Contacts of the helix formed by residues 315 - 330 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B SER* 4.2 4.7 - - - -
313B GLY 2.7 8.5 + - - -
314B SER* 1.3 82.9 - - - +
316B MET* 1.3 61.3 + - - -
317B VAL* 3.4 20.8 - - - +
318B MET* 3.3 30.1 - - - +
319B SER* 3.9 2.4 + - - -
465B HIS* 4.4 8.7 + - - -
504B ARG* 6.0 0.4 - - - +
506B GLN* 5.4 0.8 + - - -
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Residues in contact with MET 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A THR 3.9 15.7 - - - +
525A GLY* 3.1 30.0 + - - +
526A ASP* 5.0 11.9 - - - +
314B SER 2.9 4.8 + - - -
315B GLY* 1.3 70.5 - - - -
317B VAL* 1.3 74.1 + - - +
318B MET 2.8 1.3 - - - -
319B SER* 2.7 29.5 + - - +
320B THR* 2.8 39.8 + - - +
504B ARG* 5.7 4.9 - - - -
535B TYR* 2.9 57.7 - - + +
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Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B SER* 5.6 0.7 - - - +
315B GLY* 3.4 20.0 - - - -
316B MET* 1.3 87.4 - - - +
318B MET* 1.3 56.8 + - - +
320B THR* 4.1 5.6 - - - -
321B PHE* 2.9 25.9 + - - +
502B LEU* 4.6 6.7 - - + +
504B ARG* 3.7 37.2 - - + +
514B VAL* 4.0 36.8 - - + -
535B TYR* 5.6 3.8 - - + -
542B LEU* 3.4 25.0 - - + +
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Residues in contact with MET 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL* 3.6 24.7 - - + +
311B THR 4.2 0.2 - - - -
312B SER* 3.0 60.3 + - - +
313B GLY 3.8 4.5 - - - +
315B GLY* 3.3 9.4 - - - +
316B MET 2.8 1.6 - - - -
317B VAL* 1.3 81.0 - - - +
319B SER* 1.3 57.5 + - - +
321B PHE* 3.1 2.9 + - - +
322B VAL* 3.0 32.9 + - - +
463B ILE* 3.1 42.0 - - + -
464B CYS 3.6 2.5 - - - +
465B HIS* 3.3 25.1 - - + +
502B LEU* 3.8 7.4 - - + +
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLY 3.9 2.1 + - - -
316B MET* 2.7 21.2 + - - -
318B MET* 1.3 75.7 - - - +
320B THR* 1.3 54.9 + - - -
322B VAL* 4.0 2.8 - - - +
323B ARG* 2.8 55.2 + - - +
344B GLU* 5.3 0.3 + - - -
424B ASP* 2.8 30.6 + - - -
463B ILE* 4.5 3.6 - - - +
465B HIS* 5.9 4.3 - - - -
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B MET* 2.8 40.0 + - - +
317B VAL 3.6 7.9 - - - -
319B SER* 1.3 71.6 - - - +
321B PHE* 1.3 70.7 + - - +
323B ARG* 2.9 6.2 + - - +
324B GLN* 2.6 48.5 + - - +
356B LEU* 4.8 8.7 - - + -
535B TYR* 4.6 2.0 - - + -
540B GLY 3.5 22.0 - - - +
542B LEU* 4.0 10.5 - - + +
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Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 4.5 9.0 - + - -
290B SER 4.3 6.3 - - - -
292B CYS* 5.7 0.2 - - + -
295B ILE* 4.7 20.9 - - + -
310B VAL* 4.2 24.0 - - + -
317B VAL 2.9 14.9 + - - +
318B MET 3.6 4.3 - - - +
320B THR* 1.3 83.7 - - - +
322B VAL* 1.3 66.6 + - - +
324B GLN* 3.2 5.9 + - + +
325B GLN* 2.9 57.3 + - + +
500B ILE* 4.6 14.8 - - + -
502B LEU* 3.6 22.0 - - + -
516B VAL* 5.5 0.4 - - + -
533B MET* 2.9 38.1 - - + -
542B LEU* 4.0 8.7 - - + -
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL* 3.9 21.5 - - + -
318B MET 3.0 7.9 + - - +
319B SER* 4.4 4.0 - - - +
321B PHE* 1.3 78.9 - - - +
323B ARG* 1.3 59.3 + - - +
325B GLN* 3.1 8.7 + - + +
326B ALA* 2.9 25.8 + - - +
341B MET* 5.9 1.8 - - - -
422B ILE* 3.1 41.4 - - + +
424B ASP* 5.1 3.4 - - - +
461B VAL* 4.9 6.7 - - + -
463B ILE* 3.1 39.3 - - + -
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Residues in contact with ARG 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B SER* 2.8 43.7 + - - +
320B THR* 2.9 7.4 + - - +
322B VAL* 1.3 77.6 - - - +
324B GLN* 1.3 67.0 + - - +
326B ALA* 3.2 8.7 + - + +
327B LEU* 2.8 23.8 + - - +
341B MET* 3.2 26.1 - - - +
344B GLU* 2.6 36.4 + - - -
349B THR* 5.2 3.1 - - - -
352B ASP* 4.4 26.8 + - + +
353B LEU* 4.1 21.6 - - + +
356B LEU* 4.1 15.5 - - + -
424B ASP* 3.2 13.7 + - - -
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B SER* 5.1 12.1 - - - +
291B GLY* 5.5 1.0 - - - -
320B THR* 2.6 32.9 + - - +
321B PHE* 3.2 12.0 - - + +
323B ARG* 1.3 72.8 - - - +
325B GLN* 1.3 67.1 + - - +
327B LEU* 3.0 22.9 + - - +
328B GLN* 3.0 9.1 + - - +
356B LEU* 4.3 7.1 - - + +
541B TRP* 2.7 50.8 - - + +
542B LEU* 2.9 45.4 + - - +
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Residues in contact with GLN 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 3.1 20.0 - - + +
290B SER* 2.3 50.3 + - - +
321B PHE* 2.9 44.5 + - + +
322B VAL* 3.1 11.2 + - + +
324B GLN* 1.3 75.8 - - - +
326B ALA* 1.3 66.8 + - - +
328B GLN* 3.2 5.9 + - - +
329B TRP* 2.9 68.2 + - + +
422B ILE* 5.3 0.4 - - + -
461B VAL* 6.5 0.2 - - + -
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL 2.9 10.8 + - - +
323B ARG* 3.2 14.4 - - + +
325B GLN* 1.3 72.2 - - - +
327B LEU* 1.3 67.4 + - - +
329B TRP* 3.4 1.3 + - - -
330B GLY 3.1 13.7 + - - -
337B VAL* 3.5 17.7 - - + +
339B LEU* 4.0 16.6 - - + -
353B LEU* 5.1 6.1 - - + -
391B PHE* 3.5 9.7 - - + -
422B ILE* 3.5 28.3 - - + +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ARG 2.8 12.6 + - - +
324B GLN* 3.0 14.7 + - - +
326B ALA* 1.3 79.7 - - - +
328B GLN* 1.3 61.4 + - - +
330B GLY* 3.0 7.6 + - - -
331B THR* 2.8 24.3 + - + +
353B LEU* 4.1 19.4 - - + +
356B LEU* 4.1 4.9 - - + -
357B HIS* 3.4 45.5 - - + +
359B ARG* 5.3 0.9 - - - +
385B LEU* 3.9 28.3 - - + -
391B PHE* 4.0 6.9 - - + -
541B TRP* 4.0 22.2 - - + -
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Residues in contact with GLN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 4.2 7.1 + - - +
290B SER* 3.6 35.7 + - - +
324B GLN 3.0 11.3 + - - +
325B GLN 3.2 2.6 + - - +
327B LEU* 1.3 78.9 - - + +
329B TRP* 1.3 66.2 + - + +
331B THR* 3.7 6.3 - - - -
332B ALA* 2.9 51.0 + - + +
333B MET* 3.1 42.7 + - - +
541B TRP* 6.1 4.5 - - + -
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Residues in contact with TRP 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B LEU* 3.3 36.3 - - + +
288B LEU 3.4 20.7 + - - -
289B PHE* 4.0 24.0 - + - -
302B ALA* 4.5 11.4 - - + -
325B GLN* 2.9 51.2 + - + +
326B ALA* 3.9 7.2 - - - +
328B GLN* 1.3 86.2 - - + +
330B GLY* 1.3 57.4 + - - +
331B THR 3.3 1.6 - - - -
333B MET* 3.1 25.1 - - + +
335B LYS* 3.0 25.5 + - + +
337B VAL* 4.1 7.2 - - + -
420B VAL* 3.7 37.2 - - + -
422B ILE* 4.5 4.0 - - + -
459B VAL* 5.2 0.2 - - + -
461B VAL* 3.9 19.1 - - + -
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Residues in contact with GLY 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ALA 3.1 5.9 + - - -
327B LEU 3.0 7.4 + - - -
329B TRP* 1.3 76.4 - - - +
331B THR* 1.3 69.9 + - - +
333B MET 3.8 3.4 - - - -
334B GLY 5.3 0.4 - - - -
335B LYS 3.2 13.5 - - - -
337B VAL* 3.9 4.9 - - - +
390B THR* 3.0 24.2 + - - +
391B PHE* 3.4 19.1 - - - -
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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