Contacts of the helix formed by residues 499 - 512 (chain A) in PDB entry 6FWF
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 VAL 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A ILE* 5.4 7.6 - - + +
458A SER* 3.5 24.9 - - - +
494A GLU 4.3 2.0 - - - +
495A GLY* 3.7 33.4 - - - +
496A PHE 3.2 1.2 + - - -
497A PHE 3.6 0.4 - - - -
498A GLU* 1.3 84.0 - - + +
500A PHE* 1.3 63.1 + - - +
502A THR* 3.0 13.3 + - - -
503A ALA* 3.3 17.0 + - - +
528A ALA* 4.1 24.5 - - + +
531A PHE* 6.0 0.7 - - + -
532A MET* 4.2 24.5 - - + -
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Residues in contact with PHE 500 (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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347A PHE* 4.5 12.1 - + - -
348A LEU* 6.5 0.2 - - + -
350A ALA* 5.2 1.1 - - + -
351A GLY* 3.6 35.0 - - - -
430A TRP* 4.0 15.3 - + - -
434A MET* 4.0 9.4 - - + -
455A PHE* 4.1 21.5 - + - -
458A SER* 3.3 30.2 - - - +
459A MET* 3.6 31.4 - - + -
462A VAL* 4.2 5.6 - - + -
496A PHE* 2.8 41.6 + + + +
499A VAL* 1.3 73.0 - - - +
501A ALA* 1.3 58.1 + - - +
503A ALA* 3.4 2.6 + - - +
504A ALA* 2.8 39.0 + - + +
649A PHE* 6.0 1.8 - + - -
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Residues in contact with ALA 501 (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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347A PHE* 3.8 27.1 - - + -
496A PHE 3.3 2.6 + - - -
497A PHE* 3.4 23.1 - - - +
499A VAL 3.6 0.2 - - - -
500A PHE* 1.3 81.8 - - - +
502A THR* 1.3 53.5 + - + +
504A ALA* 3.5 8.5 - - - +
505A PHE* 2.8 30.7 + - - +
645A LEU* 4.6 5.8 - - + -
649A PHE* 3.9 19.2 - - + -
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Residues in contact with THR 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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497A PHE 4.6 3.8 - - - +
498A GLU* 2.9 41.6 + - + +
499A VAL* 3.0 14.9 + - - +
501A ALA* 1.3 74.3 - - + +
503A ALA* 1.3 57.5 + - - +
504A ALA 3.2 1.3 - - - -
505A PHE* 3.1 12.8 + - + +
506A ALA* 2.8 28.8 + - - +
527A ALA* 5.3 11.0 - - + -
528A ALA* 5.1 3.2 - - - +
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Residues in contact with ALA 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A LEU* 3.5 5.9 - - - +
454A ILE* 3.8 17.5 - - + -
455A PHE* 3.4 43.1 - - + +
458A SER* 4.5 0.4 - - - +
499A VAL 3.3 16.9 + - - +
500A PHE 4.0 0.7 - - - +
502A THR* 1.3 76.1 + - - +
504A ALA* 1.3 57.3 + - - +
506A ALA* 4.0 6.7 - - - -
507A PHE* 3.2 25.1 + - - +
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Residues in contact with ALA 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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354A LEU* 4.2 18.6 - - + -
455A PHE* 3.5 19.2 - - + -
500A PHE* 2.8 25.2 + - + +
501A ALA* 3.5 9.6 - - - +
503A ALA* 1.3 75.6 - - - +
505A PHE* 1.3 56.2 + - - +
507A PHE* 3.5 2.8 - - - +
508A VAL* 2.8 40.7 + - - +
649A PHE* 5.1 8.3 - - + -
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Residues in contact with PHE 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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501A ALA 2.8 19.9 + - - +
502A THR* 3.1 16.8 + - + +
504A ALA* 1.3 72.4 - - - +
506A ALA* 1.3 57.4 + - + +
508A VAL* 4.8 1.8 - - - -
509A PHE* 2.8 91.1 + + + +
515A VAL* 5.6 6.3 - - + -
597A PHE* 5.7 9.9 - + - -
649A PHE* 5.6 4.9 - + + -
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Residues in contact with ALA 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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451A LEU* 4.0 19.4 - - + +
454A ILE* 6.4 0.7 - - + -
502A THR 2.8 18.1 + - - +
503A ALA* 4.1 7.9 - - - +
505A PHE* 1.3 78.7 - - + +
507A PHE* 1.3 52.8 + - - +
509A PHE 3.7 0.5 - - - -
510A TYR* 2.8 36.4 + - - +
515A VAL* 4.0 12.4 - - + +
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Residues in contact with PHE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 4.2 10.8 - - + -
357A ILE* 3.7 23.1 - - + -
358A VAL* 3.6 43.1 - - + -
451A LEU* 3.9 22.1 - - + +
452A LEU* 4.1 19.5 - - + -
455A PHE* 4.9 9.2 - + + -
503A ALA 3.2 19.5 + - - +
504A ALA* 3.5 7.4 - - - +
505A PHE 3.3 0.2 - - - -
506A ALA* 1.3 78.2 - - - +
508A VAL* 1.3 62.9 + - + +
510A TYR* 3.3 8.0 + + - +
511A ASN* 2.8 62.7 + - - +
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Residues in contact with VAL 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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354A LEU* 3.4 39.3 - - + -
357A ILE* 5.9 1.3 - - + -
504A ALA 2.8 25.1 + - - +
505A PHE* 4.1 2.9 - - - +
507A PHE* 1.3 78.1 - - + +
509A PHE* 1.3 64.3 + - + +
511A ASN* 3.2 5.2 + - - +
512A MET* 2.9 57.7 + - + +
652A LEU* 4.5 17.7 - - + -
656A TYR* 4.7 5.4 - - + +
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Residues in contact with PHE 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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505A PHE* 2.8 70.8 + + + +
508A VAL* 1.3 80.6 - - + +
510A TYR* 1.3 52.7 + - - +
512A MET* 4.2 12.8 - - + -
514A PHE* 2.8 61.9 + + + -
515A VAL* 2.8 33.2 + - + -
590A LEU* 6.4 1.8 - - + -
594A LEU* 6.1 4.5 - - + -
597A PHE* 5.6 11.9 - + - -
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Residues in contact with TYR 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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451A LEU* 4.6 15.5 - - + -
506A ALA 2.8 20.8 + - - +
507A PHE* 3.4 9.6 - + - +
509A PHE* 1.3 75.9 - - - +
511A ASN* 1.3 76.8 + - - +
512A MET 3.3 0.2 - - - -
513A GLY* 3.4 13.0 + - - -
515A VAL* 3.7 24.4 - - + +
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Residues in contact with ASN 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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271A VAL* 5.0 12.5 - - - +
357A ILE* 3.2 34.2 + - + +
507A PHE* 2.8 45.7 + - - +
508A VAL* 3.2 5.4 + - - +
510A TYR* 1.3 85.3 - - - +
512A MET* 1.3 61.3 + - + +
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Residues in contact with MET 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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267A PRO* 4.6 4.9 - - - +
268A ILE 4.1 11.6 - - - +
269A SER* 3.8 32.0 + - - +
270A LYS 5.9 0.2 - - - +
271A VAL* 6.0 4.5 - - + -
508A VAL* 2.9 39.0 + - + +
509A PHE* 4.6 13.0 - - + -
511A ASN* 1.3 78.8 - - + +
513A GLY* 1.3 59.9 + - - +
514A PHE* 3.5 35.4 - - + -
590A LEU* 4.2 22.4 - - + -
652A LEU* 5.5 3.6 - - + -
656A TYR* 3.0 28.5 - - - +
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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