Contacts of the helix formed by residues 502 - 517 (chain A) in PDB entry 2FY2
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 ILE 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A THR* 3.4 43.1 - - + +
27A THR* 3.6 17.7 - - + -
28A TYR* 3.7 35.4 - - + -
31A CYS* 3.9 18.8 - - + -
453A ARG* 3.9 13.2 - - - +
492A TYR* 3.6 11.8 + - - +
500A MET 5.5 0.7 - - - +
501A ALA* 1.4 83.3 - - - +
503A ASP* 1.3 74.5 + - - +
504A ASN 3.6 1.6 - - - -
505A HIS* 3.4 2.6 + - - +
506A LEU* 3.0 31.9 + - + +
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Residues in contact with ASP 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A TYR* 5.5 0.2 - - - -
450A ASP* 3.3 15.5 + - - +
451A ASN* 3.3 31.9 + - + +
453A ARG* 2.9 44.3 + - - +
492A TYR* 4.6 0.3 + - - -
501A ALA* 4.0 0.6 - - - +
502A ILE* 1.3 80.6 - - - +
504A ASN* 1.3 65.7 + - - +
506A LEU* 3.3 6.1 + - - +
507A LEU* 3.0 23.5 + - - +
529A TYR* 5.6 0.2 + - - -
533A ASN* 4.0 4.4 - - - +
535A PHE* 3.8 6.9 - - - -
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Residues in contact with ASN 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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16A LEU* 4.7 3.0 - - + +
75A TRP* 3.5 18.8 - - + -
76A VAL* 3.9 24.8 - - + +
80A TRP* 3.5 24.4 + - - -
441A ILE* 3.8 13.5 - - - +
449A VAL 3.1 17.3 + - - +
450A ASP* 3.1 36.8 + - - +
502A ILE 3.6 0.2 - - - -
503A ASP* 1.3 79.6 - - - +
505A HIS* 1.3 63.1 + - - +
507A LEU* 3.3 8.7 + - - +
508A ALA 3.0 19.8 + - - -
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Residues in contact with HIS 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.0 0.4 - - - +
19A PRO* 2.9 51.8 + - + +
20A PRO 4.0 3.8 - - - -
21A LEU* 4.1 4.9 - - - -
24A THR* 2.6 36.5 + - + +
62A GLN* 2.9 25.0 + - - -
65A LEU* 3.5 19.6 - - + +
75A TRP* 3.9 8.9 - + + -
501A ALA 4.2 5.5 + - - +
502A ILE 3.4 8.7 + - - +
503A ASP 3.2 0.4 - - - -
504A ASN* 1.3 80.9 - - - +
506A LEU* 1.3 61.5 + - - +
508A ALA* 3.3 1.7 + - - +
509A LEU* 3.0 31.1 + - + +
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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
----------------------------------------------------------
24A THR* 3.7 19.5 - - + -
25A LEU* 4.6 13.2 - - + -
28A TYR* 4.0 29.8 - - + -
51A PHE* 5.9 0.4 - - + -
453A ARG* 6.1 2.5 - - - +
502A ILE* 3.0 33.1 + - + +
503A ASP* 3.9 4.3 - - - +
505A HIS* 1.3 77.0 - - - +
507A LEU* 1.3 57.7 + - - +
509A LEU* 3.2 14.2 + - + +
510A ARG* 2.8 31.8 + - - +
523A MET* 4.6 7.0 - - + -
524A PHE* 3.6 16.3 - - + -
529A TYR* 4.1 26.9 - - + +
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Residues in contact with LEU 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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76A VAL* 4.1 9.0 - - + -
79A TYR* 3.8 12.8 - - + +
80A TRP* 3.7 39.7 - - + +
83A ASP* 3.8 20.2 - - + +
503A ASP 3.0 14.3 + - - +
504A ASN* 3.4 10.3 - - - +
506A LEU* 1.3 76.5 - - - +
508A ALA* 1.3 58.5 + - - +
510A ARG* 3.1 40.4 + - - +
511A GLU* 2.9 37.8 + - + +
529A TYR* 4.5 6.0 + - - +
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Residues in contact with ALA 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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65A LEU* 3.8 15.3 - - + -
75A TRP* 3.5 37.7 - - + -
76A VAL* 4.9 0.4 - - + -
79A TYR* 3.5 24.4 - - + -
504A ASN 3.0 7.3 + - - +
505A HIS 3.7 3.1 - - - +
507A LEU* 1.3 76.2 - - - +
509A LEU* 1.3 58.5 + - - +
512A LEU* 2.9 36.7 + - - +
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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
----------------------------------------------------------
21A LEU* 3.9 20.0 - - + -
24A THR* 5.6 0.9 - - + -
25A LEU* 5.6 0.2 - - + -
51A PHE* 4.6 9.9 - - + -
58A GLY 4.7 1.3 - - - +
61A LEU* 3.5 46.2 - - + +
62A GLN* 3.9 13.9 - - - +
65A LEU* 4.0 10.5 - - + -
505A HIS* 3.0 40.3 + - + +
506A LEU* 3.6 20.0 - - + +
508A ALA* 1.3 76.4 - - - +
510A ARG* 1.3 62.7 + - - +
512A LEU* 3.5 3.4 + - + +
513A ALA* 3.1 23.2 + - - +
524A PHE* 3.9 10.3 - - + -
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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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83A ASP* 2.8 31.3 + - - +
506A LEU 2.8 17.3 + - - +
507A LEU* 3.2 22.6 - - - +
509A LEU* 1.3 77.1 - - - +
511A GLU* 1.3 82.7 + - - +
513A ALA* 3.2 5.4 + - - +
514A ARG* 3.0 31.0 + - - +
520A LEU* 3.6 19.2 - - + +
524A PHE* 3.5 33.6 - - + -
529A TYR* 3.1 38.3 + - - -
533A ASN* 4.6 4.9 - - - +
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Residues in contact with GLU 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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79A TYR* 3.7 40.8 + - + +
507A LEU* 2.9 29.3 + - + +
508A ALA 4.1 0.2 - - - +
510A ARG* 1.3 99.8 + - - +
512A LEU* 1.3 65.5 + - - +
514A ARG* 2.6 49.7 + - - +
515A ALA* 3.1 21.5 + - - +
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Residues in contact with LEU 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.9 16.6 - - + +
64A LYS* 4.0 20.7 - - + +
65A LEU* 3.6 47.6 - - + +
68A ARG* 4.4 13.5 - - + +
79A TYR* 3.4 20.0 - - + +
508A ALA 2.9 26.4 + - - +
509A LEU* 3.9 5.8 - - - +
511A GLU* 1.3 75.6 - - - +
513A ALA* 1.3 62.8 + - - +
515A ALA* 3.4 11.2 + - + +
516A MET* 3.3 22.3 + - - +
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Residues in contact with ALA 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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57A LEU* 5.4 0.9 - - + -
61A LEU* 3.7 21.9 - - + +
509A LEU 3.1 14.3 + - - +
510A ARG* 3.3 11.2 - - - +
511A GLU 3.2 0.2 - - - -
512A LEU* 1.3 75.7 - - - +
514A ARG* 1.3 57.5 + - - +
516A MET* 2.7 28.3 + - - +
517A CYS* 2.9 13.8 + - - +
520A LEU* 4.7 0.4 - - - -
521A PRO* 3.7 31.0 - - + -
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Residues in contact with ARG 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* 3.0 24.1 + - - +
511A GLU* 2.6 52.7 + - - +
513A ALA* 1.3 75.7 - - - +
515A ALA* 1.3 61.4 + - - +
517A CYS 3.2 24.3 - - - +
518A ALA* 3.6 15.5 + - - -
520A LEU* 3.3 41.0 - - + +
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Residues in contact with ALA 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 5.9 0.9 - - - +
511A GLU 3.1 13.2 + - - +
512A LEU* 3.5 15.7 - - + +
513A ALA 3.1 0.2 - - - -
514A ARG* 1.3 76.8 - - - +
516A MET* 1.3 62.1 + - + +
517A CYS* 4.8 0.2 - - - -
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Residues in contact with MET 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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57A LEU* 4.1 19.7 - - + -
60A THR* 4.7 6.7 - - + -
61A LEU* 3.6 27.6 - - - -
64A LYS* 2.9 34.5 - - + +
512A LEU 3.3 9.1 + - - +
513A ALA* 2.7 9.8 + - - +
515A ALA* 1.3 79.9 - - + +
517A CYS* 1.3 64.0 + - + +
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Residues in contact with CYS 517 (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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513A ALA 2.9 10.9 + - - +
514A ARG* 3.2 14.0 + - - +
516A MET* 1.3 84.0 - - + +
518A ALA* 1.3 68.4 + - - +
519A ALA* 3.0 36.6 + - - +
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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