 - - - -
265B TYR* 1.3 81.4 - - - +
267B GLU* 1.3 63.0 + - - -
268B PRO* 3.7 2.9 - - - +
353B PHE* 4.4 0.3 - - - -
354B LYS* 4.1 10.8 - - - -
426B TYR* 2.6 31.0 + - - -
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Residues in contact with GLU 267 (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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212B PRO* 3.4 28.7 - - + +
213B THR 4.9 6.1 - - - +
214B LEU* 4.9 4.8 - - + +
265B TYR 4.9 1.4 - - - +
266B GLY* 1.3 73.3 - - - -
268B PRO* 1.3 75.3 - - + +
269B ILE* 4.8 1.4 - - - +
281B TYR* 4.1 15.9 + - - -
353B PHE* 5.1 0.9 - - - -
354B LYS* 4.8 5.9 + - - +
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Residues in contact with PRO 268 (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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214B LEU* 3.7 28.5 - - + -
218B LEU* 4.6 17.7 - - + +
266B GLY 3.7 4.9 - - - +
267B GLU* 1.3 91.9 - - + +
269B ILE* 1.3 64.6 + - - +
270B VAL* 4.1 3.0 + - + +
351B LEU* 4.1 22.0 - - + -
352B LYS 3.2 15.5 - - - +
353B PHE* 3.6 29.4 - - + -
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Residues in contact with ILE 269 (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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267B GLU 4.8 0.9 - - - +
268B PRO* 1.3 77.2 - - - +
270B VAL* 1.3 75.3 + - - +
271B PHE* 3.7 0.8 + - + -
281B TYR* 3.7 33.4 - - + +
351B LEU* 3.5 2.7 - - - -
352B LYS* 2.9 59.4 + - + +
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Residues in contact with VAL 270 (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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218B LEU* 4.4 15.0 - - + -
268B PRO 5.5 2.5 - - - +
269B ILE* 1.3 83.9 - - - +
271B PHE* 1.3 68.4 + - - +
272B GLU* 4.2 14.8 - - - +
349B SER* 5.4 3.8 - - - +
350B GLY 3.5 10.8 - - - +
351B LEU* 3.6 20.9 - - + -
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Residues in contact with PHE 271 (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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269B ILE* 4.1 2.0 - - + -
270B VAL* 1.3 77.3 - - - +
272B GLU* 1.3 74.3 + - - +
273B GLY 3.5 8.7 - - - -
274B LYS 4.3 0.9 - - - -
275B TYR* 3.4 55.9 - + + -
276B VAL 5.8 0.4 - - - -
284B HIS* 4.0 3.4 - + + -
285B ILE 3.9 4.9 - - - -
286B GLN* 3.6 7.6 - - - -
349B SER* 3.3 6.2 - - - -
350B GLY* 2.9 56.4 + - - +
351B LEU 3.4 26.5 - - - -
352B LYS* 3.8 25.1 - - + +
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Residues in contact with GLU 272 (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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270B VAL* 4.2 17.0 - - - +
271B PHE* 1.3 83.2 - - - +
273B GLY* 1.3 66.2 + - - +
274B LYS 3.7 4.5 + - - +
348B ILE 4.0 5.6 - - - +
349B SER* 3.9 11.9 - - - -
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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