Contacts of the helix formed by residues 497 - 514 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423D HIS* 3.7 18.1 - - + +
483D ARG* 3.7 45.3 - - + +
486D GLU* 4.7 2.2 + - - +
494D THR 3.7 3.5 + - - +
495D SER 3.1 1.4 + - - -
496D GLY* 1.3 75.5 - - - +
498D ALA* 1.3 64.8 + - - +
499D ASN 3.2 2.5 - - - -
500D ASP* 3.2 9.4 + - + +
501D ILE* 2.9 30.3 + - + +
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Residues in contact with ALA 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D SER 3.2 15.6 + - - +
496D GLY 3.3 1.6 - - - -
497D ALA* 1.3 77.1 - - - +
499D ASN* 1.3 68.1 + - - +
501D ILE* 3.2 6.9 + - - +
502D GLU* 3.0 22.0 + - - +
514E GLN* 3.9 18.7 - - + +
515E LEU* 3.8 22.2 - - + +
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Residues in contact with ASN 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D ARG* 5.5 7.7 - - - +
450D TYR* 4.2 31.7 + - - -
496D GLY 4.7 6.9 + - - +
497D ALA 3.2 0.6 - - - -
498D ALA* 1.3 80.4 - - - +
500D ASP* 1.3 68.9 + - - +
502D GLU* 3.2 12.2 + - - +
503D ARG* 2.9 24.3 + - - +
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Residues in contact with ASP 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D HIS* 2.9 11.4 + - - -
427D HIS* 2.8 15.1 + - - -
448D ARG* 4.0 13.3 + - - -
479D LEU* 3.3 30.9 - - + +
480D LEU* 5.4 2.0 - - + -
483D ARG* 6.3 0.4 - - + -
496D GLY 5.3 0.7 - - - -
497D ALA* 3.2 13.1 + - + +
499D ASN* 1.3 80.6 - - - +
501D ILE* 1.3 58.4 + - + +
503D ARG* 3.7 6.7 - - - +
504D ALA* 2.9 29.5 + - - +
1607D ZN 2.0 38.1 - - - -
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Residues in contact with ILE 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480D LEU* 4.8 8.7 - - + -
483D ARG* 3.6 32.1 - - + +
497D ALA* 2.9 26.1 + - + +
498D ALA 3.4 4.7 - - - +
499D ASN 3.1 0.2 - - - -
500D ASP* 1.3 75.1 - - + +
502D GLU* 1.3 62.9 + - - +
504D ALA* 3.1 7.3 + - - +
505D THR* 2.8 32.7 + - - -
514E GLN 4.0 8.7 - - - +
515E LEU 4.0 18.4 - - - -
516E GLY* 4.1 5.4 - - - +
523E PRO* 4.0 16.1 - - + +
524E LEU* 3.6 11.2 - - - +
525E ALA* 3.5 28.0 - - + +
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Residues in contact with GLU 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D ALA 3.0 13.6 + - - +
499D ASN* 3.7 13.9 - - - +
501D ILE* 1.3 77.3 - - - +
503D ARG* 1.3 62.1 + - - +
505D THR* 3.1 2.9 + - - -
506D GLU* 3.0 42.3 + - + +
525E ALA* 3.8 21.3 - - + +
527E GLY 4.9 1.0 - - - +
528E LYS* 4.0 30.8 + - - +
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Residues in contact with ARG 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D LYS* 4.0 23.8 - - - +
479D LEU* 4.1 17.0 - - + -
499D ASN 2.9 15.7 + - - +
500D ASP* 3.7 7.4 - - - +
502D GLU* 1.3 79.0 - - - +
504D ALA* 1.3 60.2 + - - +
506D GLU* 2.9 42.2 + - - +
507D ILE* 3.2 35.7 + - - +
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Residues in contact with ALA 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476D LEU* 3.6 29.4 - - + +
479D LEU* 4.2 11.6 - - + +
480D LEU* 4.2 23.3 - - + -
500D ASP 2.9 19.6 + - - +
501D ILE* 3.5 6.1 - - - +
503D ARG* 1.3 73.4 - - - +
505D THR* 1.3 66.1 + - - +
507D ILE* 3.5 1.0 + - - -
508D ALA* 3.3 17.2 + - - +
561D VAL* 4.1 7.3 - - + +
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Residues in contact with THR 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D ILE 2.8 15.2 + - - -
502D GLU 3.6 4.5 - - - -
504D ALA* 1.3 75.2 - - - +
506D GLU* 1.3 68.1 + - + +
508D ALA* 3.2 7.1 + - - +
509D ARG* 2.9 39.0 + - + +
557D VAL* 4.6 12.1 - - + -
561D VAL* 4.6 3.7 - - - +
523E PRO 4.6 0.9 + - - -
524E LEU* 3.5 14.4 - - + +
525E ALA* 2.9 46.1 + - + +
526E TRP* 6.4 0.9 - - + -
544E ASN* 6.3 0.7 - - - +
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Residues in contact with GLU 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D GLU* 3.0 36.1 + - + +
503D ARG* 2.9 37.9 + - - +
505D THR* 1.3 78.5 - - + +
507D ILE* 1.3 67.8 + - - +
509D ARG* 3.1 9.5 + - - +
510D ASN* 3.0 20.6 + - - +
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Residues in contact with ILE 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D LEU* 4.2 30.3 - - + +
475D LYS* 3.8 25.1 - - + +
476D LEU* 3.9 19.5 - - + +
479D LEU* 3.6 31.2 - - + -
503D ARG* 3.2 26.5 + - - +
504D ALA* 3.9 6.5 - - - +
505D THR 3.2 0.4 - - - -
506D GLU* 1.3 75.3 - - - +
508D ALA* 1.3 59.8 + - - +
510D ASN* 2.8 25.3 + - - +
511D MET* 2.9 23.8 + - + +
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Residues in contact with ALA 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476D LEU* 4.1 3.3 - - + +
504D ALA 3.3 10.3 + - - +
505D THR 3.2 8.0 + - - +
507D ILE* 1.3 80.1 - - - +
509D ARG* 1.3 64.1 + - - +
511D MET* 3.1 13.6 + - - +
512D VAL* 3.0 26.0 + - - +
557D VAL* 3.9 15.5 - - + +
560D ILE* 4.1 15.9 - - + -
561D VAL* 3.8 21.5 - - + -
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Residues in contact with ARG 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D THR* 2.9 36.9 + - + +
506D GLU* 3.1 10.1 + - - +
508D ALA* 1.3 73.3 - - - +
510D ASN* 1.3 58.2 + - - +
512D VAL* 3.2 0.4 + - - -
513D CYS* 2.8 45.5 + - + +
542D LEU* 6.3 1.2 - - - +
545D TYR* 3.8 19.6 + - - -
553D ILE* 3.9 20.9 - - - +
554D ASP* 3.6 17.2 + - - -
557D VAL* 3.9 19.6 - - + +
526E TRP* 5.8 3.0 - - - -
544E ASN* 3.2 48.6 + - - +
545E TYR* 5.5 0.2 - - - +
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Residues in contact with ASN 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D GLU 3.0 10.8 + - - +
507D ILE* 2.8 15.4 + - - +
509D ARG* 1.3 75.9 - - - +
511D MET* 1.3 64.1 + - + +
513D CYS* 5.1 0.2 - - - -
514D GLN* 2.6 55.5 + - - +
515D LEU* 3.1 35.5 + - + +
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Residues in contact with MET 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D ARG* 3.8 45.5 - - + +
472D LEU* 4.0 32.8 - - + -
473D LEU* 4.1 24.9 - - + -
476D LEU* 5.0 0.9 - - - -
507D ILE* 2.9 27.3 + - - +
508D ALA* 3.1 9.8 + - - +
510D ASN* 1.3 79.3 - - - +
512D VAL* 1.3 59.7 + - - +
515D LEU* 3.6 10.2 + - - +
516D GLY 3.5 5.0 + - - -
517D MET* 2.9 38.2 + - + +
560D ILE* 4.4 19.5 - - + -
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Residues in contact with VAL 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508D ALA 3.0 17.6 + - - +
509D ARG 3.8 2.9 - - - +
511D MET* 1.3 80.1 - - - +
513D CYS* 1.3 73.8 - - - +
516D GLY* 4.6 5.4 + - - -
518D SER* 4.2 19.3 - - - -
521D LEU* 3.6 29.2 - - + +
522D GLY 5.1 1.0 - - - +
524D LEU 4.4 2.9 - - - +
526D TRP* 4.0 11.5 - - + -
553D ILE* 4.1 12.6 - - + -
556D GLU* 3.9 21.8 - - + +
557D VAL* 3.9 11.4 - - + -
560D ILE* 3.9 16.8 - - + -
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Residues in contact with CYS 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509D ARG* 2.8 37.7 + - + +
512D VAL* 1.3 88.5 - - - +
514D GLN* 1.3 65.8 + - + +
524D LEU 4.2 2.7 - - - -
525D ALA* 3.4 6.1 - - - +
526D TRP* 2.8 48.1 + - - +
545D TYR* 5.4 0.7 - - - -
553D ILE* 3.8 31.6 - - - -
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Residues in contact with GLN 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510D ASN* 2.6 45.0 + - - +
513D CYS* 1.3 88.2 - - + +
515D LEU* 1.3 68.9 + - + +
516D GLY 3.5 2.6 + - - -
524D LEU 5.2 2.6 - - - -
525D ALA* 5.0 8.6 - - + +
526D TRP 5.6 0.7 - - - +
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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
------------------------------------------------------------
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