Contacts of the helix formed by residues 497 - 514 (chain F) in PDB entry 2CEA
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 ALA 497 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423F HIS* 4.1 13.8 - - + -
483F ARG* 3.6 47.3 - - + +
486F GLU* 4.2 2.3 + - - +
494F THR 3.6 3.4 + - - +
495F SER 3.1 1.4 + - - -
496F GLY* 1.3 73.0 - - - +
498F ALA* 1.3 66.9 + - - +
499F ASN* 3.1 7.6 - - - +
500F ASP* 2.9 16.5 + - + -
501F ILE* 2.9 18.0 + - + +
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Residues in contact with ALA 498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483F ARG* 5.3 0.6 - - - +
494F THR 5.1 0.4 + - - -
495F SER* 3.1 18.5 + - - +
496F GLY 3.2 1.6 - - - +
497F ALA* 1.3 79.0 - - - +
499F ASN* 1.3 57.3 + - - +
501F ILE* 3.2 11.7 + - - +
502F GLU* 3.0 26.7 + - - +
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Residues in contact with ASN 499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448F ARG* 5.5 4.5 + - - -
452F ALA* 6.0 2.4 - - - +
496F GLY 3.4 19.7 + - - +
497F ALA 3.5 1.0 + - - -
498F ALA* 1.3 73.5 - - - +
500F ASP* 1.3 107.9 + - - +
502F GLU* 3.4 11.4 + - - +
503F ARG* 3.1 25.3 + - - +
1606F ZN 4.4 1.2 - - - -
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Residues in contact with ASP 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F HIS* 3.0 10.6 + - - -
427F HIS* 2.9 8.2 + - - -
479F LEU* 3.3 44.0 - - - +
480F LEU* 5.1 3.8 - - + -
483F ARG* 5.2 1.3 + - + -
497F ALA* 2.9 11.2 + - + +
499F ASN* 1.3 97.2 + - - +
501F ILE* 1.3 58.5 + - + +
503F ARG* 3.3 2.4 + - - +
504F ALA* 2.8 31.2 + - - +
1606F ZN 2.0 36.8 - - - -
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Residues in contact with ILE 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480F LEU* 4.4 16.4 - - + -
483F ARG* 3.6 42.2 - - - +
497F ALA* 2.9 21.4 + - + +
498F ALA* 3.3 11.2 - - - +
500F ASP* 1.3 73.6 - - - +
502F GLU* 1.3 66.2 + - - +
504F ALA* 3.4 6.5 + - - +
505F THR* 2.8 37.2 + - - +
561F VAL* 5.9 0.3 - - - +
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Residues in contact with GLU 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498F ALA 3.0 13.0 + - - +
499F ASN* 3.8 12.8 - - - +
500F ASP 3.3 0.2 - - - -
501F ILE* 1.3 77.9 - - - +
503F ARG* 1.3 57.9 + - - +
505F THR* 3.3 5.4 + - - -
506F GLU* 3.0 49.2 + - + +
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Residues in contact with ARG 503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F ASP* 5.5 6.7 + - - +
454F GLY 4.9 15.2 + - - -
475F LYS* 4.7 14.3 - - - +
479F LEU* 3.7 22.2 - - + -
499F ASN 3.1 17.0 + - - +
500F ASP 3.6 4.5 - - - +
502F GLU* 1.3 74.7 - - - +
504F ALA* 1.3 65.6 + - - +
506F GLU* 3.2 35.0 + - - +
507F ILE* 3.1 53.8 + - - +
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Residues in contact with ALA 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476F LEU* 3.1 34.9 - - + +
479F LEU* 3.9 6.0 - - + +
480F LEU* 4.1 20.0 - - + -
500F ASP 2.8 21.0 + - - +
501F ILE* 3.8 4.7 - - - +
503F ARG* 1.3 72.6 - - - +
505F THR* 1.3 63.8 + - - +
507F ILE* 3.3 7.8 + - - +
508F ALA* 3.0 23.0 + - - +
561F VAL* 4.4 7.2 - - + -
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Residues in contact with THR 505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501F ILE* 2.8 28.9 + - - +
502F GLU* 3.6 7.1 - - - -
504F ALA* 1.3 76.7 - - - +
506F GLU* 1.3 58.1 + - + +
508F ALA* 3.1 3.2 + - - +
509F ARG* 2.8 47.2 + - + +
557F VAL* 4.6 8.3 - - + -
561F VAL* 4.4 15.7 - - + +
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Residues in contact with GLU 506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502F GLU* 3.0 38.4 + - + +
503F ARG* 3.2 42.5 + - - +
505F THR* 1.3 76.5 - - + +
507F ILE* 1.3 64.6 + - - +
509F ARG* 3.3 8.1 + - - +
510F ASN* 2.9 24.3 + - - +
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Residues in contact with ILE 507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472F LEU* 3.9 31.4 - - + +
475F LYS* 4.3 21.3 - - + +
476F LEU* 4.2 18.4 - - + -
479F LEU* 3.5 26.5 - - + -
503F ARG* 3.1 39.7 + - - +
504F ALA* 3.7 5.8 - - - +
506F GLU* 1.3 76.7 - - - +
508F ALA* 1.3 58.9 + - - +
510F ASN* 3.0 9.0 + - + +
511F MET* 2.9 38.3 + - + +
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Residues in contact with ALA 508 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476F LEU* 4.2 3.8 - - + +
504F ALA 3.0 13.6 + - - +
505F THR 3.6 6.5 - - - +
507F ILE* 1.3 75.3 - - - +
509F ARG* 1.3 64.6 + - - +
510F ASN 3.2 0.3 + - - -
511F MET* 3.2 10.1 + - - +
512F VAL* 3.2 28.1 + - - +
557F VAL* 3.7 17.9 - - + +
560F ILE* 4.1 15.5 - - + -
561F VAL* 3.6 23.1 - - + -
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Residues in contact with ARG 509 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505F THR* 2.8 35.3 + - + +
506F GLU* 3.9 7.0 - - - +
508F ALA* 1.3 72.2 - - - +
510F ASN* 1.3 57.2 + - - +
512F VAL 3.3 0.3 + - - -
513F CYS* 2.9 41.8 + - - +
545F TYR* 4.3 14.1 + - - -
550F ALA* 6.4 0.2 - - - +
553F ILE* 3.8 22.7 - - - +
554F ASP* 3.2 24.4 + - - +
557F VAL* 3.9 25.5 - - + +
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Residues in contact with ASN 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506F GLU 2.9 13.6 + - - +
507F ILE* 3.3 12.6 - - + +
509F ARG* 1.3 77.9 - - - +
511F MET* 1.3 64.8 + - + +
512F VAL 3.1 0.2 - - - -
514F GLN* 2.5 49.8 + - - +
515F LEU* 3.1 38.5 + - + +
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Residues in contact with MET 511 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469F ARG* 3.7 44.9 - - + +
472F LEU* 4.0 32.8 - - + -
473F LEU* 4.7 7.2 - - + -
476F LEU* 4.6 4.5 - - - -
507F ILE* 2.9 22.4 + - - +
508F ALA* 3.6 8.1 - - - +
510F ASN* 1.3 78.8 - - + +
512F VAL* 1.3 65.5 + - + +
515F LEU* 3.7 9.8 + - - -
516F GLY 3.4 4.9 + - - -
517F MET* 2.9 42.6 + - + +
560F ILE* 4.5 22.4 - - + -
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Residues in contact with VAL 512 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508F ALA 3.2 17.2 + - - +
509F ARG 3.9 2.5 - - - +
510F ASN 3.1 0.4 - - - -
511F MET* 1.3 81.7 - - - +
513F CYS* 1.3 61.6 + - - +
516F GLY* 4.5 6.4 + - - -
518F SER* 4.2 20.1 - - - -
521F LEU* 3.5 32.3 - - + +
522F GLY 5.2 0.9 - - - +
524F LEU 4.3 3.3 - - - +
526F TRP* 4.2 10.4 - - - -
553F ILE* 4.3 17.0 - - + -
556F GLU* 4.2 11.2 - - + -
557F VAL* 4.1 12.1 - - + -
560F ILE* 3.6 25.6 - - + -
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Residues in contact with CYS 513 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509F ARG* 2.9 29.2 + - - +
512F VAL* 1.3 77.7 - - - +
514F GLN* 1.3 67.4 + - + +
524F LEU 4.1 3.6 - - - -
525F ALA* 3.2 6.2 - - - +
526F TRP* 2.7 52.6 + - - +
545F TYR* 5.2 1.6 - - - -
553F ILE* 3.8 40.2 - - - -
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Residues in contact with GLN 514 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498E ALA* 3.8 20.9 - - + +
501E ILE* 4.2 9.5 - - - +
502E GLU* 5.9 2.0 + - - -
510F ASN* 2.5 37.4 + - - +
513F CYS* 1.3 90.5 - - + +
515F LEU* 1.3 67.9 + - + +
516F GLY 3.3 4.8 + - - -
524F LEU 5.3 0.2 - - - -
525F ALA* 4.8 6.8 - - + +
526F TRP 5.5 1.3 - - - +
527F GLY 5.7 2.8 + - - -
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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
------------------------------------------------------------
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