Contacts of the helix formed by residues 505 - 518 (chain A) in PDB entry 4F6M
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 CYS 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A TYR* 3.8 8.7 - - - -
503A TYR* 3.6 9.0 - - - +
504A VAL* 1.3 82.4 - - + +
506A LEU* 1.3 66.1 + - - +
507A THR* 3.3 17.5 - - + +
508A SER* 3.4 22.5 + - - -
509A LEU* 3.4 8.5 + - - +
10D G 3.5 37.2 + - - -
11D C 4.8 7.2 - - - -
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Residues in contact with LEU 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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483A HIS* 3.8 34.3 - - + +
485A GLU* 5.6 0.7 - - - +
494A TYR* 3.6 41.5 - - + +
505A CYS* 1.3 69.9 - - - +
507A THR* 1.3 67.0 + - + +
509A LEU* 3.2 18.6 + - + +
510A ARG* 3.0 47.7 + - + +
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Residues in contact with THR 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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505A CYS* 3.9 16.3 - - + +
506A LEU* 1.3 77.3 - - + +
508A SER* 1.3 63.8 + - - +
510A ARG* 3.3 8.0 + - - +
511A ARG* 2.9 29.6 + - - +
11D C 5.0 2.3 + - - -
12D C 4.0 16.9 + - - +
25E T 5.6 7.4 - - + -
26E T 4.0 30.2 - - + +
27E G 4.5 4.5 + - - -
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Residues in contact with SER 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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503A TYR* 3.7 13.8 - - - -
505A CYS* 3.4 13.9 + - - -
506A LEU 3.3 0.6 - - - -
507A THR* 1.3 82.1 + - - +
509A LEU* 1.3 57.8 + - - +
511A ARG* 3.3 16.0 + - - +
512A HIS* 2.9 31.2 + - - +
9D T 3.6 6.7 - - - +
10D G 2.7 48.5 + - - -
11D C 5.0 1.0 + - - -
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Residues in contact with LEU 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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482A ASP 4.4 15.3 - - - +
483A HIS* 3.8 23.3 - - + +
494A TYR* 3.7 17.5 - - + +
495A ILE 3.7 6.7 - - - -
496A CYS* 3.5 36.8 - - + +
503A TYR* 3.7 21.5 - - + -
505A CYS 3.4 8.2 + - - +
506A LEU* 3.2 24.0 + - + +
508A SER* 1.3 78.6 - - - +
510A ARG* 1.3 63.3 + - - +
512A HIS* 3.2 5.0 + - + +
513A PHE* 2.8 32.7 + - + +
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Residues in contact with ARG 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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482A ASP* 3.6 28.0 + - - +
483A HIS* 3.7 23.6 + - - -
506A LEU* 3.0 40.9 + - + +
507A THR* 3.6 7.6 - - - +
509A LEU* 1.3 77.8 - - - +
511A ARG* 1.3 65.8 + - - +
513A PHE* 3.1 17.8 + - - +
514A ASN* 3.5 9.4 + - - +
26E T 6.1 1.3 - - - +
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Residues in contact with ARG 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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507A THR 2.9 17.5 + - - +
508A SER* 3.5 19.2 + - - +
510A ARG* 1.3 76.6 - - - +
512A HIS* 1.3 63.5 + - - +
514A ASN* 3.6 12.2 + - - +
532A PRO 4.8 0.3 - - - +
533A LEU* 3.8 39.6 - - + +
535A GLU* 4.2 6.8 + - - -
9D T 3.3 26.5 - - - +
10D G 3.0 36.7 + - - -
11D C 3.7 5.2 - - - +
27E G 4.3 22.2 + - + +
28E G 2.8 29.7 + - - -
29E C 4.1 4.9 - - - +
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Residues in contact with HIS 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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496A CYS* 3.6 8.7 - - + +
499A CYS* 3.5 9.2 - - - -
501A ARG* 4.1 9.6 - - - -
503A TYR* 3.0 40.6 + + + +
508A SER 2.9 17.4 + - - +
509A LEU* 3.5 4.9 - - - +
511A ARG* 1.3 77.9 - - - +
513A PHE* 1.3 69.6 + + + +
515A ILE* 3.1 40.4 + - + +
516A HIS* 3.4 8.6 + + - -
533A LEU* 5.0 2.2 - - - -
701A ZN 2.1 36.3 - - - -
9D T 4.3 6.4 + - - +
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Residues in contact with PHE 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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482A ASP* 3.7 40.6 - - + +
496A CYS* 4.0 23.3 - - + -
497A ILE* 4.1 20.6 - - + -
498A VAL* 4.2 10.3 - - + -
509A LEU* 2.8 24.7 + - + +
510A ARG* 3.1 11.3 + - - +
512A HIS* 1.3 77.4 - + - +
514A ASN* 1.3 58.5 + - - +
515A ILE 3.0 0.2 - - - -
516A HIS* 2.8 33.9 + + + -
517A SER* 3.1 30.8 + - - -
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Residues in contact with ASN 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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510A ARG 3.5 6.7 + - - +
511A ARG* 3.8 9.9 - - - +
512A HIS 3.2 1.0 - - - -
513A PHE* 1.3 78.5 - - - +
515A ILE* 1.3 55.8 + - - +
517A SER* 3.7 8.6 + - - -
518A TRP* 2.9 29.5 + - - -
519A GLU* 3.3 15.7 + - - +
520A LYS* 2.9 62.7 - - - +
522A TYR* 3.9 3.7 - - + -
532A PRO* 3.1 27.7 - - - +
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Residues in contact with ILE 515 (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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512A HIS* 3.1 34.7 + - + +
513A PHE 3.0 1.2 - - - -
514A ASN* 1.3 78.9 - - - +
516A HIS* 1.3 69.6 + - + +
518A TRP* 3.7 17.7 + - + +
532A PRO* 3.8 28.5 - - + -
533A LEU* 3.9 15.7 - - + -
536A TYR* 5.0 0.4 - - - +
8D C 3.7 27.4 - - - +
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Residues in contact with HIS 516 (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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496A CYS* 3.6 6.7 - - - -
498A VAL* 3.7 43.0 - - + +
499A CYS* 3.6 9.8 - - + -
501A ARG* 6.0 0.2 - - - -
512A HIS* 3.4 11.4 + + - -
513A PHE* 2.8 24.3 + + + +
515A ILE* 1.3 91.0 + - + +
517A SER* 1.3 60.1 + - - +
518A TRP* 3.6 7.0 + - - -
701A ZN 2.1 36.7 - - - -
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Residues in contact with SER 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A PHE* 3.1 32.3 + - - -
514A ASN* 3.7 8.0 + - - -
516A HIS* 1.3 76.3 - - - +
518A TRP* 1.3 72.7 + - - +
519A GLU* 2.9 21.3 + - - +
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Residues in contact with TRP 518 (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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514A ASN* 2.9 17.7 + - - +
515A ILE* 3.7 21.3 + - + +
516A HIS 4.4 7.0 - - - -
517A SER* 1.3 77.8 + - - +
519A GLU* 1.3 63.6 - - - +
520A LYS 3.3 16.4 - - - -
521A LYS* 3.6 39.9 + - + +
530A VAL* 3.9 27.6 - - + -
531A PHE 3.7 20.9 - - - -
532A PRO* 3.6 35.7 - - + -
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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