Contacts of the helix formed by residues 502 - 514 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B TYR* 5.5 5.0 - - + -
501B SER* 1.3 85.4 - - - +
503B VAL* 1.3 65.8 + - + +
504B ASP 3.4 0.2 - - - -
505B MET* 3.6 8.6 + - - +
506B PHE* 3.3 21.0 + - - +
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Residues in contact with VAL 503 (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 SER 3.4 4.8 - - - +
502B ASP* 1.3 80.3 - - + +
504B ASP* 1.3 62.7 + - - +
505B MET 3.2 0.2 - - - -
506B PHE* 3.4 5.8 + - - +
507B CYS* 3.0 41.3 + - - -
532B PRO* 5.7 6.5 - - + -
535B PHE* 4.3 27.4 - - + -
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Residues in contact with ASP 504 (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 SER* 3.8 20.1 + - - +
502B ASP 3.4 0.4 - - - -
503B VAL* 1.3 81.9 - - - +
505B MET* 1.3 57.5 + - + +
507B CYS* 3.4 6.9 + - - +
508B ARG* 3.0 39.8 + - - +
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Residues in contact with MET 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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492B TYR* 5.6 0.4 - - - -
501B SER 3.7 13.6 + - - +
502B ASP* 3.6 11.2 + - - +
503B VAL 3.2 0.6 - - - -
504B ASP* 1.3 77.9 - - + +
506B PHE* 1.3 64.3 + - - +
508B ARG* 3.5 9.3 + - - +
509B GLU* 3.1 25.2 + - - +
608B GLY 3.8 16.6 - - - +
609B GLU* 4.7 14.4 - - - +
611B ARG* 3.5 37.0 + - - +
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Residues in contact with PHE 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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492B TYR* 3.5 40.7 + + + -
502B ASP 3.3 12.1 + - - +
503B VAL* 3.7 8.3 - - - +
505B MET* 1.3 79.9 - - - +
507B CYS* 1.3 69.9 + - - +
509B GLU* 3.5 4.0 + - - +
510B VAL* 3.2 36.4 + - + +
527B ALA* 4.5 1.1 - - + -
528B CYS 4.0 11.4 - - - -
529B LEU* 3.5 26.5 - - + -
535B PHE* 3.6 45.3 - + + -
536B ALA 4.1 9.4 - - - -
537B ILE* 3.7 25.8 - - + -
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Residues in contact with CYS 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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503B VAL* 3.0 39.6 + - - +
504B ASP* 3.8 8.5 - - - +
505B MET 3.3 0.2 - - - -
506B PHE* 1.3 84.0 - - - +
508B ARG* 1.3 56.0 + - - +
510B VAL* 3.6 5.4 + - - +
511B SER* 2.4 38.7 + - - +
529B LEU* 5.9 3.6 - - - -
535B PHE* 6.0 0.9 - - - -
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Residues in contact with ARG 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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504B ASP* 3.0 28.2 + - - +
505B MET* 3.7 10.2 - - - +
507B CYS* 1.3 73.4 - - - +
509B GLU* 1.3 67.3 + - - +
511B SER* 3.0 18.5 + - - -
512B ILE* 3.0 20.9 + - + +
610B SER 3.8 11.9 - - - +
611B ARG* 3.0 59.9 - - - +
612B PHE* 5.6 5.8 - - + +
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Residues in contact with GLU 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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490B LYS* 2.8 31.7 + - - +
492B TYR* 3.0 10.0 + - - -
505B MET 3.1 14.4 + - - +
506B PHE 3.8 5.6 - - - +
508B ARG* 1.3 79.0 - - - +
510B VAL* 1.3 50.5 + - - +
512B ILE* 3.2 8.1 + - - +
513B LEU* 2.8 46.1 + - + +
537B ILE* 3.5 19.9 - - + +
606B ASP* 4.8 0.5 - - - +
607B PHE 3.4 23.9 - - - +
608B GLY* 3.7 20.4 + - - +
610B SER 5.5 0.4 - - - -
611B ARG* 5.8 0.2 - - - +
801B 4CW 3.5 20.6 + - - -
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Residues in contact with VAL 510 (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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452B LEU* 3.6 36.6 - - + -
506B PHE* 3.2 43.4 + - + +
507B CYS* 3.9 5.6 - - - +
509B GLU* 1.3 73.1 - - - +
511B SER* 1.3 66.4 + - - +
513B LEU* 4.0 7.3 - - - +
514B CYS* 3.0 25.1 + - - +
524B PHE* 4.6 4.2 - - + -
527B ALA* 4.0 10.8 - - + -
529B LEU* 5.2 4.7 - - + -
537B ILE* 4.0 17.7 - - + -
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Residues in contact with SER 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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452B LEU* 5.7 0.2 - - - -
507B CYS* 2.4 28.0 + - - +
508B ARG* 3.0 10.8 + - - -
510B VAL* 1.3 77.3 - - - +
512B ILE* 1.3 58.8 + - - +
514B CYS* 3.5 14.0 - - - -
515B GLN* 3.3 25.3 + - - +
612B PHE* 3.9 17.3 - - - -
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Residues in contact with ILE 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 ARG* 3.0 20.8 + - + +
509B GLU* 3.5 9.0 - - - +
511B SER* 1.3 75.3 - - - +
513B LEU* 1.3 65.7 + - - +
514B CYS 3.2 1.8 - - - -
515B GLN* 3.1 19.3 + - - +
516B LEU* 3.5 8.3 - - + +
584B ILE* 3.9 17.3 - - + -
607B PHE* 3.8 31.4 - - + -
610B SER* 3.1 38.1 - - - +
611B ARG* 3.8 13.7 - - - +
612B PHE* 3.6 31.0 - - + +
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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 GLU* 2.8 35.7 + - + +
510B VAL* 3.3 2.9 + - - +
512B ILE* 1.3 73.1 - - - +
514B CYS* 1.3 60.0 + - - +
516B LEU* 3.3 34.9 + - + +
522B ILE* 4.1 16.4 - - + -
524B PHE* 3.3 42.9 - - + +
537B ILE* 3.4 43.7 - - + -
539B THR* 4.8 4.5 - - + -
607B PHE* 4.0 18.4 - - + -
801B 4CW 4.7 5.2 - - - +
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Residues in contact with CYS 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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451B GLY 5.6 0.9 - - - -
452B LEU* 3.6 32.8 - - + -
453B PRO* 4.3 12.0 - - - +
456B PHE* 3.7 27.2 - - + -
510B VAL 3.0 12.5 + - - +
511B SER* 3.5 20.9 - - - -
512B ILE 3.2 0.6 - - - -
513B LEU* 1.3 76.4 - - - +
515B GLN* 1.3 70.5 + - - +
516B LEU 3.4 2.9 + - - +
524B PHE* 3.8 9.8 - - + -
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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