Contacts of the helix formed by residues 502 - 515 (chain A) in PDB entry 4F1P
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 SER 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500A SER 3.8 0.8 + - - -
501A CYS* 1.3 78.4 - - - +
503A ARG* 1.3 62.4 + - - +
504A GLN* 2.8 33.4 + - - +
505A GLU* 3.4 15.9 + - - +
506A LYS* 3.1 22.3 + - - +
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Residues in contact with ARG 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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442A GLN* 3.5 43.0 + - - +
445A GLY* 4.2 10.5 + - - -
446A ILE* 3.4 36.0 - - + +
449A SER* 4.4 8.5 + - - -
502A SER* 1.3 72.6 + - - +
504A GLN* 1.3 65.9 + - - +
506A LYS* 3.3 4.6 + - - +
507A GLU* 2.7 59.9 + - + +
409B ALA* 4.8 7.1 - - - +
410B GLN* 6.3 0.6 - - - +
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Residues in contact with GLN 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A SER* 2.8 25.9 + - - +
503A ARG* 1.3 92.8 + - - +
505A GLU* 1.3 59.4 + - - +
507A GLU* 3.4 20.3 + - - +
508A ALA* 3.0 29.3 + - - +
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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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495A LYS* 4.7 14.3 - - - +
497A PRO* 4.3 18.7 - - + +
501A CYS* 3.9 25.1 - - + +
502A SER* 3.4 23.1 + - - +
503A ARG 3.3 0.4 - - - -
504A GLN* 1.3 77.6 - - - +
506A LYS* 1.3 63.0 + - - +
508A ALA* 3.4 6.8 + - - +
509A TRP* 3.1 22.6 + - + +
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Residues in contact with LYS 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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423A CYS* 3.5 20.6 - - + -
425A GLU* 4.7 2.2 + - - -
440A CYS* 4.6 2.0 - - - -
442A GLN* 2.6 37.4 + - + +
443A CYS* 3.8 22.4 - - - -
446A ILE* 3.8 13.0 - - + -
497A PRO* 4.2 15.7 - - + -
498A GLY 3.4 21.5 - - - -
499A PRO* 2.9 19.0 + - - +
501A CYS* 3.6 12.1 - - + +
502A SER 3.1 14.0 + - - +
503A ARG 3.7 4.3 - - - +
505A GLU* 1.3 73.8 - - - +
507A GLU* 1.3 59.3 + - - +
509A TRP* 3.2 5.8 + - - +
510A ILE* 2.9 34.8 + - + +
801A ZN 4.5 0.2 - - - -
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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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446A ILE* 3.8 31.7 - - + +
449A SER* 5.6 1.2 + - - +
503A ARG* 2.7 55.0 + - - +
504A GLN* 3.6 24.8 + - - +
505A GLU 3.3 0.2 - - - -
506A LYS* 1.3 72.6 - - - +
508A ALA* 1.3 57.7 + - - +
510A ILE* 3.9 0.7 - - - +
511A HIS* 3.0 33.5 + - - +
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Residues in contact with ALA 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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504A GLN 3.0 17.6 + - - +
505A GLU* 3.8 6.7 - - - +
506A LYS 3.3 0.2 - - - -
507A GLU* 1.3 75.5 - - - +
509A TRP* 1.3 57.9 + - - +
511A HIS* 4.2 4.4 - - - +
512A ALA* 3.2 28.8 + - - +
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Residues in contact with TRP 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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422A ASP* 3.8 23.2 + - + -
486A GLU* 2.9 30.4 + - - -
489A VAL* 3.7 23.1 - - + -
494A VAL* 3.7 31.4 - - + -
495A LYS 3.4 23.1 - - - -
496A LYS* 3.7 20.4 - - + -
497A PRO* 3.4 20.2 - - + -
505A GLU 3.1 16.8 + - - +
506A LYS 3.6 4.0 - - - +
508A ALA* 1.3 75.7 - - - +
510A ILE* 1.3 63.8 + - + +
512A ALA* 3.3 3.7 + - + +
513A LYS* 2.8 44.2 + - + +
519A PHE* 3.6 26.2 - + - -
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Residues in contact with ILE 510 (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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422A ASP* 3.5 30.1 - - + +
443A CYS* 3.8 31.9 - - + +
446A ILE* 3.8 33.0 - - + -
447A HIS* 3.9 6.7 - - + +
450A LEU* 3.9 21.4 - - + +
506A LYS* 2.9 21.5 + - + +
507A GLU 4.0 2.5 - - - +
509A TRP* 1.3 78.9 - - + +
511A HIS* 1.3 57.3 + - - +
513A LYS* 4.3 4.5 - - - -
514A TYR* 3.0 45.3 + - + +
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Residues in contact with HIS 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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450A LEU* 4.8 9.8 - - + +
507A GLU 3.0 19.3 + - - +
508A ALA* 4.2 4.5 - - - +
510A ILE* 1.3 77.5 - - - +
512A ALA* 1.3 60.9 + - - +
515A VAL* 3.1 51.2 + - + +
516A GLU* 2.9 34.6 + - + +
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Residues in contact with ALA 512 (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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508A ALA 3.2 21.5 + - - +
509A TRP* 3.3 5.1 + - - +
511A HIS* 1.3 76.7 + - - +
513A LYS* 1.3 56.6 + - - +
516A GLU* 3.5 22.2 - - - +
517A LYS 3.0 8.7 + - - -
518A LYS* 2.8 39.9 + - + +
519A PHE* 4.1 18.4 - - + -
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Residues in contact with LYS 513 (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* 3.1 9.6 + - - -
422A ASP* 2.8 21.7 + - - +
481A ILE* 5.8 0.2 - - - -
482A ASN* 2.8 27.8 + - - -
485A TYR* 3.4 45.3 - - + +
486A GLU* 2.8 29.8 + - + +
509A TRP* 2.8 25.5 + - + +
510A ILE* 3.6 4.3 - - - +
512A ALA* 1.3 80.1 - - - +
514A TYR* 1.3 89.6 + - + +
517A LYS* 3.5 14.2 - - - -
519A PHE* 3.9 15.0 - - + -
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Residues in contact with TYR 514 (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* 3.6 13.2 - - - +
422A ASP* 2.7 30.9 + - - -
435A LEU* 3.7 31.2 - - + -
437A VAL* 4.4 4.5 - - - +
447A HIS* 3.4 26.1 + + - -
450A LEU* 4.5 13.0 - - + -
454A PHE* 3.7 12.1 - - + +
481A ILE* 4.9 2.9 - - + -
485A TYR* 3.9 29.1 - + + -
510A ILE* 3.0 33.6 + - + +
513A LYS* 1.3 101.6 + - + +
515A VAL* 1.3 59.1 - - + +
517A LYS* 2.5 35.0 + - - -
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Residues in contact with VAL 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LEU* 3.9 23.6 - - + -
454A PHE* 3.9 36.7 - - + -
511A HIS* 3.1 47.2 + - + +
514A TYR* 1.3 79.3 - - - +
516A GLU* 1.3 65.5 + - - +
517A LYS* 3.4 10.6 + - - +
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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