Contacts of the strand formed by residues 263 - 268 (chain A) in PDB entry 3JRQ
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 ARG 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A VAL* 4.2 6.2 - - - +
262A SER* 1.3 77.4 - - - +
264A ALA* 1.3 69.2 + - - +
265A VAL* 3.9 8.3 - - + -
274A PRO* 5.0 3.8 - - - -
276A SER* 3.3 22.9 + - - +
278A ASP* 2.8 37.3 + - - +
343A ILE 3.8 1.2 - - - +
344A LEU* 3.6 1.0 - - - -
345A ALA 2.9 31.6 + - - +
350A TRP* 3.3 54.8 + - + +
353A MET 5.1 1.4 + - - -
354A THR* 5.3 1.6 - - - +
355A ASP* 3.1 34.1 + - - +
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Residues in contact with ALA 264 (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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245A VAL* 3.9 12.0 - - + +
256A VAL* 4.0 25.4 - - + -
263A ARG* 1.3 73.3 - - - +
265A VAL* 1.3 68.5 + - - +
274A PRO* 3.7 0.9 - - - +
275A LEU* 2.9 28.2 + - + -
276A SER* 3.1 8.7 + - - +
342A LEU* 4.6 2.9 - - + -
343A ILE 3.2 5.8 - - - +
344A LEU* 3.6 22.9 - - + -
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ARG* 3.9 13.5 - - + -
264A ALA* 1.3 81.0 - - - +
266A LEU* 1.3 60.7 + - - +
267A CYS 4.2 0.2 + - - -
273A LEU 3.7 9.6 - - - +
274A PRO* 4.2 5.8 - - + -
275A LEU* 4.4 0.4 - - - +
341A CYS 4.1 0.2 - - - +
342A LEU* 3.3 6.2 - - - +
343A ILE* 2.8 54.0 + - + +
350A TRP* 3.9 16.4 - - + -
355A ASP* 3.3 33.4 - - + +
359A CYS* 3.6 26.7 - - - -
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Residues in contact with LEU 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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254A ILE* 4.4 8.5 - - + -
265A VAL* 1.3 74.9 - - - +
267A CYS* 1.3 82.5 + - - +
268A ARG* 3.8 33.7 - - + +
271A THR 3.6 1.0 - - - +
272A ALA* 3.4 1.9 - - - -
273A LEU* 2.6 61.2 + - + +
275A LEU* 3.9 22.0 - - + -
333A VAL* 4.6 13.5 - - + -
339A ASP* 3.9 10.5 - - - +
341A CYS 3.6 9.2 - - - +
342A LEU* 4.3 2.9 - - + -
359A CYS* 4.4 2.7 - - - -
422A LEU* 3.7 20.4 - - + -
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Residues in contact with CYS 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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265A VAL 4.2 0.4 + - - -
266A LEU* 1.3 80.5 - - - +
268A ARG* 1.3 55.6 + - - +
269A GLY 4.3 1.6 - - - -
271A THR 3.4 9.9 - - - -
339A ASP 3.6 0.2 - - - -
340A ASP* 2.7 45.1 + - - -
341A CYS* 2.9 33.7 + - - -
359A CYS* 3.8 23.1 - - + -
363A ARG* 3.3 45.8 - - - -
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Residues in contact with ARG 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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266A LEU* 3.8 19.3 + - + +
267A CYS* 1.3 72.3 - - - +
269A GLY* 1.3 71.3 + - - +
271A THR* 3.1 22.6 + - + +
273A LEU* 3.7 31.1 - - + +
333A VAL* 4.8 6.1 - - - +
334A LYS 3.3 24.5 + - - -
335A ARG* 4.8 0.2 - - - +
336A VAL* 3.5 20.7 - - - +
338A GLU* 3.2 28.9 - - + +
339A ASP* 3.1 22.7 + - - +
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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