Contacts of the helix formed by residues 361 - 379 (chain A) in PDB entry 3QPV
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 361 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A ILE* 3.7 8.6 - - - +
352A TYR 3.7 6.1 - - - -
353A TYR 3.5 16.4 - - - -
354A TYR 3.0 24.2 - - - -
355A ARG* 4.0 7.4 + - - -
360A GLU* 1.3 76.9 - - - +
362A TYR* 1.4 56.1 + - - +
363A GLN* 3.1 8.5 + - - +
364A ASP* 2.8 44.8 + - - +
365A LEU* 3.2 8.3 + - - +
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Residues in contact with TYR 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 4.2 7.2 - - + -
347A ARG* 3.6 13.9 - - - -
351A LYS* 3.4 17.9 - - - -
352A TYR* 3.2 28.7 + - + +
361A SER* 1.4 67.6 - - - +
363A GLN* 1.3 66.6 + - - +
365A LEU* 3.2 11.5 + - + +
366A VAL* 3.1 25.1 + - - +
389A ALA* 3.5 32.6 - - + +
392A ARG* 3.0 25.0 + - + -
393A CYS* 3.6 19.4 - - - -
406A MET* 4.2 6.1 - - + -
407A PRO* 3.8 33.5 + - + -
720A F6P 2.5 30.1 + - - -
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Residues in contact with GLN 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 2.8 33.1 + - - +
352A TYR* 3.2 37.2 + - + +
353A TYR* 3.5 21.3 + - + +
355A ARG* 4.7 8.6 - - - +
361A SER* 3.1 10.8 + - - +
362A TYR* 1.3 78.2 - - - +
364A ASP* 1.3 62.7 + - - +
366A VAL* 3.3 13.0 + - - +
367A GLN* 3.4 12.1 + - - +
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Residues in contact with ASP 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ARG* 3.1 35.0 + - - -
359A GLY 4.2 0.3 - - - +
360A GLU* 3.2 28.4 - - + +
361A SER* 2.8 39.7 + - - +
363A GLN* 1.3 73.8 - - - +
365A LEU* 1.4 61.9 + - - +
367A GLN* 3.1 10.3 + - - +
368A ARG* 3.0 29.8 + - + +
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Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ILE* 4.0 18.4 - - + -
360A GLU* 4.6 1.1 - - - +
361A SER 3.2 9.8 + - - +
362A TYR* 3.2 13.2 + - + +
364A ASP* 1.4 76.0 - - - +
366A VAL* 1.3 55.9 + - - +
368A ARG* 3.3 40.6 + - - +
369A LEU* 2.7 45.9 + - + +
389A ALA* 3.7 32.8 - - + -
390A VAL* 3.8 18.4 - - + +
393A CYS* 3.4 25.6 - - - -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 3.3 62.0 - - + +
61A ILE* 4.0 11.0 - - + -
352A TYR* 3.9 18.2 - - - +
362A TYR 3.1 13.7 + - - +
363A GLN 3.5 8.3 - - - +
364A ASP 3.2 0.4 - - - -
365A LEU* 1.3 75.7 - - - +
367A GLN* 1.3 59.1 + - - +
369A LEU* 3.0 3.0 + - - -
370A GLU* 3.0 26.9 + - - +
393A CYS* 4.7 3.1 - - - -
406A MET* 4.2 21.1 - - + -
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Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLN 3.4 8.2 + - - +
364A ASP* 3.1 12.3 + - - +
366A VAL* 1.3 80.8 - - + +
368A ARG* 1.3 66.0 + - - +
370A GLU* 3.7 12.2 + - - +
371A PRO* 3.9 7.1 - - - +
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Residues in contact with ARG 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS 3.9 3.6 + - - -
319A ALA* 2.8 59.6 + - + +
321A ASN* 2.7 35.5 + - - +
322A GLU 3.2 10.5 + - - -
324A ASP* 5.1 0.4 - - - +
360A GLU* 2.7 42.6 + - - +
364A ASP* 3.0 15.8 + - + +
365A LEU* 3.3 25.1 - - - +
367A GLN* 1.3 77.7 - - - +
369A LEU* 1.3 62.5 + - - +
370A GLU 3.3 0.2 - - - -
371A PRO* 3.3 13.5 - - - +
372A VAL* 4.6 0.2 - - - +
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Residues in contact with LEU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TRP* 3.9 11.2 - - + -
319A ALA 3.3 26.2 - - - +
320A LEU* 3.8 25.4 - - + -
365A LEU* 2.7 33.6 + - + +
366A VAL 3.0 3.8 + - - +
368A ARG* 1.3 78.1 - - + +
370A GLU* 1.3 67.0 + - - +
371A PRO 3.2 1.3 - - - -
372A VAL* 2.7 22.2 + - + +
373A ILE* 3.0 11.6 + - - +
390A VAL* 4.0 23.6 - - + +
393A CYS* 3.6 29.4 - - + -
394A LEU* 4.3 13.0 - - + -
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Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 2.6 36.6 + - - -
60A TRP* 3.8 22.9 - - + -
61A ILE* 4.2 5.7 - - + +
233A ARG* 3.3 18.5 + - - +
236A TYR* 4.9 5.4 - - - -
366A VAL* 3.0 10.9 + - + +
367A GLN* 4.2 7.4 - - - +
368A ARG 3.3 0.2 - - - -
369A LEU* 1.3 77.7 - - - +
371A PRO* 1.4 80.5 - - + +
373A ILE* 3.2 2.5 + - - +
374A MET* 2.9 36.0 + - - +
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Residues in contact with PRO 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A TRP* 4.2 11.3 - - + -
319A ALA* 5.9 1.8 - - + -
367A GLN 3.9 3.8 - - - +
368A ARG* 3.3 20.4 - - - +
370A GLU* 1.4 104.3 - - + +
372A VAL* 1.3 60.9 - - + +
374A MET* 3.8 5.3 - - + +
375A GLU* 3.0 23.7 + - - +
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TRP* 3.8 18.5 - - + -
317A TRP* 3.5 31.4 - - + -
319A ALA* 3.8 22.4 - - + -
320A LEU* 3.8 25.1 - - + -
368A ARG 4.6 0.2 - - - +
369A LEU* 2.7 27.0 + - + +
371A PRO* 1.3 72.3 - - + +
373A ILE* 1.3 50.9 + - - +
375A GLU* 3.2 4.2 + - - +
376A LEU* 2.8 44.7 + - + +
384A VAL* 5.5 0.4 - - + -
394A LEU* 4.3 8.3 - - + -
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 4.6 12.1 - - + -
60A TRP* 3.4 31.2 - - + -
237A TYR* 5.3 0.2 - - + -
369A LEU 3.0 7.4 + - - +
370A GLU* 3.5 9.4 - - - +
372A VAL* 1.3 73.4 - - - +
374A MET* 1.3 66.8 + - - +
376A LEU* 3.1 7.6 + - + +
377A GLU* 2.9 25.1 + - + +
394A LEU* 3.4 28.3 - - + -
397A TYR* 3.5 57.8 - - + +
398A PHE* 4.1 11.7 - - + -
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Residues in contact with MET 374 (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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57A TYR* 3.6 28.7 - - + +
233A ARG* 5.0 2.2 - - - +
236A TYR* 3.4 48.0 - - + +
237A TYR* 3.7 39.9 - - + +
240A ASN* 4.3 15.4 - - - +
370A GLU* 2.9 27.4 + - - +
371A PRO* 3.8 7.0 - - + +
372A VAL 3.3 0.2 - - - -
373A ILE* 1.3 80.8 - - + +
375A GLU* 1.3 59.3 + - - +
377A GLU* 3.5 13.0 + - - +
378A ARG* 3.6 16.3 + - - +
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TRP* 3.4 28.3 - - + -
317A TRP* 3.8 15.9 - - + -
371A PRO 3.0 18.1 + - - +
372A VAL 3.7 1.1 - - - +
374A MET* 1.3 73.0 - - - +
376A LEU* 1.3 67.1 + - - +
377A GLU 3.1 1.6 - - - -
378A ARG* 3.0 32.7 + - - +
379A GLN* 3.1 40.9 + - - +
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Residues in contact with LEU 376 (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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246A ARG* 3.0 27.2 + - - -
248A ILE* 4.5 13.5 - - + -
250A LEU* 5.1 0.7 - - + -
296A TRP* 3.5 21.1 - - + -
372A VAL* 2.8 30.7 + - + +
373A ILE* 3.1 15.7 + - + +
375A GLU* 1.3 75.0 - - - +
377A GLU* 1.3 63.4 + - - +
379A GLN* 3.2 6.6 + - - +
382A VAL* 3.9 29.2 - - + -
384A VAL* 4.1 14.6 - - + -
394A LEU* 4.7 6.5 - - + -
398A PHE* 3.9 35.7 - - + -
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Residues in contact with GLU 377 (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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53A LYS* 2.6 37.3 + - - -
56A ARG* 4.7 1.7 + - - -
237A TYR* 4.2 7.9 - - + -
240A ASN* 3.3 11.2 - - + +
241A ILE* 3.6 23.0 - - + +
242A HIS* 3.1 24.4 + - - -
246A ARG* 3.6 11.8 + - - +
373A ILE 2.9 17.2 + - - +
374A MET* 3.6 12.3 - - - +
375A GLU 3.1 0.2 - - - -
376A LEU* 1.3 77.9 - - - +
378A ARG* 1.3 55.9 + - - +
397A TYR* 2.5 39.8 + - - +
398A PHE* 4.3 8.5 - - - -
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Residues in contact with ARG 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MET 3.8 13.5 + - - -
240A ASN* 2.8 55.4 + - + +
242A HIS* 3.8 9.1 + - - -
374A MET* 3.6 14.3 + - + +
375A GLU* 3.0 30.2 + - - +
377A GLU* 1.3 77.4 - - - +
379A GLN* 1.3 65.7 + - - +
380A GLU* 5.1 2.6 - - - +
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Residues in contact with GLN 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A HIS* 2.7 26.7 - - - -
246A ARG* 2.9 10.0 + - - -
294A ARG* 3.1 53.3 + - - +
296A TRP* 3.9 21.5 - - + -
375A GLU* 3.1 36.5 + - - +
376A LEU 3.2 5.8 + - - +
378A ARG* 1.3 81.4 - - - +
380A GLU* 1.3 63.6 + - - +
381A ASN 5.0 0.4 + - - -
382A VAL* 3.5 16.9 - - + +
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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