Contacts of the helix formed by residues 315 - 330 (chain A) in PDB entry 1Q57
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 GLY 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A SER* 3.8 10.1 - - - -
313A GLY 2.4 15.8 + - - +
314A SER* 1.3 78.9 - - - +
316A MET* 1.3 61.3 + - - -
317A VAL* 2.6 26.5 - - - +
318A MET* 3.4 15.9 - - - +
319A SER* 3.9 3.1 + - - -
465A HIS* 4.4 12.3 + - - -
506A GLN* 5.4 1.2 + - - -
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Residues in contact with MET 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 SER 3.0 5.1 + - - +
315A GLY* 1.3 69.6 - - - -
317A VAL* 1.3 80.0 + - - +
318A MET 2.8 0.9 - - - -
319A SER* 2.6 31.3 + - - +
320A THR* 2.6 35.8 + - - +
361A ARG* 5.8 0.2 - - - +
504A ARG* 5.5 5.8 - - - -
535A TYR* 3.0 56.1 - - + +
522C ARG 5.6 7.0 - - - +
524C THR 5.4 3.4 - - - +
525C GLY* 5.2 18.8 - - - +
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A SER* 4.8 2.5 - - - +
315A GLY* 2.6 41.3 - - - +
316A MET* 1.3 99.3 - - + +
318A MET* 1.3 54.0 + - - +
320A THR 3.4 0.2 + - - -
321A PHE* 2.9 24.9 + - - +
502A LEU* 4.6 6.9 - - + +
504A ARG* 3.7 41.7 - - + +
514A VAL* 4.2 29.6 - - + -
535A TYR* 5.4 3.6 - - + -
542A LEU* 3.2 25.0 - - + +
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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
----------------------------------------------------------
310A VAL* 3.6 18.8 - - + +
311A THR* 3.0 4.9 - - - -
312A SER* 2.5 56.3 + - - +
313A GLY 4.6 0.7 - - - +
315A GLY 3.4 11.7 - - - +
316A MET 2.8 1.4 - - - -
317A VAL* 1.3 81.8 - - - +
319A SER* 1.3 62.6 + - - +
320A THR 3.1 0.8 + - - -
321A PHE* 3.1 3.5 + - - +
322A VAL* 3.1 28.1 + - - +
463A ILE* 2.9 43.7 - - + -
464A CYS 3.0 17.3 - - - +
465A HIS* 3.8 13.5 - - + -
502A LEU* 3.8 11.4 - - + +
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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
----------------------------------------------------------
315A GLY 3.9 2.8 + - - -
316A MET* 2.6 22.0 + - - -
318A MET* 1.3 76.6 - - - +
320A THR* 1.3 54.5 + - - -
322A VAL* 4.4 1.0 - - - +
323A ARG* 3.1 48.5 + - - +
344A GLU* 5.3 0.7 + - - -
424A ASP* 2.8 30.1 + - - -
463A ILE* 4.6 2.6 - - - +
465A HIS* 5.9 3.6 + - - -
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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
----------------------------------------------------------
316A MET* 2.6 37.3 + - - +
317A VAL 3.6 9.2 - - - -
319A SER* 1.3 70.7 - - - +
321A PHE* 1.3 58.2 + - - +
322A VAL 3.2 0.2 - - - -
323A ARG* 3.0 6.2 + - - +
324A GLN* 2.7 54.9 + - - +
356A LEU* 4.7 8.5 - - + -
535A TYR* 4.8 2.2 + - + -
540A GLY 3.6 20.5 + - - +
542A LEU* 4.1 10.3 - - + +
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Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 4.6 9.9 - + - -
290A SER 4.3 8.1 - - - -
292A CYS* 5.7 0.2 - - + -
295A ILE* 4.7 20.9 - - + -
310A VAL* 4.1 21.5 - - + -
317A VAL 2.9 17.5 + - - +
318A MET 3.5 3.8 - - - +
320A THR* 1.3 78.0 - - - +
322A VAL* 1.3 66.3 + - + +
324A GLN* 3.2 6.7 + - + +
325A GLN* 2.8 56.4 + - + +
500A ILE* 4.7 17.7 - - + -
502A LEU* 3.7 22.4 - - + -
516A VAL* 5.7 0.2 - - + -
533A MET* 2.9 37.5 - - + -
542A LEU* 3.9 8.1 - - + -
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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
----------------------------------------------------------
310A VAL* 3.8 21.1 - - + -
318A MET 3.1 7.2 + - - +
319A SER* 4.4 4.7 - - - +
321A PHE* 1.3 78.5 - - + +
323A ARG* 1.3 66.3 + - - +
325A GLN* 3.1 7.9 + - + +
326A ALA* 2.9 20.6 + - - +
341A MET* 5.8 2.0 - - - -
422A ILE* 3.1 41.7 - - + +
424A ASP* 5.1 3.4 - - - +
461A VAL* 5.0 5.4 - - + -
463A ILE* 3.2 39.5 - - + -
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Residues in contact with ARG 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER* 3.1 38.6 + - - +
320A THR* 3.0 11.8 + - - +
322A VAL* 1.3 80.4 - - - +
324A GLN* 1.3 58.1 + - - +
326A ALA* 3.3 9.3 - - + +
327A LEU* 2.8 28.2 + - - +
339A LEU* 6.5 1.6 - - + -
341A MET* 3.0 36.3 - - - +
344A GLU* 2.7 35.3 + - - -
349A THR* 4.6 4.6 - - - -
352A ASP* 4.4 25.1 + - + -
353A LEU* 4.1 22.4 - - + +
356A LEU* 4.1 16.2 - - + -
424A ASP* 3.5 5.9 + - - -
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Residues in contact with GLN 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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290A SER* 5.1 13.5 - - - +
291A GLY* 5.5 1.0 - - - -
320A THR* 2.7 34.8 + - - +
321A PHE* 3.3 11.9 - - + +
323A ARG* 1.3 73.2 - - - +
325A GLN* 1.3 65.6 + - - +
327A LEU* 3.0 10.1 + - - +
328A GLN* 3.0 23.7 + - - +
356A LEU* 4.3 7.3 - - + +
541A TRP* 2.6 50.6 - - + +
542A LEU* 3.0 45.2 + - - +
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Residues in contact with GLN 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 3.1 22.2 - - + +
290A SER* 2.3 48.9 + - - +
321A PHE* 2.8 43.9 + - + +
322A VAL* 3.1 10.3 + - - +
324A GLN* 1.3 76.8 - - - +
326A ALA* 1.3 66.9 + - - +
327A LEU 3.2 0.2 + - - -
328A GLN* 3.2 3.4 + - - -
329A TRP* 2.9 68.6 + - + +
422A ILE* 5.2 0.9 - - + -
461A VAL* 6.5 0.9 - - + -
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Residues in contact with ALA 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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322A VAL 2.9 5.4 + - - +
323A ARG* 3.3 13.9 - - + +
325A GLN* 1.3 77.7 - - - +
327A LEU* 1.3 65.7 + - - +
329A TRP* 4.6 1.6 - - - -
330A GLY 3.2 13.7 + - - -
337A VAL* 3.6 14.4 - - + +
339A LEU* 3.9 21.1 - - + -
353A LEU* 5.1 4.0 - - + -
391A PHE* 3.3 14.3 - - + -
422A ILE* 3.4 27.6 - - + +
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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 ARG 2.8 16.0 + - - +
324A GLN* 3.0 14.3 + - - +
326A ALA* 1.3 76.3 - - - +
328A GLN* 1.3 61.6 + - + +
330A GLY 3.1 5.7 + - - -
331A THR* 2.7 23.4 + - + +
353A LEU* 4.1 18.1 - - + +
356A LEU* 4.2 4.9 - - + -
357A HIS* 3.5 44.9 - - + +
359A ARG* 5.4 0.9 - - - +
385A LEU* 3.9 28.9 - - + -
391A PHE* 3.8 8.4 - - + -
541A TRP* 4.1 21.1 - - + -
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Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 4.1 9.9 + - - +
290A SER* 3.5 34.5 + - - +
324A GLN 3.0 11.4 + - - +
325A GLN* 3.2 2.2 + - - +
327A LEU* 1.3 77.0 - - - +
329A TRP* 1.3 70.3 + - + +
330A GLY 3.3 0.2 - - - -
331A THR* 3.6 7.0 - - - -
332A ALA* 3.1 36.4 + - + +
333A MET* 3.2 42.9 + - - +
541A TRP* 6.0 5.6 - - + -
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Residues in contact with TRP 329 (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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287A LEU* 3.4 35.9 - - + +
288A LEU 3.6 19.8 + - - -
289A PHE* 4.0 23.1 - + - -
302A ALA* 4.5 13.0 - - + -
325A GLN* 2.9 51.9 + - + +
326A ALA* 4.0 6.7 - - - +
328A GLN* 1.3 87.9 - - + +
330A GLY* 1.3 57.6 + - - +
331A THR 3.2 0.7 - - - -
333A MET* 3.0 29.6 - - + +
335A LYS* 3.1 20.7 + - + +
337A VAL* 4.0 7.9 - - + -
420A VAL* 3.5 41.5 - - + -
422A ILE* 4.7 2.7 - - + -
459A VAL* 5.1 0.7 - - + -
461A VAL* 3.9 18.4 - - + -
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Residues in contact with GLY 330 (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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326A ALA 3.2 6.3 + - - -
327A LEU 3.1 4.4 + - - -
329A TRP* 1.3 77.2 - - - +
331A THR* 1.3 69.1 + - - +
333A MET 3.8 3.4 - - - -
334A GLY 5.2 0.4 - - - -
335A LYS 3.1 15.0 - - - -
337A VAL* 3.8 5.4 - - - +
390A THR* 3.0 29.9 + - - +
391A PHE* 3.4 13.3 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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