Contacts of the helix formed by residues 504 - 518 (chain B) in PDB entry 3F7F
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 504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493B TRP* 3.7 20.7 + - - +
503B GLY* 1.3 75.9 - - - +
505B GLU* 1.3 66.3 + - - +
506B LEU* 3.8 4.8 + - - +
507B PHE* 3.2 17.1 + - - +
508B LYS* 3.0 23.3 + - - +
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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
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504B SER* 1.3 74.4 - - - +
506B LEU* 1.3 53.8 + - - +
508B LYS* 3.1 24.5 + - - +
509B TYR* 2.7 36.6 + - - +
576B SER 4.0 9.0 - - - +
577B PHE* 3.5 28.3 - - - -
578B ASP 5.5 0.7 + - - -
582B VAL* 4.4 16.8 - - + +
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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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493B TRP* 3.2 37.2 - - + -
504B SER* 3.3 5.3 + - - +
505B GLU* 1.3 75.4 - - - +
507B PHE* 1.3 60.4 + - - +
509B TYR* 3.6 8.1 - - + +
510B LEU* 2.8 39.4 + - + +
582B VAL* 3.3 33.3 - - + +
585B ASP* 3.4 25.4 - - - +
586B LEU* 3.7 41.5 - - + +
590B GLN* 4.4 3.1 - - + +
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Residues in contact with PHE 507 (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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493B TRP* 3.4 57.3 - + + +
496B ASN 3.9 6.3 - - - -
497B MET* 3.8 27.1 - - - -
500B GLU* 3.2 37.7 - - + -
502B ASP 3.6 16.4 - - - -
503B GLY* 3.9 6.7 - - - -
504B SER* 3.2 19.8 + - - +
506B LEU* 1.3 79.5 - - - +
508B LYS* 1.3 62.9 + - + +
510B LEU* 3.2 2.2 + - - +
511B ARG* 2.9 58.5 + - - +
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Residues in contact with LYS 508 (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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501B THR 5.3 2.0 - - - -
502B ASP* 3.9 14.5 - - - +
503B GLY 3.2 23.8 + - - -
504B SER 3.0 9.5 + - - +
505B GLU* 3.5 25.8 + - - +
507B PHE* 1.3 88.5 - - + +
509B TYR* 1.3 62.2 + - - +
511B ARG* 3.5 25.5 + - - +
512B THR* 3.1 32.2 + - + +
577B PHE* 3.6 13.7 - - + -
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Residues in contact with TYR 509 (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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505B GLU 2.7 20.2 + - - +
506B LEU* 3.6 11.4 - - + +
507B PHE 3.2 0.2 - - - -
508B LYS* 1.3 70.9 - - - +
510B LEU* 1.3 72.1 + - + +
512B THR* 3.2 5.0 + - - -
513B LEU* 3.1 59.4 + - + +
574B LEU* 3.9 11.7 - - + -
577B PHE* 3.5 35.6 - + + -
579B ILE* 4.6 17.8 - - + +
582B VAL* 3.5 27.1 - - + -
583B LEU* 3.6 35.9 - - + +
586B LEU* 4.9 0.7 - - + -
633B VAL* 3.9 10.7 - - + +
636B THR* 4.2 7.3 + - - -
637B PHE* 5.4 0.5 - - - -
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Residues in contact with LEU 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B TRP* 3.4 44.2 - - + -
497B MET* 3.7 14.5 - - + +
506B LEU* 2.8 26.3 + - + +
507B PHE* 3.7 3.1 - - - +
509B TYR* 1.3 87.8 - - + +
511B ARG* 1.3 58.3 + - - +
513B LEU* 3.0 8.1 + - + +
514B ASN* 2.8 30.5 + - - +
586B LEU* 4.2 17.5 - - + -
629B ILE* 3.9 44.4 - - + -
632B GLN* 4.1 4.5 + - - +
633B VAL* 4.9 3.6 - - + -
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Residues in contact with ARG 511 (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 MET* 3.3 45.1 + - + +
498B HIS* 6.1 1.8 - - + +
499B SER 5.7 0.4 - - - +
500B GLU 3.4 23.6 + - - -
501B THR 4.7 4.2 + - - -
502B ASP 4.7 1.8 + - - -
507B PHE* 2.9 35.9 + - + +
508B LYS* 3.7 24.6 + - - +
510B LEU* 1.3 77.8 - - - +
512B THR* 1.3 63.9 + - + +
514B ASN* 3.3 3.4 + - + +
515B GLY* 2.8 24.8 + - - -
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Residues in contact with THR 512 (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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508B LYS* 3.1 17.3 + - + +
509B TYR 3.2 11.3 + - - -
511B ARG* 1.3 86.0 - - + +
513B LEU* 1.3 64.2 + - - +
515B GLY* 3.4 3.3 + - - +
516B PHE* 3.4 15.1 + - - +
570B LEU* 3.9 13.3 - - - +
573B GLU* 3.3 47.9 - - + +
574B LEU* 4.3 9.2 - - - +
577B PHE* 3.8 18.6 - - + -
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Residues in contact with LEU 513 (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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509B TYR* 3.1 36.7 + - + +
510B LEU* 3.0 13.6 + - + +
512B THR* 1.3 76.8 + - - +
514B ASN* 1.3 64.1 + - - +
516B PHE* 3.4 4.0 + - - +
517B ALA* 3.1 23.4 + - - +
570B LEU* 4.4 4.9 - - + +
574B LEU* 3.7 26.2 - - + -
632B GLN* 3.9 14.7 - - + +
633B VAL* 3.5 45.8 - - + +
635B LEU* 5.8 0.2 - - - +
636B THR* 3.6 26.0 - - + -
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Residues in contact with ASN 514 (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 MET* 3.4 39.4 - - + +
498B HIS* 4.6 13.0 + - - -
510B LEU 2.8 6.1 + - - +
511B ARG* 3.5 4.7 - - - +
513B LEU* 1.3 76.0 - - - +
515B GLY* 1.3 67.2 + - - +
518B SER* 2.8 42.0 + - - +
628B ARG* 3.4 30.0 + - - +
632B GLN* 2.9 29.5 + - - +
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Residues in contact with GLY 515 (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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511B ARG 2.8 16.5 + - - -
512B THR* 3.4 5.8 + - - -
513B LEU 3.3 0.4 - - - -
514B ASN* 1.3 77.5 + - - +
516B PHE* 1.3 57.2 + - - +
518B SER* 3.0 17.2 + - - -
519B THR* 3.5 12.8 - - - +
573B GLU* 6.0 0.2 - - - -
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Residues in contact with PHE 516 (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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512B THR 3.4 7.1 + - - +
513B LEU 3.4 5.1 + - - +
514B ASN 3.1 0.6 - - - -
515B GLY* 1.3 73.6 - - - +
517B ALA* 1.3 64.4 + - - +
518B SER 3.2 2.2 - - - -
519B THR* 2.6 29.0 + - - -
520B LEU* 4.0 10.9 + - + +
558B LEU* 5.6 0.9 - - + -
562B PHE* 3.9 38.8 - + + -
566B ASN* 3.7 29.6 - - + +
567B LEU* 4.0 19.3 - - + -
570B LEU* 3.3 35.0 - - + -
635B LEU* 4.1 19.7 - - + -
636B THR* 6.2 0.4 - - + -
639B LEU* 3.5 29.8 - - + -
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Residues in contact with ALA 517 (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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513B LEU 3.1 10.3 + - - +
516B PHE* 1.3 84.1 - - - +
518B SER* 1.3 62.5 + - - +
519B THR 3.2 1.0 + - - -
520B LEU* 3.2 20.6 + - - +
525B LEU* 4.0 19.7 - - + +
632B GLN* 3.5 37.0 - - + +
635B LEU* 4.1 18.4 - - + -
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Residues in contact with SER 518 (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 HIS* 6.1 1.6 - - - -
514B ASN* 2.8 33.6 + - - +
515B GLY* 3.0 15.6 + - - -
517B ALA* 1.3 77.8 - - - +
519B THR* 1.3 62.5 + - - +
520B LEU 3.3 7.8 - - - +
525B LEU* 5.9 0.9 - - - -
628B ARG* 6.0 1.1 - - - -
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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
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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