Contacts of the helix formed by residues 502 - 516 (chain A) in PDB entry 4YFI
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 ASP 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A PHE* 5.0 2.1 - - - +
492A TYR* 4.0 18.1 - - + +
493A ARG* 4.3 19.6 + - - +
501A SER* 1.3 77.1 - - - +
503A VAL* 1.3 61.5 + - + +
505A MET* 3.5 30.1 - - - +
506A PHE* 3.2 25.6 + - - +
535A PHE* 4.4 5.3 - - + -
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Residues in contact with VAL 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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441A GLU* 3.5 59.2 - - + +
444A ASP* 4.6 5.4 - - + +
445A ILE* 4.3 8.3 - - + -
501A SER 3.4 0.6 - - - -
502A ASP* 1.3 76.8 - - + +
504A ASP* 1.3 69.2 + - - +
505A MET 3.2 0.2 - - - -
506A PHE* 3.2 1.9 + - - +
507A CYS* 3.0 38.6 + - - -
532A PRO* 4.5 11.9 - - + -
535A PHE* 4.2 19.1 - - + -
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Residues in contact with ASP 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLU* 6.0 0.7 - - - +
444A ASP* 4.4 13.0 - - - +
501A SER* 3.5 17.3 + - - +
503A VAL* 1.3 78.1 - - - +
505A MET* 1.3 58.1 + - - +
507A CYS* 3.6 5.0 + - - +
508A ARG* 3.0 42.4 + - - +
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Residues in contact with MET 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PHE* 4.7 17.7 - - + -
492A TYR* 4.0 24.7 - - - +
501A SER* 3.6 12.6 + - - +
502A ASP* 3.5 33.4 - - - +
503A VAL 3.2 0.2 - - - -
504A ASP* 1.3 79.2 - - - +
506A PHE* 1.3 57.0 + - - +
508A ARG* 3.5 20.0 + - - +
509A GLU* 2.9 30.5 + - - +
608A GLY 4.8 13.7 - - - +
611A ARG* 5.1 4.3 - - - +
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Residues in contact with PHE 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ILE* 5.9 0.2 - - + -
448A LEU* 4.4 7.6 - - + -
492A TYR* 3.7 24.9 - + + -
502A ASP 3.2 13.9 + - - +
503A VAL 3.2 5.2 + - - +
505A MET* 1.3 75.7 - - - +
507A CYS* 1.3 70.8 + - - +
509A GLU* 3.2 1.6 + - - +
510A VAL* 3.0 46.3 + - + +
527A ALA* 4.2 2.5 - - + -
528A CYS 3.3 23.6 - - - -
529A LEU* 3.9 13.0 - - + -
535A PHE* 3.5 57.4 - + + -
536A ALA* 3.6 22.4 - - - -
537A ILE* 3.8 14.1 - - + -
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Residues in contact with CYS 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ASP* 4.0 30.7 - - + -
445A ILE* 4.4 6.1 - - - -
448A LEU* 3.7 28.6 - - + +
503A VAL* 3.0 34.1 + - - +
504A ASP* 3.9 5.6 - - - +
506A PHE* 1.3 78.1 - - - +
508A ARG* 1.3 57.7 + - - +
511A SER* 2.9 32.9 + - - +
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Residues in contact with ARG 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ASP* 3.0 24.5 + - - +
505A MET* 3.8 26.1 + - - +
507A CYS* 1.3 74.9 - - - +
509A GLU* 1.3 58.8 + - - +
511A SER* 3.1 6.9 + - - -
512A ILE* 2.9 40.0 + - + +
610A SER 3.4 23.1 - - - -
611A ARG* 3.2 49.8 - - - +
612A PHE* 5.2 9.2 - - + +
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Residues in contact with GLU 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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490A LYS* 3.0 31.1 + - - +
492A TYR* 2.8 25.8 + - - +
505A MET* 2.9 20.7 + - + +
506A PHE 3.2 3.3 + - - +
508A ARG* 1.3 74.8 - - - +
510A VAL* 1.3 57.6 + - - +
512A ILE* 3.5 5.4 + - - +
513A LEU* 3.0 37.3 + - + +
537A ILE* 3.5 24.2 - - + +
607A PHE 3.6 20.5 + - - +
608A GLY* 3.3 25.3 + - - +
610A SER 6.1 0.2 - - - -
801A 4CW 4.1 5.2 + - - -
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Residues in contact with VAL 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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448A LEU* 4.2 18.8 - - + -
452A LEU* 4.0 26.0 - - + -
506A PHE* 3.0 48.5 + - + +
507A CYS 4.0 2.5 - - - +
509A GLU* 1.3 73.4 - - - +
511A SER* 1.3 66.7 + - - +
513A LEU* 3.2 7.5 + - - +
514A CYS* 3.1 23.0 + - - -
524A PHE* 4.2 11.9 - - + -
527A ALA* 4.0 15.3 - - + -
537A ILE* 4.0 13.0 - - + -
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Residues in contact with SER 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 3.9 13.0 - - - +
507A CYS 2.9 22.6 + - - -
508A ARG* 3.1 9.4 + - - -
510A VAL* 1.3 78.1 - - - +
512A ILE* 1.3 65.5 + - - +
514A CYS* 3.4 18.7 - - - -
515A GLN* 3.5 15.2 + - - +
612A PHE* 4.5 14.1 - - - -
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Residues in contact with ILE 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 ARG* 2.9 22.8 + - - +
509A GLU* 3.9 4.5 - - - +
511A SER* 1.3 78.4 - - - +
513A LEU* 1.3 63.6 + - - +
515A GLN* 3.1 20.0 + - - +
516A LEU* 3.4 8.9 - - + +
584A ILE* 3.9 18.1 - - + +
607A PHE* 3.9 35.0 - - + +
610A SER* 3.7 34.5 - - - +
611A ARG* 3.9 15.7 - - - +
612A PHE* 3.5 33.7 - - + +
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Residues in contact with LEU 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A GLU* 3.0 37.2 + - + +
510A VAL* 3.2 4.7 + - - +
512A ILE* 1.3 76.3 - - - +
514A CYS* 1.3 57.1 + - - +
516A LEU* 3.0 37.8 + - + +
522A ILE* 3.9 28.3 - - + -
524A PHE* 3.7 37.5 - - + +
537A ILE* 3.4 35.0 - - + -
539A THR* 4.8 3.8 - - + -
607A PHE* 4.2 15.5 - - + +
801A 4CW 5.5 3.8 - - - +
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Residues in contact with CYS 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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448A LEU* 6.2 1.1 - - - -
451A GLY 5.6 1.6 - - - -
452A LEU* 3.9 20.6 - - + -
453A PRO* 5.0 7.0 - - + -
456A PHE* 3.9 29.8 - - + -
510A VAL* 3.1 21.3 + - - +
511A SER* 3.4 15.3 - - - -
513A LEU* 1.3 75.4 - - - +
515A GLN* 1.3 70.6 + - - +
516A LEU 3.3 2.9 - - - +
524A PHE* 4.1 12.5 - - + -
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Residues in contact with GLN 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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511A SER 3.5 17.8 + - - +
512A ILE 3.1 10.4 + - - +
514A CYS* 1.3 86.0 + - - +
516A LEU* 1.3 61.6 + - - +
517A ASN* 3.4 5.9 + - - +
576A TYR* 3.5 9.5 + - - -
580A LEU* 5.1 10.1 - - + +
584A ILE* 4.7 9.9 - - + -
612A PHE* 4.2 21.1 - - + -
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Residues in contact with LEU 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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512A ILE* 3.4 15.3 - - + +
513A LEU* 3.0 36.3 + - + +
514A CYS 3.3 2.3 - - - +
515A GLN* 1.3 76.9 - - + +
517A ASN* 1.3 63.1 + - - +
518A HIS 4.1 0.7 - - - -
521A VAL* 3.7 27.1 - - + -
522A ILE 4.1 12.9 - - - +
523A GLN* 5.7 1.4 - - - -
524A PHE* 5.4 4.7 + - - +
576A TYR* 4.0 7.9 - - + -
577A LEU* 3.6 28.0 - - + -
580A LEU* 4.9 0.7 - - + -
584A ILE* 4.2 12.6 - - + -
607A PHE* 3.8 26.5 - - + -
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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