Contacts of the strand formed by residues 309 - 315 (chain A) in PDB entry 3JPX
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 VAL 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A LEU* 3.5 4.4 - - - +
254A CYS* 3.4 36.2 - - + -
255A GLY* 2.9 29.8 + - - +
258A HIS 3.6 27.4 - - - +
259A SER 4.3 2.9 - - - +
260A LEU* 4.1 10.5 - - + -
305A HIS* 3.7 32.1 - - + +
307A ASN 3.4 13.7 - - - +
308A TYR* 1.3 70.4 - - - +
310A ASP* 1.3 58.0 + - - +
311A CYS 3.6 0.9 - - - +
321A SER* 4.1 4.0 - - - -
322A LYS 3.2 17.9 - - - +
323A SER* 4.3 0.2 - - - +
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Residues in contact with ASP 310 (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 LEU* 3.8 21.5 - - + +
241A SER* 3.7 9.6 - - - -
308A TYR 4.6 3.1 - - - +
309A VAL* 1.3 73.7 - - - +
311A CYS* 1.3 62.9 + - - +
322A LYS* 2.6 46.1 + - - +
323A SER* 3.9 7.2 - - - +
363A ILE 4.5 0.3 - - - +
364A TRP* 3.6 9.1 - - + -
365A TYR* 2.7 36.0 + - + +
366A MET* 3.0 7.5 + - - +
367A ARG* 2.9 29.9 + - - +
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Residues in contact with CYS 311 (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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195A GLU* 5.7 1.1 - - - -
241A SER* 3.5 11.3 - - - -
254A CYS* 3.9 1.3 - - - -
309A VAL* 3.6 2.3 - - - +
310A ASP* 1.3 85.0 + - - +
312A VAL* 1.3 64.9 + - - +
321A SER* 3.2 5.9 - - - -
322A LYS* 3.0 44.7 + - + +
366A MET 4.2 7.2 - - - +
367A ARG* 3.9 11.2 - - - -
368A PHE* 3.6 49.5 - - - -
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Residues in contact with VAL 312 (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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197A LYS* 4.4 4.7 + - - -
241A SER* 3.2 10.8 + - - +
242A ALA* 3.7 18.9 - - - +
243A ASP* 3.4 11.7 - - + +
252A MET* 3.5 35.9 - - + +
253A SER* 4.5 0.7 - - - -
254A CYS* 3.8 17.5 - - - -
260A LEU* 3.8 15.3 - - + -
311A CYS* 1.3 79.4 - - - +
313A ARG* 1.3 69.3 + - - +
314A TRP 5.1 0.2 - - - +
319A ILE* 3.5 28.5 - - + -
320A LEU 3.3 4.3 - - - +
368A PHE* 4.4 2.5 - - - -
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Residues in contact with ARG 313 (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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103A TRP* 5.9 6.1 - - - -
197A LYS* 5.0 5.2 - - - +
243A ASP* 2.9 42.1 + - - -
244A TYR 4.5 4.2 + - - -
245A ASP 6.1 0.6 - - - -
312A VAL* 1.3 82.0 - - - +
314A TRP* 1.3 73.4 + - - +
319A ILE* 3.8 1.3 - - - +
320A LEU* 2.8 35.0 + - + +
368A PHE* 3.7 22.9 - - + -
369A SER* 6.4 0.7 - - - +
370A MET* 3.9 31.0 - - - +
371A ASP 5.1 2.6 + - - -
372A PHE 5.5 1.2 + - - -
374A GLN* 3.4 37.9 + - - +
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Residues in contact with TRP 314 (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 ASP* 2.8 44.1 + - + +
244A TYR 3.3 14.8 - - - +
245A ASP* 3.5 24.2 - - + +
246A LEU 5.1 1.1 - - - +
250A LYS* 3.6 31.4 - - + -
251A ILE 4.0 0.8 - - - -
252A MET* 3.4 20.6 - - + +
262A LEU* 3.5 30.7 - - + -
313A ARG* 1.3 80.7 + - - +
315A LEU* 1.3 59.2 + - - +
316A GLY 3.5 22.7 - - - +
317A ASP 3.8 16.2 - - - -
318A LEU 3.6 7.6 - - - -
319A ILE* 3.4 26.7 - - + -
320A LEU* 5.6 0.2 - - - -
340A ILE* 3.9 15.3 - - + -
374A GLN* 2.9 20.3 + - - +
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Residues in contact with LEU 315 (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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313A ARG 3.7 0.8 + - - -
314A TRP* 1.3 73.3 - - - +
316A GLY* 1.3 58.7 + - - +
317A ASP 3.3 0.5 + - - -
318A LEU* 2.8 44.7 + - + +
320A LEU* 4.1 26.7 - - + -
330A CYS* 5.0 9.9 - - - -
370A MET* 4.1 10.8 - - + -
374A GLN* 4.0 38.4 - - + +
391A LEU* 4.2 21.3 - - + -
396A PRO* 5.4 7.4 - - + -
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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