Contacts of the strand formed by residues 310 - 323 (chain A) in PDB entry 4JVA
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 SER 310 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.1 6.6 - - - +
308A ALA 3.7 0.4 - - - -
309A ASP* 1.3 89.0 - - - +
311A PHE* 1.3 59.3 + - - +
312A PHE* 3.5 20.7 - - - -
349A GLY 3.6 8.0 - - - +
353A LEU* 4.2 8.4 - - - +
359A ARG* 2.8 26.0 + - - +
373A ALA* 4.0 10.0 - - - +
374A MET 3.0 27.1 + - - -
375A ASP* 4.3 1.1 - - - +
376A VAL 4.5 0.9 - - - +
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Residues in contact with PHE 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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274A PHE* 4.5 6.1 - + - -
310A SER* 1.3 73.6 - - - +
312A PHE* 1.3 67.3 + - - +
313A ILE* 3.8 23.6 - - + -
347A TYR* 3.4 43.5 - + + -
348A PHE 3.8 4.7 - - - -
349A GLY 4.5 0.7 - - - -
350A GLU* 3.4 34.5 - - + -
353A LEU* 3.6 15.9 - - + +
372A LEU 4.2 0.6 - - - +
373A ALA* 3.3 7.1 - - - +
374A MET* 2.9 50.3 + - + +
379A PHE* 4.0 7.6 - + + -
383A LEU* 3.7 30.1 - - + -
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Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LYS* 5.0 3.8 - - + -
295A TYR* 3.4 24.5 - - - -
301A ILE* 3.7 15.0 - - + -
302A ILE* 3.6 29.6 - - + -
310A SER* 3.5 34.3 - - - -
311A PHE* 1.3 77.1 - - - +
313A ILE* 1.3 64.6 + - - +
314A VAL 4.2 0.2 - - - -
347A TYR* 3.2 9.0 - - - +
348A PHE* 3.0 68.0 + + + +
349A GLY* 4.6 1.8 - - - -
359A ARG* 3.9 3.6 - - - -
371A CYS* 4.2 15.0 - - + -
372A LEU 4.2 2.2 - - - -
373A ALA* 4.3 15.0 - - + -
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Residues in contact with ILE 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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268A PHE* 4.3 17.9 - - + -
269A ILE* 6.3 1.8 - - + -
272A LEU* 4.3 16.8 - - + -
274A PHE* 4.1 18.8 - - + -
275A LEU* 5.3 4.3 - - + -
286A VAL* 6.0 2.9 - - + -
290A ILE* 5.6 4.0 - - + -
311A PHE* 3.8 26.2 - - + -
312A PHE* 1.3 80.0 - - - +
314A VAL* 1.3 74.2 + - - +
315A GLU* 3.2 0.9 + - - -
345A GLY 4.7 5.2 - - - -
346A GLN 3.8 8.3 - - - +
347A TYR* 4.2 4.3 - - + +
371A CYS* 4.3 2.0 - - - +
372A LEU* 3.0 48.2 + - + +
374A MET* 5.3 8.5 - - + -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A PHE* 3.5 5.0 - - - -
313A ILE* 1.3 72.4 - - - +
315A GLU* 1.3 61.0 + - - +
316A SER 3.9 13.0 - - - +
317A GLY 3.8 17.7 - - - +
319A VAL* 3.4 30.5 - - + -
342A CYS* 3.9 15.3 - - + +
343A LEU 3.6 11.4 - - - +
344A ARG 3.8 16.2 - - - +
345A GLY 2.9 26.9 + - - -
346A GLN 3.1 14.6 + - - +
348A PHE* 3.6 13.4 - - + -
369A VAL* 4.8 1.3 - - + -
370A LYS 4.0 4.0 - - - +
371A CYS* 4.4 4.3 - - - +
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A TYR* 3.9 32.4 + - + -
268A PHE* 3.9 18.2 - - + -
313A ILE 3.2 0.4 + - - -
314A VAL* 1.3 76.0 - - - +
316A SER* 1.3 64.1 + - - +
344A ARG* 2.6 65.6 + - - +
370A LYS* 2.7 40.1 + - - +
372A LEU* 3.9 17.4 - - + +
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Residues in contact with SER 316 (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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314A VAL* 3.7 2.7 - - - +
315A GLU* 1.3 89.1 - - - +
317A GLY* 1.3 63.7 + - - +
344A ARG* 4.7 4.7 - - - +
368A THR 4.3 2.8 + - - -
369A VAL* 3.3 5.7 - - - +
370A LYS* 2.9 62.6 + - - +
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Residues in contact with GLY 317 (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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314A VAL* 3.8 10.5 - - - +
316A SER* 1.3 78.2 - - - +
318A GLU* 1.3 61.5 + - - +
342A CYS 4.2 2.1 - - - +
343A LEU* 4.2 4.3 - - - +
344A ARG* 4.2 7.7 + - - +
366A ILE 5.0 1.8 - - - -
368A THR 3.5 17.7 - - - -
369A VAL* 4.2 0.9 - - - -
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Residues in contact with GLU 318 (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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317A GLY* 1.3 75.0 - - - +
319A VAL* 1.3 64.9 + - - +
341A ARG* 5.7 3.1 - - - +
342A CYS 3.5 4.7 - - - -
343A LEU* 4.2 16.6 - - + -
366A ILE* 2.9 55.2 + - + +
369A VAL* 3.1 10.8 - - - +
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Residues in contact with VAL 319 (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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301A ILE* 3.8 17.7 - - + -
314A VAL* 3.4 28.5 - - + -
318A GLU* 1.3 78.7 - - - +
320A ARG* 1.3 62.5 + - - +
321A ILE* 3.8 9.0 + - + +
341A ARG* 3.2 8.7 - - - -
342A CYS* 2.8 43.0 + - + +
348A PHE* 3.9 12.8 - - + -
363A ALA* 3.9 20.6 - - + -
364A HIS 3.5 10.1 - - - +
369A VAL* 4.0 19.5 - - + -
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Residues in contact with ARG 320 (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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298A GLY* 5.1 5.9 - - - -
319A VAL* 1.3 71.9 - - - +
321A ILE* 1.3 63.7 + - - +
322A THR* 3.7 28.1 + - + +
338A GLU* 3.7 23.1 - - + +
340A ALA 3.9 3.4 - - - -
341A ARG* 3.9 15.0 - - - +
362A SER 3.8 0.3 - - - +
363A ALA* 3.3 3.5 - - - -
364A HIS* 2.8 73.3 + - - +
365A ALA 4.5 9.1 + - - -
366A ILE* 3.5 25.4 - - + +
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Residues in contact with ILE 321 (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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319A VAL* 4.1 9.9 - - + +
320A ARG* 1.3 74.6 - - - +
322A THR* 1.3 64.8 + - - +
338A GLU* 3.6 1.4 - - - +
339A ILE* 2.9 39.5 + - + -
340A ALA* 3.1 27.5 + - + +
342A CYS* 4.0 23.1 - - - -
348A PHE* 4.2 12.3 - - + -
361A ALA* 3.8 9.0 - - + -
362A SER 3.3 7.2 - - - +
363A ALA* 3.8 24.9 - - + -
502A 1OR 3.3 34.8 - - + +
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Residues in contact with THR 322 (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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320A ARG* 3.7 34.5 + - + +
321A ILE* 1.3 79.3 - - - +
323A MET* 1.3 64.7 + - - +
336A ALA* 4.7 16.2 - - + +
337A VAL 3.3 10.8 - - - -
338A GLU* 3.9 13.0 - - + +
339A ILE* 4.3 1.1 - - - +
361A ALA* 3.3 6.8 - - - +
362A SER* 3.0 45.2 + - - -
364A HIS* 4.6 6.6 + - - -
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Residues in contact with MET 323 (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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304A GLN* 4.0 8.7 - - - +
322A THR* 1.3 76.0 - - - +
324A LYS* 1.3 67.3 - - - +
325A ARG* 6.2 2.0 - - - +
336A ALA* 3.3 3.7 - - - -
337A VAL* 2.7 49.5 + - + +
339A ILE* 3.3 38.6 - - + -
360A ALA 3.8 15.7 - - - +
361A ALA* 3.8 8.3 - - + -
502A 1OR 4.0 26.5 - - + +
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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