Contacts of the helix formed by residues 494 - 511 (chain A) in PDB entry 2Q0N
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 494 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A HIS* 3.3 61.2 - - + +
435A GLY* 5.2 0.9 - - - +
436A VAL 4.9 0.9 - - - +
437A ILE* 3.8 24.7 - - + -
465A VAL* 4.6 15.0 - - + -
470A PRO 5.5 0.4 - - - +
471A ARG* 4.4 4.3 - - - +
493A GLY* 1.4 83.1 - - - +
495A GLU* 1.3 69.0 + - - +
496A VAL 3.1 0.4 - - - -
497A ASP* 3.0 14.1 + - - +
498A ILE 3.9 0.7 + - - -
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Residues in contact with GLU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ARG* 2.9 42.3 + - - -
485A GLU* 4.0 1.6 - - - +
493A GLY 3.2 10.6 - - - -
494A PRO* 1.3 82.6 - - - +
496A VAL* 1.3 62.2 + - - +
498A ILE* 3.1 21.6 + - - +
499A TRP 3.4 3.5 + - - -
557A PRO* 3.6 36.8 - - + +
558A ALA* 4.9 1.2 + - - -
560A ARG* 2.9 32.2 + - + +
561A ALA 5.8 1.8 - - - +
562A THR* 6.3 3.8 - - + -
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Residues in contact with VAL 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A ILE* 3.6 20.6 - - + -
439A ARG* 4.5 7.4 - - + -
483A ALA* 3.8 22.8 - - + +
485A GLU* 3.4 18.4 - - + +
486A LEU* 4.1 18.2 - - + -
492A TYR* 3.5 31.0 - - + -
493A GLY 3.4 17.5 - - - +
494A PRO 3.0 1.2 + - - -
495A GLU* 1.3 77.3 - - - +
497A ASP* 1.3 68.2 + - - +
499A TRP* 3.4 4.7 + - - +
500A SER* 3.1 26.3 + - - +
560A ARG* 4.0 0.7 - - - +
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Residues in contact with ASP 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LEU* 3.9 8.7 - - + +
432A HIS* 2.8 30.2 + - + +
437A ILE* 3.7 9.0 - - - +
438A HIS* 2.9 30.3 + - - +
439A ARG* 2.9 29.3 + - - -
441A ILE* 4.0 15.5 + - + +
494A PRO 3.0 9.4 + - - +
496A VAL* 1.3 80.8 - - - +
498A ILE* 1.3 57.5 + - - +
500A SER* 3.4 6.2 + - - -
501A LEU* 2.9 29.1 + - - +
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Residues in contact with ILE 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 4.2 14.4 - - + -
428A LEU* 4.4 5.2 - - + -
432A HIS* 4.2 11.7 - - + +
494A PRO 4.4 7.0 - - - +
495A GLU* 3.1 15.1 + - - +
497A ASP* 1.3 74.8 - - - +
499A TRP* 1.3 65.0 + - - +
501A LEU* 3.3 6.6 + - + +
502A GLY 3.0 17.2 + - - -
552A LEU* 3.5 17.1 - - + +
560A ARG* 3.9 14.4 - - + -
561A ALA 3.3 25.6 - - - +
562A THR* 4.6 1.8 - - - -
563A ALA* 3.8 33.9 - - + +
566A LEU* 3.7 16.4 - - + -
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Residues in contact with TRP 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A TRP 3.7 7.6 - - - -
482A MET 3.4 23.6 + - - -
483A ALA* 3.6 16.2 - - + -
484A PRO* 3.5 22.4 - - + -
495A GLU 3.4 2.6 + - - -
496A VAL 3.4 8.8 + - - +
497A ASP 3.4 0.2 - - - -
498A ILE* 1.3 78.1 - - - +
500A SER* 1.3 64.3 + - - +
502A GLY* 2.9 12.8 + - - -
503A ILE* 3.1 25.0 + - + +
527A ILE* 3.9 23.9 - - + +
532A PRO* 4.2 10.1 - - + -
533A PRO* 3.9 25.4 - - + -
552A LEU 3.8 8.5 - - - -
553A LEU* 3.5 39.0 - - + +
554A VAL 3.5 30.5 - - - -
555A ARG* 3.9 9.0 - - + -
560A ARG* 3.8 11.0 - - - +
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Residues in contact with SER 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ARG* 5.5 4.2 + - - -
441A ILE* 3.5 32.0 + - - +
481A TRP* 2.8 32.3 + - - +
482A MET* 4.6 3.3 - - - -
483A ALA 4.6 0.9 + - - -
496A VAL* 3.1 16.9 + - - +
497A ASP* 3.7 7.4 + - - -
498A ILE 3.3 0.2 - - - -
499A TRP* 1.3 76.7 - - - +
501A LEU* 1.3 58.3 + - - +
503A ILE* 3.1 7.4 + - - +
504A MET* 2.9 25.6 + - - +
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Residues in contact with LEU 501 (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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421A CYS* 4.7 15.9 - - - +
424A VAL* 4.2 22.4 - - + -
425A LEU* 3.5 39.9 - - + -
428A LEU* 4.6 5.8 - - + -
441A ILE* 3.8 11.3 - - + +
497A ASP 2.9 18.0 + - - +
498A ILE* 3.5 7.6 - - + +
499A TRP 3.2 0.2 - - - -
500A SER* 1.3 75.6 - - - +
502A GLY* 1.3 56.7 + - - +
504A MET* 3.0 28.3 + - + -
505A VAL* 2.9 28.7 + - + +
548A PHE* 5.4 1.6 - - + -
552A LEU* 3.6 17.9 - - + -
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Residues in contact with GLY 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ILE 3.0 7.9 + - - -
499A TRP 2.9 9.4 + - - -
501A LEU* 1.3 75.2 - - - +
503A ILE* 1.3 61.9 + - - +
505A VAL* 3.1 5.5 + - - +
506A ILE* 3.1 21.1 + - - +
549A LEU* 3.4 25.1 - - - +
552A LEU* 3.7 16.9 - - - +
553A LEU* 4.0 7.9 - - - -
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Residues in contact with ILE 503 (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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480A TYR 3.7 17.0 - - - +
481A TRP* 3.4 24.2 - - + -
499A TRP* 3.1 37.7 + - + +
500A SER 3.1 7.1 + - - +
502A GLY* 1.3 76.4 - - - +
504A MET* 1.3 58.0 + - - +
506A ILE* 3.1 8.4 + - + +
507A GLU* 2.9 24.9 + - - +
513A PRO* 3.6 26.4 - - + +
514A PRO* 3.8 13.2 - - + -
527A ILE* 4.2 3.1 - - + -
533A PRO* 4.0 20.6 - - + -
553A LEU* 3.9 11.7 - - + -
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Residues in contact with MET 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 3.8 6.7 - - + -
420A VAL* 3.8 28.9 - - + -
424A VAL* 4.3 4.9 - - + -
441A ILE* 4.5 4.0 - - + -
442A LYS* 3.5 29.8 - - - +
443A SER* 3.5 9.2 - - - +
446A ILE* 3.6 24.0 - - + -
481A TRP* 4.2 0.4 - - - -
500A SER 2.9 12.8 + - - +
501A LEU* 3.0 27.6 + - + +
503A ILE* 1.3 75.6 - - - +
505A VAL* 1.3 59.5 + - - +
507A GLU* 3.1 28.0 + - + +
508A MET* 2.9 39.7 + - + +
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Residues in contact with VAL 505 (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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417A ILE* 4.7 9.4 - - + -
421A CYS* 3.8 28.7 - - - -
501A LEU* 2.9 21.1 + - + +
502A GLY* 3.1 12.3 + - - +
504A MET* 1.3 75.9 - - - +
506A ILE* 1.3 61.2 + - - +
508A MET* 3.0 10.9 + - + +
509A VAL* 3.0 34.4 + - + +
545A LEU* 4.5 12.1 - - + -
548A PHE* 4.4 14.6 - - + -
549A LEU* 3.8 24.9 - - + -
552A LEU* 5.1 1.1 - - + -
571A PHE* 6.2 0.2 - - + -
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Residues in contact with ILE 506 (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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502A GLY 3.1 11.4 + - - +
503A ILE* 3.1 10.5 + - + +
505A VAL* 1.3 70.6 - - - +
507A GLU* 1.3 57.8 + - - +
509A VAL 3.2 0.5 + - - -
510A ASP* 2.7 52.3 + - - +
512A GLU 3.6 16.2 - - - +
514A PRO* 3.8 34.3 - - + -
533A PRO* 4.1 15.3 - - + +
534A ARG 4.5 7.9 - - - +
535A LEU* 3.8 20.4 - - + -
549A LEU* 4.3 5.4 - - + -
553A LEU* 3.6 27.1 - - + -
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Residues in contact with GLU 507 (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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407A VAL* 3.7 22.0 - - + +
443A SER* 2.6 47.0 + - - -
481A TRP* 2.9 28.2 + - - +
503A ILE 2.9 16.9 + - - +
504A MET* 3.1 14.6 + - + +
506A ILE* 1.3 79.1 - - - +
508A MET* 1.3 57.4 + - - +
511A GLY* 2.7 29.3 + - - +
512A GLU* 4.0 12.3 - - - +
513A PRO* 4.0 17.2 - - + +
-2B ARG* 2.9 15.8 + - - -
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Residues in contact with MET 508 (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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403A LEU* 4.1 8.3 - - + -
407A VAL* 3.9 17.6 - - + +
411A ARG* 5.5 1.6 - - - -
412A MET* 3.8 48.8 + - - +
417A ILE* 3.9 29.6 - - + +
420A VAL* 4.0 17.5 - - + -
421A CYS* 3.9 23.8 - - - -
501A LEU* 5.3 0.2 - - + -
504A MET* 2.9 43.1 + - + +
505A VAL* 3.0 18.1 + - + +
507A GLU* 1.3 73.6 - - + +
509A VAL* 1.3 61.1 + - - +
511A GLY 4.8 0.4 + - - -
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Residues in contact with VAL 509 (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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411A ARG* 5.6 5.7 - - - +
412A MET 6.1 0.2 - - - -
417A ILE* 4.0 17.5 - - + -
505A VAL* 3.0 18.7 + - + +
508A MET* 1.3 81.1 - - - +
510A ASP* 1.3 72.8 + - - +
511A GLY 3.7 0.2 - - - -
535A LEU* 3.7 26.5 - - + -
537A ASN* 3.7 23.2 + - + +
540A LYS* 5.6 1.3 - - + -
541A VAL* 3.7 21.5 - - + -
545A LEU* 4.2 17.7 - - + -
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Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ILE* 2.7 30.7 + - - +
509A VAL* 1.3 79.3 - - - +
511A GLY* 1.3 55.4 + - - +
512A GLU* 3.3 21.2 + - + +
534A ARG 4.4 0.9 - - - +
535A LEU* 3.6 7.6 - - - -
536A LYS* 2.9 33.1 + - + +
537A ASN* 2.9 40.9 + - - +
599A EDO 5.0 4.0 + - - -
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Residues in contact with GLY 511 (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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407A VAL* 3.5 23.2 - - - +
408A THR* 4.0 22.3 - - - +
507A GLU* 2.7 28.7 + - - +
508A MET 4.8 0.2 - - - -
509A VAL 3.7 1.0 - - - -
510A ASP* 1.3 71.4 - - - +
512A GLU* 1.3 60.8 + - - +
599A EDO 4.5 9.2 - - - -
-2B ARG* 5.2 2.1 + - - -
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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
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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