Contacts of the strand formed by residues 263 - 269 (chain A) in PDB entry 5JPM
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 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A PRO* 3.4 2.4 - - - +
248A GLY* 2.5 46.4 + - - -
249A LYS* 5.3 3.0 - - + +
261A GLU* 3.6 39.1 + - + +
262A MET* 1.3 74.1 - - - +
264A LEU* 1.3 59.9 + - - +
311A HIS* 3.9 27.9 + - + -
312A ILE 3.7 7.6 - - - +
313A SER* 4.2 8.5 + - - +
360A TRP* 3.6 7.3 - - - -
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 3.9 15.9 - - + -
246A THR 3.2 12.8 - - - +
247A PRO* 3.8 8.5 - - + -
248A GLY* 3.9 1.6 - - - +
262A MET 5.1 1.1 - - - +
263A GLN* 1.3 79.6 - - - +
265A ASP* 1.3 62.7 + - - +
266A ILE* 4.1 19.7 - - + -
282A VAL* 5.0 0.4 - - + -
284A PHE* 4.2 15.7 - - + -
311A HIS* 3.0 8.8 + - - -
312A ILE* 3.0 51.3 + - + +
313A SER* 5.5 0.7 - - - -
314A LEU* 5.7 2.0 - - + +
340A VAL* 3.6 27.8 - - + -
357A LEU* 5.5 1.1 - - + -
360A TRP* 4.0 22.4 - - + -
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS 3.8 0.7 - - - +
245A ILE* 3.7 2.4 - - - -
246A THR* 2.6 48.4 + - + +
264A LEU* 1.3 73.2 - - - +
266A ILE* 1.3 65.5 + - - +
267A GLN* 4.3 2.4 + - + +
309A GLN* 5.5 7.9 - - + +
310A SER 3.4 4.4 - - - +
311A HIS* 2.5 42.7 + - - +
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Residues in contact with ILE 266 (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 VAL* 5.0 1.6 - - + -
244A LYS 3.5 9.0 - - - +
245A ILE* 4.9 4.7 - - + -
264A LEU* 4.1 16.2 - - + -
265A ASP* 1.3 78.2 - - - +
267A GLN* 1.3 62.5 + - - +
280A ALA* 4.6 14.1 - - + -
282A VAL* 4.2 13.9 - - + -
305A LEU* 4.6 3.2 - - + +
309A GLN* 3.1 6.6 - - - +
310A SER* 2.7 45.3 + - - +
312A ILE* 3.8 27.1 - - + -
342A ALA* 4.1 25.4 - - + -
344A ILE* 3.7 30.5 - - + -
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Residues in contact with GLN 267 (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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242A GLU* 3.9 0.7 - - - +
243A VAL* 3.5 6.4 - - - +
244A LYS* 2.9 74.9 + - + +
246A THR* 5.9 1.1 - - - +
265A ASP* 4.2 2.0 - - + +
266A ILE* 1.3 74.9 - - - +
268A ALA* 1.3 66.7 + - - +
269A ARG* 4.6 16.3 + - + +
305A LEU* 6.0 0.2 - - - -
308A GLY 3.5 3.8 - - - +
309A GLN* 3.2 34.0 + - + +
344A ILE* 4.7 1.3 - - - -
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Residues in contact with ALA 268 (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 PHE* 4.3 4.5 - - + -
242A GLU 3.5 8.3 - - - +
243A VAL* 4.7 0.2 - - + -
267A GLN* 1.3 75.7 - - - +
269A ARG* 1.3 62.6 + - - +
275A PRO* 4.1 0.2 - - - +
276A VAL* 3.1 28.3 + - + -
305A LEU* 4.0 13.5 - - + -
308A GLY* 2.7 24.9 + - - +
344A ILE* 3.6 30.3 - - + -
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Residues in contact with ARG 269 (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 PHE* 3.5 0.9 - - - +
242A GLU* 2.4 72.0 + - + +
244A LYS* 5.1 4.1 - - - +
267A GLN* 4.6 17.1 + - + +
268A ALA* 1.3 75.2 - - - +
270A TYR* 1.3 73.1 + - - +
271A ILE 4.1 11.1 + - - -
272A TYR 4.8 0.6 + - - -
273A GLY* 3.6 28.1 + - - +
274A LYS 3.5 12.1 - - - +
275A PRO* 3.8 8.5 - - + -
276A VAL* 3.8 9.8 - - - +
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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