Contacts of the helix formed by residues 312 - 328 (chain A) in PDB entry 3J8B
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 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A LEU 3.5 3.6 + - - +
311A THR* 1.3 69.5 - - - +
313A ASP* 1.3 61.1 + - - +
314A GLU 3.2 2.2 - - - -
315A MET* 3.3 9.8 + - - +
316A GLN* 3.0 27.0 + - - +
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Residues in contact with ASP 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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311A THR* 3.3 6.2 - - - -
312A GLN* 1.3 80.2 - - - +
314A GLU* 1.3 59.3 + - - +
316A GLN* 3.3 18.3 - - - +
317A ARG* 3.4 9.5 + - - +
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Residues in contact with GLU 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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311A THR* 3.8 18.6 + - - +
312A GLN 3.2 0.4 - - - -
313A ASP* 1.3 75.8 - - - +
315A MET* 1.3 58.4 + - - +
316A GLN 3.0 1.3 - - - -
317A ARG* 3.0 5.9 + - - +
318A MET* 2.8 38.2 + - + +
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Residues in contact with MET 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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311A THR 3.8 8.1 + - - +
312A GLN* 3.3 13.4 + - - +
314A GLU* 1.3 76.9 - - - +
316A GLN* 1.3 64.6 + - - +
318A MET* 4.7 5.4 - - - +
319A SER* 3.2 24.4 + - - -
382A TYR* 3.3 16.6 - - + +
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Residues in contact with GLN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLN 3.0 13.3 + - - +
313A ASP* 3.3 15.3 - - - +
314A GLU 3.0 0.2 - - - -
315A MET* 1.3 78.7 - - - +
317A ARG* 1.3 61.8 - - - +
320A THR* 3.2 18.5 + - - -
382A TYR* 3.2 21.5 - - - +
384A VAL* 4.5 3.2 + - + +
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Residues in contact with ARG 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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313A ASP 3.4 8.4 + - - +
314A GLU* 3.0 7.1 + - - +
316A GLN* 1.3 77.6 - - - +
318A MET* 1.3 61.3 + - - +
320A THR* 3.6 5.5 - - - -
321A ARG* 2.9 30.0 + - - +
419A GLU* 4.3 27.8 - - + +
423A GLU* 4.6 6.5 - - + +
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Residues in contact with MET 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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300A TYR* 5.5 13.0 - - + -
314A GLU* 2.8 22.1 + - + +
315A MET* 4.6 4.0 - - - +
317A ARG* 1.3 72.6 - - - +
319A SER* 1.3 58.8 + - - +
321A ARG* 3.1 8.6 + - - +
322A VAL* 2.9 29.9 + - - +
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Residues in contact with SER 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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300A TYR* 6.2 2.0 - - - +
315A MET 3.2 19.6 + - - -
318A MET* 1.3 76.5 - - - +
320A THR* 1.3 63.4 + - - +
322A VAL* 3.4 8.8 + - - +
323A LEU* 3.0 24.3 + - - +
378A ASN 5.0 0.4 - - - -
379A VAL* 3.6 30.1 - - - +
382A TYR* 3.7 18.6 - - - -
383A VAL* 4.6 1.8 - - - -
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Residues in contact with THR 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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316A GLN 3.2 16.1 + - - -
317A ARG* 3.6 6.7 - - - -
318A MET 3.2 0.4 - - - -
319A SER* 1.3 78.6 - - - +
321A ARG* 1.3 52.8 + - - +
323A LEU* 3.0 6.9 + - - +
324A LEU* 2.8 37.7 + - - +
383A VAL* 4.3 6.8 - - - +
384A VAL* 4.1 24.5 - - - +
387A VAL* 5.3 7.2 - - - +
420A LYS* 6.1 3.4 - - - -
423A GLU* 5.1 8.3 - - - -
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Residues in contact with ARG 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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317A ARG 2.9 15.5 + - - +
318A MET* 3.1 11.2 + - - +
320A THR* 1.3 76.3 - - - +
322A VAL* 1.3 57.3 + - - +
324A LEU* 3.7 4.0 - - - +
325A ALA* 2.8 34.3 + - - +
423A GLU* 4.4 19.2 - - + +
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Residues in contact with VAL 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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293A ALA* 4.7 7.9 - - + +
296A LEU* 4.7 22.6 - - + +
297A HIS* 5.5 7.4 - - + +
300A TYR* 6.1 4.3 - - + -
318A MET 2.9 16.3 + - - +
319A SER* 3.6 11.7 - - - +
321A ARG* 1.3 73.7 - - - +
323A LEU* 1.3 61.9 + - - +
325A ALA* 3.5 6.8 + - - +
326A THR* 3.3 19.4 + - - -
374A MET* 5.6 0.6 - - - +
379A VAL* 6.0 4.7 - - + -
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Residues in contact with LEU 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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319A SER 3.0 17.5 + - - +
320A THR* 3.5 6.3 - - - +
322A VAL* 1.3 74.3 - - - +
324A LEU* 1.3 64.5 + - - +
326A THR* 3.0 13.3 + - - -
327A LEU* 3.1 13.6 + - - +
374A MET* 4.5 24.2 - - + +
379A VAL* 5.6 3.6 - - + +
383A VAL* 5.0 11.0 - - + -
387A VAL* 5.1 9.4 - - + -
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Residues in contact with LEU 324 (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 THR 2.8 21.2 + - - +
321A ARG* 3.7 6.1 - - - +
323A LEU* 1.3 73.3 - - - +
325A ALA* 1.3 57.7 + - - +
327A LEU* 3.3 7.5 + - - +
328A SER* 2.9 32.6 + - - -
387A VAL* 5.5 8.2 - - + +
423A GLU* 5.5 9.2 - - + +
424A LEU* 6.0 2.2 - - - -
427A TYR* 5.0 11.8 - - + +
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Residues in contact with ALA 325 (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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289A ALA* 4.9 9.9 - - - +
292A HIS* 6.0 3.6 - - + -
293A ALA* 4.7 16.7 - - + +
296A LEU* 6.3 0.7 - - + -
321A ARG 2.8 17.7 + - - +
322A VAL* 3.8 7.4 - - - +
323A LEU 3.2 0.4 - - - -
324A LEU* 1.3 76.9 - - - +
326A THR* 1.3 59.8 + - - +
328A SER* 3.8 8.1 - - - -
329A ILE* 3.5 18.2 + - - +
427A TYR* 5.6 3.1 - - - +
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Residues in contact with THR 326 (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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293A ALA* 4.9 10.8 - - - -
322A VAL 3.3 10.4 + - - -
323A LEU* 3.0 11.5 + - - -
325A ALA* 1.3 78.5 - - - +
327A LEU* 1.3 62.6 + - - +
328A SER 3.2 1.3 - - - -
329A ILE* 3.5 17.4 - - - +
367A ARG* 4.5 11.5 - - - +
370A LEU* 5.1 8.5 - - - -
371A ILE* 4.7 24.5 - - - +
374A MET* 4.7 6.5 - - - -
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Residues in contact with LEU 327 (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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323A LEU 3.1 12.1 + - - +
324A LEU* 3.3 9.8 + - - +
326A THR* 1.3 74.4 - - - +
328A SER* 1.3 57.6 + - - +
329A ILE 3.1 12.6 + - - +
371A ILE* 6.4 0.2 - - - -
390A LEU* 6.4 1.6 - - + -
391A TYR* 6.0 8.7 - - + +
431A LEU* 5.4 1.0 - - - -
434A ASN* 4.2 12.0 - - - +
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Residues in contact with SER 328 (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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289A ALA* 5.7 0.6 - - - +
324A LEU 2.9 19.9 + - - -
325A ALA* 3.9 9.6 - - - -
326A THR 3.2 0.4 - - - -
327A LEU* 1.3 76.9 - - - +
329A ILE* 1.3 61.0 + - - +
330A PRO* 3.7 1.2 - - - +
427A TYR* 4.3 15.5 - - - -
430A GLN* 3.2 38.1 - - - +
431A LEU* 4.2 20.6 - - - +
434A ASN* 5.2 1.3 - - - +
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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