Contacts of the helix formed by residues 489 - 506 (chain B) in PDB entry 4U7D
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 ILE 489 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487B LYS* 4.1 26.2 - - + +
488B ASN* 1.3 75.5 - - - +
490B THR* 1.3 63.6 + - - +
491B GLU* 3.4 2.5 - - - -
492B TYR* 3.2 41.9 + - + +
493B CYS 3.5 5.7 + - - -
545B ILE* 4.6 14.6 - - + -
548B HIS* 3.8 15.9 - - + -
549B PHE* 3.5 31.0 - - + -
586B ILE* 2.6 27.4 + - + +
588B MET* 3.8 31.0 - - + +
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Residues in contact with THR 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ASN* 2.6 25.6 + - - -
489B ILE* 1.3 76.2 - - - +
491B GLU* 1.3 62.1 + - - +
493B CYS* 2.8 22.7 + - - +
494B ARG* 3.0 24.9 + - - +
579B LEU* 3.7 26.7 - - + -
584B HIS 3.6 18.2 - - - +
585B ALA* 3.4 3.5 - - - -
586B ILE* 2.6 34.2 + - + +
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Residues in contact with GLU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ASN* 4.7 1.7 + - - +
489B ILE 3.4 0.6 - - - -
490B THR* 1.3 80.5 - - - +
492B TYR* 1.3 62.2 + - + +
494B ARG* 3.1 40.5 + - - +
495B ASP* 2.7 44.7 + - - +
498B LYS* 4.9 5.0 + - - -
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Residues in contact with TYR 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B LYS* 4.6 17.4 + - - -
488B ASN 5.2 2.0 - - - -
489B ILE* 3.2 39.3 + - + +
491B GLU* 1.3 81.8 - - + +
493B CYS* 1.3 57.1 + - - +
495B ASP* 3.4 12.0 + - - +
496B LEU* 2.9 35.3 + - - +
519B TRP* 3.6 31.3 - + + -
533B VAL 5.1 4.7 - - - -
535B PRO* 3.5 37.1 - - + +
537B LEU* 4.7 0.7 - - + +
545B ILE* 4.3 17.3 - - + -
549B PHE* 4.2 7.9 - - + -
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Residues in contact with CYS 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ILE 3.5 1.2 + - - -
490B THR 2.8 10.5 + - - +
492B TYR* 1.3 77.4 - - - +
494B ARG* 1.3 65.7 + - - +
496B LEU* 3.0 3.9 + - - +
497B ILE* 2.8 47.1 + - - +
549B PHE* 3.6 46.3 - - + -
554B TYR* 4.0 17.0 - - - -
555B LEU* 5.0 3.6 - - - -
579B LEU* 4.1 5.4 - - + -
586B ILE* 3.9 12.8 - - + -
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Residues in contact with ARG 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B THR* 3.0 27.0 + - + +
491B GLU* 3.1 38.7 + - - +
493B CYS* 1.3 76.0 - - - +
495B ASP* 1.3 64.3 + - - +
497B ILE* 3.3 9.8 + - - +
498B LYS* 3.0 38.4 + - - +
579B LEU* 2.7 46.2 + - + +
581B ASN 3.6 9.3 + - - -
582B GLU* 3.3 30.6 + - - +
584B HIS* 3.7 15.8 + - - +
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Residues in contact with ASP 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B GLU* 2.7 35.3 + - - +
492B TYR* 3.5 16.1 - - - +
493B CYS 3.1 0.2 - - - -
494B ARG* 1.3 74.7 - - - +
496B LEU* 1.3 60.8 + - - +
498B LYS* 3.3 27.0 + - - +
499B ILE* 3.3 25.6 + - - +
519B TRP* 4.6 6.3 + - - +
531B GLY 5.5 1.1 - - - +
532B VAL* 4.0 34.6 - - + +
533B VAL 4.7 7.4 + - - +
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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 TYR 2.9 22.3 + - - +
493B CYS* 3.0 4.0 + - - +
495B ASP* 1.3 77.0 - - - +
497B ILE* 1.3 57.9 + - - +
499B ILE* 3.3 8.8 + - + +
500B LEU* 3.1 31.7 + - - +
515B LEU* 3.8 35.5 - - + +
519B TRP* 3.9 39.7 - - + -
546B ILE* 4.2 15.9 - - + -
549B PHE* 3.4 33.7 - - + -
555B LEU* 4.8 12.3 - - + -
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Residues in contact with ILE 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B CYS* 2.8 25.6 + - - +
494B ARG* 3.7 5.6 - - - +
496B LEU* 1.3 74.1 - - - +
498B LYS* 1.3 61.7 + - + +
500B LEU* 4.0 5.3 - - - +
501B LYS* 2.9 30.7 + - + +
554B TYR 4.6 3.1 - - - +
555B LEU* 4.4 13.2 - - + -
572B ILE* 4.0 27.4 - - + -
576B ALA* 3.9 20.0 - - + +
579B LEU* 3.5 32.5 - - + -
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Residues in contact with LYS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B GLU* 4.9 5.3 + - - -
494B ARG* 3.0 31.3 + - - +
495B ASP* 3.4 29.2 + - - +
496B LEU 3.3 0.2 - - - -
497B ILE* 1.3 77.2 - - - +
499B ILE* 1.3 60.5 + - - +
501B LYS* 3.8 5.7 - - - +
502B GLN* 3.2 23.2 + - - +
529B VAL* 3.9 21.3 - - + +
532B VAL* 4.6 8.7 - - + -
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Residues in contact with ILE 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ASP 3.3 17.4 + - - +
496B LEU* 3.4 19.3 - - + +
497B ILE 3.2 0.2 - - - -
498B LYS* 1.3 75.4 - - - +
500B LEU* 1.3 60.8 + - - +
502B GLN* 3.4 4.5 + - - +
503B ALA* 3.1 24.9 + - - +
510B LEU* 3.9 11.0 - - + -
515B LEU* 3.7 23.1 - - + -
518B SER* 3.6 20.9 - - - +
519B TRP* 4.0 33.4 - - + +
527B LEU 3.7 9.8 - - - +
529B VAL* 3.7 21.8 - - + +
532B VAL* 4.6 6.5 - - + -
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Residues in contact with LEU 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LEU 3.1 18.5 + - - +
497B ILE* 4.0 3.6 - - - +
499B ILE* 1.3 76.5 - - - +
501B LYS* 1.3 66.8 + - - +
503B ALA* 3.0 16.2 + - + +
504B GLU* 3.2 14.8 + - - +
510B LEU* 3.9 23.6 - - + -
515B LEU* 4.3 16.4 - - + -
555B LEU* 3.8 28.9 - - + -
570B LEU* 3.5 28.7 - - + +
571B LYS* 4.0 17.9 - - - +
572B ILE* 4.1 16.6 - - + +
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Residues in contact with LYS 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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497B ILE* 2.9 21.1 + - + +
498B LYS* 3.8 7.0 - - - +
500B LEU* 1.3 75.8 - - - +
502B GLN* 1.3 63.5 + - - +
504B GLU* 3.3 20.0 - - - +
505B GLU* 3.1 40.9 + - + +
572B ILE* 4.2 11.2 - - + +
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Residues in contact with GLN 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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498B LYS 3.2 15.5 + - - +
499B ILE 3.5 5.6 - - - +
500B LEU 3.2 0.2 - - - -
501B LYS* 1.3 78.5 - - - +
503B ALA* 1.3 58.6 + - - +
505B GLU* 3.2 12.2 + - + +
506B LEU* 2.9 39.9 + - + +
526B LYS 2.7 29.3 + - - -
527B LEU* 3.8 6.8 - - - +
528B ARG 3.0 22.5 + - - +
529B VAL* 3.5 20.8 - - + +
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Residues in contact with ALA 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 ILE 3.1 13.1 + - - +
500B LEU* 3.0 13.1 + - + +
502B GLN* 1.3 77.9 - - - +
504B GLU* 1.3 53.7 + - - +
506B LEU* 3.1 9.1 + - - -
507B ASN 2.9 6.6 + - - -
508B GLU* 2.5 52.5 + - + +
510B LEU* 4.1 23.6 - - + -
527B LEU* 5.3 4.5 - - + +
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Residues in contact with GLU 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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500B LEU 3.2 10.2 + - - +
501B LYS* 3.3 27.9 - - - +
503B ALA* 1.3 71.7 - - - +
505B GLU* 1.3 65.0 + - + +
506B LEU 2.8 4.9 - - - -
507B ASN* 2.6 35.2 + - - +
508B GLU 4.3 4.0 + - - +
571B LYS* 5.1 12.3 - - - -
572B ILE* 4.9 10.9 - - - +
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Residues in contact with GLU 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LYS* 3.1 30.5 - - + +
502B GLN* 3.4 12.0 - - - +
504B GLU* 1.3 86.1 - - + +
506B LEU* 1.3 64.8 + - + +
507B ASN* 4.8 4.0 - - - +
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Residues in contact with LEU 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 GLN* 2.9 29.4 + - + +
503B ALA* 3.4 10.5 - - - +
504B GLU 2.8 1.0 - - - -
505B GLU* 1.3 84.3 - - + +
507B ASN* 1.3 70.2 + - - +
508B GLU* 3.2 21.3 + - + +
526B LYS* 3.8 34.8 - - + +
527B LEU* 5.0 3.8 - - + -
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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