Contacts of the helix formed by residues 490 - 507 (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 ASP 490 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B ARG* 4.4 9.2 - - - +
434B CYS* 4.2 8.7 - - - -
488B HIS 4.4 6.2 - - - +
489B TRP* 1.3 76.5 - - - +
491B ASP* 1.3 65.2 + - - +
492B GLU* 3.1 42.9 + - - +
493B ASP* 2.9 23.8 + - - +
494B ILE* 3.1 13.7 + - - +
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Residues in contact with ASP 491 (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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228B ARG* 5.8 1.2 + - - -
433B ARG* 4.6 7.8 - - - +
434B CYS* 5.6 0.9 - - - +
437B ARG* 3.7 37.0 + - + +
490B ASP* 1.3 76.9 + - - +
492B GLU* 1.3 62.0 + - + +
494B ILE* 3.4 4.0 + - - +
495B SER* 2.6 39.1 + - - +
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Residues in contact with GLU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B ASP* 3.1 31.3 + - - +
491B ASP* 1.3 83.8 + - + +
493B ASP* 1.3 66.0 + - - +
495B SER* 3.5 7.0 + - - -
496B LEU* 3.0 31.2 + - + +
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Residues in contact with ASP 493 (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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463B ARG* 4.9 6.8 + - - -
488B HIS 4.5 1.0 - - - +
489B TRP* 3.4 53.9 + - + -
490B ASP* 2.9 31.4 + - - +
492B GLU* 1.3 80.3 - - - +
494B ILE* 1.3 60.5 + - - +
496B LEU* 3.6 7.3 + - - +
497B LEU* 3.3 21.0 + - - +
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Residues in contact with ILE 494 (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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430B VAL* 4.8 7.0 - - + -
434B CYS* 3.6 39.7 - - + +
437B ARG* 4.0 9.6 - - + -
438B LEU* 3.6 41.7 - - + +
489B TRP* 4.0 23.3 - - + -
490B ASP 3.1 10.7 + - - +
491B ASP 3.9 6.3 - - - +
493B ASP* 1.3 76.1 - - - +
495B SER* 1.3 59.5 + - - +
497B LEU* 3.4 14.3 + - + +
498B LEU* 3.0 37.0 + - + +
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Residues in contact with SER 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TRP* 6.1 0.3 - - - -
221B SER 5.4 0.2 + - - -
437B ARG* 3.5 26.2 + - - +
491B ASP* 2.6 25.3 + - - +
492B GLU* 3.9 7.6 - - - -
494B ILE* 1.3 72.0 - - - +
496B LEU* 1.3 66.6 + - - +
498B LEU* 3.4 3.9 + - - +
499B ALA* 3.1 24.1 + - - +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B GLU* 3.0 23.4 + - + +
493B ASP* 3.8 7.9 - - - +
495B SER* 1.3 76.6 - - - +
497B LEU* 1.3 62.7 + - - +
499B ALA* 3.2 8.7 + - - +
500B GLU* 3.0 30.5 + - + +
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Residues in contact with LEU 497 (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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426B LEU* 5.1 3.4 - - + -
430B VAL* 5.7 1.3 - - + -
438B LEU* 5.0 4.0 - - + -
456B VAL* 3.9 25.6 - - + +
459B ALA* 3.5 15.6 - - + +
460B PHE* 3.3 54.7 - - + +
463B ARG* 4.9 5.6 - - + -
489B TRP* 4.1 17.5 - - + -
493B ASP 3.3 10.9 + - - +
494B ILE* 3.5 21.3 - - + +
496B LEU* 1.3 78.1 - - - +
498B LEU* 1.3 57.3 + - + +
500B GLU* 3.3 6.9 + - + +
501B ALA* 2.9 29.2 + - - +
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Residues in contact with LEU 498 (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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220B TRP* 4.0 14.4 - - + +
437B ARG* 3.5 23.3 - - - +
438B LEU* 3.6 25.1 - - + -
441B THR* 3.2 32.3 - - - +
442B TYR* 4.6 2.7 - - + -
452B PHE* 3.8 28.2 - - + -
456B VAL* 3.8 9.9 - - + -
494B ILE* 3.0 31.4 + - + +
495B SER* 3.9 4.3 - - - +
496B LEU 3.2 0.2 - - - -
497B LEU* 1.3 76.4 - - - +
499B ALA* 1.3 57.7 + - - +
501B ALA* 3.3 4.8 + - - +
502B TYR* 3.0 29.3 + - - +
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Residues in contact with ALA 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TRP* 4.6 8.3 - - + -
495B SER 3.1 14.1 + - - +
496B LEU* 3.2 11.6 + - - +
498B LEU* 1.3 76.1 - - - +
500B GLU* 1.3 60.7 + - + +
502B TYR* 3.4 7.6 + - - +
503B ARG* 3.2 20.1 + - - +
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Residues in contact with GLU 500 (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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459B ALA* 3.9 13.2 - - + -
496B LEU* 3.0 20.8 + - + +
497B LEU* 3.7 7.0 - - + +
499B ALA* 1.3 72.7 - - + +
501B ALA* 1.3 59.8 + - - +
503B ARG* 3.1 15.6 + - - +
504B LEU* 2.9 36.4 + - + +
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Residues in contact with ALA 501 (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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452B PHE* 3.9 9.4 - - + -
455B TYR* 3.5 43.5 - - + +
456B VAL* 3.6 20.6 - - + +
459B ALA* 3.9 3.1 - - + +
497B LEU 2.9 16.7 + - - +
498B LEU 3.6 4.7 - - - +
500B GLU* 1.3 76.0 - - - +
502B TYR* 1.3 57.4 + - - +
504B LEU* 3.3 2.6 + - - +
505B LYS* 2.9 26.0 + - - +
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Residues in contact with TYR 502 (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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220B TRP* 3.7 29.2 - + + -
445B GLU* 3.6 25.6 - - - -
452B PHE* 3.9 15.0 - + + -
498B LEU 3.0 17.3 + - - +
499B ALA* 3.6 7.0 - - - +
501B ALA* 1.3 74.8 - - - +
503B ARG* 1.3 66.4 + - - +
505B LYS* 3.3 19.3 + - + +
506B PHE* 3.4 48.1 - + - -
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Residues in contact with ARG 503 (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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499B ALA 3.2 12.1 + - - +
500B GLU* 3.1 15.8 + - - +
502B TYR* 1.3 77.8 - - - +
504B LEU* 1.3 87.4 + - - +
506B PHE* 3.1 14.8 + - - +
507B ALA* 3.3 23.0 + - + +
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Residues in contact with LEU 504 (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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395B LEU* 4.9 5.1 - - + +
399B ILE* 3.7 48.3 - - + +
455B TYR* 3.9 24.2 - - + +
458B ALA* 4.1 1.8 - - + -
459B ALA* 3.9 33.9 - - + +
462B VAL* 5.5 4.5 - - + -
500B GLU* 2.9 21.2 + - + +
501B ALA* 3.3 6.3 + - - +
503B ARG* 1.3 103.6 - - - +
505B LYS* 1.3 62.6 - - - +
506B PHE 3.2 0.7 + - - -
507B ALA 3.6 18.4 + - - +
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Residues in contact with LYS 505 (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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445B GLU* 3.1 29.0 + - - +
446B PRO* 5.3 9.1 + - - +
452B PHE* 4.0 16.3 - - + +
455B TYR* 3.7 35.4 + - + +
501B ALA 2.9 13.0 + - - +
502B TYR* 3.3 18.8 - - + +
503B ARG 3.2 0.2 - - - -
504B LEU* 1.3 77.0 - - - +
506B PHE* 1.3 84.4 + - + +
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Residues in contact with PHE 506 (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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502B TYR* 3.4 53.2 - + - +
503B ARG* 3.1 8.6 + - - +
505B LYS* 1.3 102.4 - - - +
507B ALA* 1.3 61.9 + - + +
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Residues in contact with ALA 507 (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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395B LEU* 6.2 0.3 - - - +
399B ILE* 5.3 11.4 - - - +
503B ARG* 3.3 23.1 + - + +
504B LEU* 3.6 16.0 + - - +
506B PHE* 1.3 80.3 - - + +
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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