Contacts of the helix formed by residues 431 - 445 (chain B) in PDB entry 2QFZ
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 PRO 431 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B VAL* 1.3 92.7 - - + +
432B LEU* 1.3 59.9 + - - +
433B ARG* 3.8 36.6 - - + +
434B CYS* 2.9 33.8 + - - +
435B THR* 3.0 10.7 + - - -
486B THR* 3.5 28.0 - - - +
487B ALA* 4.1 9.4 - - - +
489B TRP* 4.4 0.9 - - + -
1010B UNX 4.0 5.6 - - - -
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Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PRO* 3.9 24.7 - - + -
292B LEU* 5.1 0.2 - - + -
327B THR* 3.8 19.1 - - + -
328B PRO* 4.0 32.3 - - + -
331B VAL* 3.7 32.5 - - + -
427B MET* 4.4 11.9 - - + -
430B VAL 3.7 0.8 + - - -
431B PRO* 1.3 71.5 - - - +
433B ARG* 1.3 65.2 + - - +
435B THR* 3.1 10.1 + - - -
436B ILE* 3.0 29.8 + - + +
1010B UNX 3.8 7.6 - - - -
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Residues in contact with ARG 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PRO* 3.8 14.4 - - + +
432B LEU* 1.3 74.8 - - - +
434B CYS* 1.3 66.3 + - - +
436B ILE* 3.5 11.8 + - - +
437B ARG* 3.3 20.6 + - - +
487B ALA 3.2 25.7 + - - -
488B HIS* 3.7 8.5 + - - +
489B TRP 2.9 28.0 + - - +
490B ASP* 4.4 8.7 - - - +
491B ASP* 4.6 6.5 - - - +
1010B UNX 3.2 27.0 - - - -
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Residues in contact with CYS 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B VAL* 4.1 10.1 - - + -
431B PRO* 2.9 30.4 + - - +
433B ARG* 1.3 78.3 - - - +
435B THR* 1.3 61.5 + - - +
437B ARG* 3.4 4.7 + - - +
438B LEU* 2.8 30.9 + - - +
489B TRP* 3.4 39.3 - - - -
490B ASP* 4.0 6.7 - - - -
491B ASP* 5.6 1.1 - - - -
494B ILE* 3.6 32.5 - - + +
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Residues in contact with THR 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PRO* 3.7 15.7 - - + -
425B LEU 5.3 0.8 + - - +
426B LEU 5.1 0.3 - - - -
427B MET* 3.6 32.6 + - + +
430B VAL* 3.8 15.1 + - - +
431B PRO 3.0 11.1 + - - -
432B LEU* 3.5 15.5 - - - -
434B CYS* 1.3 77.6 - - - +
436B ILE* 1.3 63.2 + - - +
438B LEU* 3.2 7.6 + - + +
439B TRP* 2.9 55.0 + - + +
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Residues in contact with ILE 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 3.4 43.1 - - - +
232B TRP* 3.4 14.4 - - + -
328B PRO* 4.1 14.8 - - + -
331B VAL* 4.2 17.7 - - + -
332B VAL* 3.8 23.8 - - + -
432B LEU* 3.0 30.6 + - + +
433B ARG* 3.7 11.7 - - - +
434B CYS 3.3 0.2 - - - -
435B THR* 1.3 75.2 - - - +
437B ARG* 1.3 61.5 + - - +
439B TRP 3.3 1.6 + - - -
440B ASP* 3.2 18.7 + - - +
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Residues in contact with ARG 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TRP* 3.8 6.7 + - - -
221B SER* 3.5 20.4 + - - +
222B GLY* 3.7 23.7 - - - +
228B ARG* 4.6 5.8 - - - +
433B ARG 3.3 7.5 + - - +
434B CYS* 3.6 9.4 - - - +
435B THR 3.2 0.2 - - - -
436B ILE* 1.3 76.5 - - - +
438B LEU* 1.3 67.7 + - - +
440B ASP* 3.1 26.4 + - - +
441B THR* 3.0 20.4 + - - -
491B ASP* 3.7 33.6 + - - +
494B ILE* 4.0 16.8 - - + -
495B SER* 3.5 27.6 + - - +
498B LEU* 3.5 16.6 - - - +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU 4.6 10.3 - - - +
426B LEU* 4.5 20.2 - - + -
430B VAL* 5.5 5.2 - - + -
434B CYS 2.8 18.7 + - - +
435B THR* 3.4 10.1 - - - +
437B ARG* 1.3 76.1 - - - +
439B TRP* 1.3 61.0 + - + +
441B THR* 3.1 20.3 + - - -
442B TYR* 3.1 41.6 + - + +
456B VAL* 4.2 13.2 - - + -
494B ILE* 3.6 24.2 - - + +
497B LEU* 5.0 3.1 - - + -
498B LEU* 3.6 29.2 - - + -
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Residues in contact with TRP 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TRP* 3.8 21.5 - + + -
325B LEU* 3.9 18.4 - - + -
328B PRO* 3.6 31.6 - - + -
329B PHE* 3.7 16.8 - + - -
370B LEU* 3.6 23.3 - - + -
425B LEU* 4.1 30.4 + - + +
427B MET* 3.9 19.3 - - + -
435B THR* 2.9 34.3 + - + +
436B ILE 3.7 4.5 - - - +
437B ARG 3.2 0.4 - - - -
438B LEU* 1.3 79.9 - - + +
440B ASP* 1.3 65.6 + - - +
441B THR 3.2 0.4 - - - -
442B TYR* 3.8 25.2 - + - +
443B GLN* 3.1 29.0 + - - +
449B PHE* 3.7 20.0 - + + -
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Residues in contact with ASP 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B SER* 3.8 17.3 - - - +
222B GLY* 3.4 4.7 - - - -
223B ILE* 2.8 35.1 + - + +
228B ARG* 2.9 36.5 + - - -
232B TRP* 2.9 18.8 + - - +
235B LEU* 4.7 1.2 - - - +
436B ILE 3.2 12.9 + - - +
437B ARG* 3.1 18.4 + - - +
439B TRP* 1.3 78.3 - - - +
441B THR* 1.3 55.0 + - - +
443B GLN* 3.5 3.7 + - - +
444B SER* 2.7 31.6 + - - -
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Residues in contact with THR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TRP* 2.8 61.0 + - + +
437B ARG* 3.0 15.3 + - - -
438B LEU 3.1 9.6 + - - -
440B ASP* 1.3 75.8 - - - +
442B TYR* 1.3 59.9 + - - +
444B SER* 2.9 5.8 + - - -
445B GLU* 2.8 30.1 + - - +
452B PHE* 4.1 9.2 - - + -
498B LEU* 3.2 23.5 - - + +
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Residues in contact with TYR 442 (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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425B LEU* 5.2 3.1 - - + -
438B LEU* 3.1 40.2 + - + +
439B TRP* 3.8 16.8 - + - -
441B THR* 1.3 77.3 - - - +
443B GLN* 1.3 62.3 + - - +
445B GLU* 3.3 16.9 - - - +
448B GLY* 3.3 24.8 + - - -
449B PHE* 3.6 49.0 - + + -
452B PHE* 4.1 14.8 - + - -
453B HIS* 2.7 44.5 + + + -
456B VAL* 3.5 40.7 - - + +
498B LEU* 4.6 1.1 - - + -
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Residues in contact with GLN 443 (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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216B ARG* 4.8 3.5 + - - +
232B TRP* 3.3 43.3 + - - -
235B LEU* 3.9 37.9 - - + +
236B SER* 4.1 22.4 - - - +
329B PHE* 3.8 31.3 - - - -
366B CYS 5.4 0.2 + - - -
370B LEU* 5.8 0.8 - - - +
439B TRP* 3.1 19.3 + - - +
440B ASP* 3.9 3.1 - - - +
442B TYR* 1.3 78.3 - - - +
444B SER* 1.3 58.3 + - - +
445B GLU 4.5 1.9 - - - +
449B PHE* 4.1 20.6 - - + -
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Residues in contact with SER 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ARG* 3.2 52.5 - - - +
219B SER* 3.1 26.0 - - - -
220B TRP* 3.8 15.4 - - - -
235B LEU* 4.2 1.6 - - - +
440B ASP 2.7 19.3 + - - -
441B THR 2.9 6.6 + - - -
443B GLN* 1.3 75.7 - - - +
445B GLU* 1.3 62.6 + - - +
446B PRO* 3.9 4.2 - - - +
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TRP* 2.9 28.6 + - - +
441B THR 2.8 19.5 + - - +
442B TYR 3.3 7.4 - - - +
443B GLN 4.5 1.7 - - - +
444B SER* 1.3 73.5 - - - +
446B PRO* 1.4 83.7 - - + +
447B ASP 3.4 0.5 + - - -
448B GLY* 3.1 17.7 + - - -
452B PHE* 3.9 31.1 - - + -
502B TYR* 3.6 15.6 - - - -
505B LYS* 3.1 36.5 + - - +
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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
------------------------------------------------------------
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