Contacts of the helix formed by residues 490 - 507 (chain A) in PDB entry 4MXP
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 THR 490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A VAL* 4.8 2.4 - - - +
432A LEU* 4.7 4.7 - - + -
475A ILE* 3.9 27.8 - - + -
479A ALA* 3.9 15.0 - - + -
480A ASP 5.2 0.2 - - - -
483A SER* 2.9 28.4 + - - +
484A LYS 3.2 23.9 + - - -
485A ILE* 3.5 22.8 + - + +
488A HIS 3.3 2.8 + - - -
489A ASN* 1.3 70.3 - - - +
491A LYS* 1.3 59.8 + - - +
493A LEU* 3.3 3.1 + - - +
494A MET* 2.9 30.1 + - + +
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Residues in contact with LYS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LYS* 3.3 52.9 + - + +
479A ALA* 4.3 18.3 + - + +
480A ASP 4.7 3.1 - - - +
481A PRO* 3.8 35.5 - - + +
489A ASN* 3.3 10.4 - - - +
490A THR* 1.3 78.7 - - - +
492A ALA* 1.3 56.1 + - - +
494A MET* 3.4 3.3 + - - +
495A ASN* 3.0 32.1 + - - +
580A ALA* 4.2 15.3 - - + +
581A GLU* 6.1 4.4 - - + +
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Residues in contact with ALA 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A ASN* 3.0 17.4 - - - +
491A LYS* 1.3 72.5 - - - +
493A LEU* 1.3 60.5 + - - +
495A ASN* 3.3 3.0 + - - +
496A HIS* 2.9 27.7 + - - +
529A TYR* 3.8 11.6 + - - +
576A LYS* 4.5 11.4 - - + +
577A ASP* 3.2 30.5 - - - +
580A ALA* 3.6 20.3 - - + +
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLU* 4.5 2.0 - - - +
485A ILE* 3.7 44.0 - - + +
488A HIS* 4.6 4.9 - - + +
489A ASN 2.9 16.4 + - - +
490A THR* 3.8 5.4 - - - +
492A ALA* 1.3 72.5 - - - +
494A MET* 1.3 68.7 + - + +
496A HIS* 3.2 7.8 + - + +
497A LYS* 3.0 51.5 + - + +
521A SER* 4.4 6.1 - - - +
522A LYS* 4.2 22.2 - - - +
523A GLY* 4.2 2.0 - - - +
529A TYR* 3.6 27.8 + - + +
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Residues in contact with MET 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 3.7 6.3 - - - +
429A GLU* 3.5 25.6 - - + +
472A MET* 3.7 39.7 - - + +
475A ILE* 3.7 26.7 - - + -
476A LYS* 3.5 24.5 - - + -
485A ILE* 4.0 22.7 - - + -
490A THR* 2.9 19.1 + - + +
491A LYS 3.6 0.7 - - - +
493A LEU* 1.3 85.5 - - + +
495A ASN* 1.3 58.4 + - - +
497A LYS* 3.2 7.3 + - + +
498A ILE* 2.8 35.1 + - - +
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Residues in contact with ASN 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LYS* 2.7 38.2 + - - +
491A LYS 3.0 13.7 + - - +
492A ALA* 3.3 9.8 + - - +
494A MET* 1.3 75.8 - - - +
496A HIS* 1.3 58.0 + - - +
498A ILE* 3.8 7.8 - - - +
499A ALA* 2.9 33.1 + - - +
579A LEU 4.7 1.4 + - - -
580A ALA* 3.5 28.4 + - + +
582A ALA 5.3 2.2 + - - -
632A THR* 5.0 12.3 + - - +
635A SER* 5.2 3.0 + - - -
639A GLN* 5.5 2.7 - - - +
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Residues in contact with HIS 496 (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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492A ALA 2.9 13.6 + - - +
493A LEU* 3.3 14.8 - - + +
495A ASN* 1.3 77.5 - - - +
497A LYS* 1.3 61.6 + - + +
499A ALA* 3.7 4.8 - - - +
500A ALA* 3.0 33.1 + - + +
521A SER* 5.6 5.8 - - - -
523A GLY* 5.7 0.9 - - - -
528A GLU* 2.9 38.1 + - - -
529A TYR* 3.4 46.6 - + + -
531A SER* 5.8 0.9 - - - -
576A LYS* 3.1 22.0 + - - +
631A GLU* 5.7 5.2 + - - -
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Residues in contact with LYS 497 (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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416A TYR* 4.3 1.6 - - - +
429A GLU* 2.8 31.1 + - - +
472A MET* 3.6 27.6 - - + -
493A LEU* 3.0 37.4 + - + +
494A MET* 3.9 5.2 - - + +
496A HIS* 1.3 76.2 - - + +
498A ILE* 1.3 67.0 + - - +
500A ALA* 3.2 2.9 + - - +
501A ILE* 2.9 28.6 + - - +
518A VAL* 3.2 30.0 + - + +
519A LEU* 3.0 22.0 + - - +
521A SER* 2.7 32.9 + - - -
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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
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469A VAL* 4.0 22.8 - - + +
472A MET* 3.7 31.4 - - + -
473A GLN* 4.2 20.4 - - + -
476A LYS* 4.2 16.6 - - + -
494A MET 2.8 29.5 + - - +
495A ASN* 3.8 9.0 - - - +
497A LYS* 1.3 72.8 - - - +
499A ALA* 1.3 56.8 + - - +
501A ILE* 3.3 3.6 + - - +
502A GLN* 2.9 52.2 + - - +
635A SER* 3.9 9.2 - - - +
639A GLN* 4.0 11.0 - - - +
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Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ASN 2.9 17.7 + - - +
496A HIS* 3.7 5.8 - - - +
498A ILE* 1.3 77.4 - - - +
500A ALA* 1.3 57.4 + - - +
502A GLN* 3.3 12.8 + - - +
503A LYS* 2.9 29.6 + - - +
506A ARG* 4.9 2.4 + - - -
631A GLU* 4.8 23.8 - - + +
635A SER* 4.6 11.2 - - - +
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Residues in contact with ALA 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A HIS* 3.0 23.3 + - + +
497A LYS* 3.2 5.8 + - - +
499A ALA* 1.3 75.4 - - - +
501A ILE* 1.3 62.2 + - - +
503A LYS* 3.4 9.5 + - - +
504A LEU* 3.1 27.2 + - - +
518A VAL* 3.9 23.6 - - + -
528A GLU* 6.1 1.6 - - - +
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Residues in contact with ILE 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A SER* 3.6 29.6 - - - -
468A LEU* 4.0 20.2 - - + -
469A VAL* 3.8 19.1 - - + -
472A MET* 3.7 33.7 - - + -
497A LYS 2.9 15.4 + - - +
498A ILE 3.7 3.4 - - - +
500A ALA* 1.3 76.3 - - - +
502A GLN* 1.3 58.3 + - - +
504A LEU* 3.1 9.4 + - + +
505A GLU* 3.0 30.4 + - - +
510A VAL* 4.7 0.2 - - - +
515A LEU* 4.1 20.4 - - + -
518A VAL* 4.1 14.6 - - + -
519A LEU* 4.6 2.5 - - + -
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Residues in contact with GLN 502 (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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466A LYS* 5.8 4.8 - - - +
469A VAL* 4.9 10.8 - - + +
498A ILE* 2.9 29.0 + - + +
499A ALA* 3.3 8.3 + - - +
501A ILE* 1.3 76.0 - - - +
503A LYS* 1.3 57.1 + - - +
505A GLU* 3.3 19.9 + - - +
506A ARG* 2.9 48.3 + - + +
635A SER* 2.6 29.5 + - - -
638A SER* 3.7 23.5 + - - +
639A GLN* 3.6 28.5 - - - +
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Residues in contact with LYS 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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499A ALA 2.9 14.0 + - - +
500A ALA* 3.5 12.3 - - - +
501A ILE 3.3 0.2 - - - -
502A GLN* 1.3 74.1 - - - +
504A LEU* 1.3 60.8 + - + +
506A ARG* 3.4 26.9 + - + +
507A SER* 3.0 40.8 + - - +
627A LYS* 5.2 8.9 - - - +
631A GLU* 5.1 10.0 + - - +
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Residues in contact with LEU 504 (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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500A ALA 3.1 19.6 + - - +
501A ILE* 3.1 8.5 + - - +
503A LYS* 1.3 76.8 - - + +
505A GLU* 1.3 62.5 + - - +
507A SER* 3.3 4.1 + - - -
508A ASN 3.1 3.5 + - - -
509A ASN* 2.8 56.9 + - + +
510A VAL* 3.6 13.3 - - + +
514A THR* 3.7 42.8 - - + +
515A LEU* 4.3 14.1 - - + -
518A VAL* 4.1 12.8 - - + -
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Residues in contact with GLU 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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465A SER* 2.5 34.8 + - - +
466A LYS* 3.2 33.8 + - - +
469A VAL* 5.3 1.0 - - - +
501A ILE* 3.0 20.3 + - - +
502A GLN* 3.4 22.9 - - - +
504A LEU* 1.3 75.9 - - - +
506A ARG* 1.3 58.4 + - + +
508A ASN* 3.0 21.4 + - - +
510A VAL* 3.5 13.4 - - + +
638A SER* 5.6 0.7 + - - -
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Residues in contact with ARG 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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499A ALA 4.9 1.4 + - - -
502A GLN* 2.9 40.2 + - - +
503A LYS* 3.4 37.0 + - - +
505A GLU* 1.3 77.3 - - + +
507A SER* 1.3 60.0 + - - +
508A ASN* 3.3 5.1 + - - -
634A GLU* 5.5 11.3 - - - +
638A SER* 5.9 3.0 + - - -
641A ARG* 6.3 1.1 - - - +
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Residues in contact with SER 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LYS* 3.0 26.9 + - - +
504A LEU* 3.8 4.7 - - - -
505A GLU 3.1 0.4 - - - -
506A ARG* 1.3 75.7 - - - +
508A ASN* 1.3 78.1 + - - +
509A ASN* 3.1 14.9 + - - +
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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
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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