Contacts of the helix formed by residues 497 - 514 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E HIS* 3.9 16.1 - - + +
483E ARG* 3.7 46.2 - - + +
486E GLU* 4.5 2.1 + - - +
494E THR 3.8 3.0 + - - +
495E SER 3.0 1.4 + - - -
496E GLY* 1.3 73.8 - - - +
498E ALA* 1.3 66.2 + - - +
499E ASN 3.2 2.9 - - - -
500E ASP* 3.0 12.2 + - + +
501E ILE* 2.9 27.6 + - + +
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Residues in contact with ALA 498 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483E ARG* 5.4 0.4 - - - +
494E THR 5.2 0.2 + - - -
495E SER 3.0 17.8 + - - +
496E GLY 3.2 1.2 - - - -
497E ALA* 1.3 77.3 - - - +
499E ASN* 1.3 57.3 + - - +
501E ILE* 3.2 8.0 + - - +
502E GLU* 3.0 26.9 + - - +
514F GLN* 3.8 15.2 - - + +
515F LEU* 3.7 24.2 - - + +
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Residues in contact with ASN 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496E GLY 3.7 16.1 + - - +
498E ALA* 1.3 73.6 - - - +
500E ASP* 1.3 106.1 + - - +
502E GLU* 3.5 11.0 + - - +
503E ARG* 3.1 22.9 + - - +
1603E ZN 4.5 2.2 - - - -
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Residues in contact with ASP 500 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E HIS* 3.0 10.9 + - - -
427E HIS* 2.8 17.4 + - - -
479E LEU* 3.3 28.1 - - + +
480E LEU* 5.2 3.1 - - + -
482E GLY* 4.8 0.5 - - - -
483E ARG* 5.1 0.7 + - + -
497E ALA* 3.0 12.4 + - + +
499E ASN* 1.3 102.4 + - - +
501E ILE* 1.3 57.6 + - + +
503E ARG* 3.3 5.1 + - - +
504E ALA* 2.9 30.1 + - - +
1603E ZN 2.0 37.5 - - - -
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Residues in contact with ILE 501 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480E LEU* 4.9 6.5 - - + -
483E ARG* 3.9 17.9 - - + +
497E ALA* 2.9 21.9 + - + +
498E ALA* 3.3 7.4 - - - +
500E ASP* 1.3 75.7 - - - +
502E GLU* 1.3 67.5 + - - +
504E ALA* 3.1 5.9 + - - +
505E THR* 2.8 27.9 + - - -
514F GLN 4.2 6.5 - - - +
515F LEU 3.9 9.9 - - - +
516F GLY* 3.9 28.0 - - - +
523F PRO* 3.7 17.2 - - + +
524F LEU* 3.4 12.1 - - - -
525F ALA* 3.2 32.5 - - + +
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Residues in contact with GLU 502 (chain E).
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 3.0 15.5 + - - +
499E ASN* 3.8 10.6 - - - +
501E ILE* 1.3 76.3 - - - +
503E ARG* 1.3 63.2 + - - +
505E THR* 3.3 2.6 + - - -
506E GLU* 2.9 48.4 + - + +
514F GLN* 5.9 1.7 + - - -
525F ALA* 3.8 22.4 - - + -
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Residues in contact with ARG 503 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475E LYS* 4.0 21.5 - - - +
479E LEU* 3.6 26.2 - - + -
499E ASN 3.1 15.1 + - - +
500E ASP* 3.7 2.2 - - - +
501E ILE 3.0 0.6 - - - -
502E GLU* 1.3 77.2 - - - +
504E ALA* 1.3 67.1 + - - +
506E GLU* 2.8 52.6 + - - +
507E ILE* 3.0 23.7 + - - +
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Residues in contact with ALA 504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476E LEU* 3.6 29.8 - - + +
479E LEU* 3.6 12.0 - - + +
480E LEU* 4.0 24.9 - - + -
500E ASP 2.9 17.2 + - - +
501E ILE* 3.1 3.8 + - - +
503E ARG* 1.3 75.4 - - - +
505E THR* 1.3 63.5 + - - +
507E ILE* 3.1 6.5 + - - +
508E ALA* 3.0 20.1 + - - +
561E VAL* 4.6 6.7 - - + -
523F PRO 5.5 0.2 - - - +
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Residues in contact with THR 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501E ILE* 2.8 19.2 + - - +
502E GLU 3.5 4.7 - - - -
504E ALA* 1.3 76.6 - - - +
506E GLU* 1.3 63.9 + - + +
508E ALA* 3.3 6.9 + - - +
509E ARG* 2.9 42.3 + - + +
557E VAL* 4.6 2.9 - - + -
561E VAL* 4.5 3.9 - - - +
523F PRO 4.5 1.0 + - - -
524F LEU* 3.5 23.6 - - + +
525F ALA* 3.1 41.7 + - + +
526F TRP* 6.2 2.0 - - + -
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Residues in contact with GLU 506 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502E GLU* 2.9 40.9 + - + +
503E ARG* 2.8 39.3 + - - +
505E THR* 1.3 75.9 - - + +
507E ILE* 1.3 68.5 + - - +
509E ARG* 3.3 7.6 + - - +
510E ASN* 3.1 21.7 + - - +
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Residues in contact with ILE 507 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472E LEU* 4.3 19.9 - - + +
475E LYS* 3.6 40.4 - - + +
476E LEU* 3.8 26.9 - - + +
479E LEU* 4.1 13.9 - - + -
503E ARG* 3.0 32.9 + - - +
504E ALA 3.5 5.8 - - - +
506E GLU* 1.3 75.1 - - - +
508E ALA* 1.3 57.8 + - - +
510E ASN* 2.9 22.9 + - - +
511E MET* 3.0 23.1 + - + +
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Residues in contact with ALA 508 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476E LEU* 4.8 1.6 - - + -
504E ALA 3.0 13.2 + - - +
505E THR 3.6 7.0 - - - +
507E ILE* 1.3 73.5 - - - +
509E ARG* 1.3 66.9 + - - +
510E ASN 2.9 1.9 + - - -
511E MET* 3.3 11.7 + - - +
512E VAL* 3.3 27.2 + - - +
557E VAL* 4.1 14.6 - - + +
560E ILE* 4.3 14.8 - - + -
561E VAL* 3.8 22.9 - - + -
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Residues in contact with ARG 509 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E THR* 2.9 40.3 + - + +
506E GLU* 4.0 6.3 - - - +
508E ALA* 1.3 73.6 - - - +
510E ASN* 1.3 56.9 + - - +
512E VAL* 3.3 0.6 + - - -
513E CYS* 2.8 41.8 + - - +
514E GLN* 5.5 0.2 - - - -
545E TYR* 4.3 13.5 + - - -
553E ILE* 3.8 18.1 - - - +
554E ASP* 3.3 24.2 + - - -
557E VAL* 3.9 23.5 - - + +
526F TRP* 4.6 12.1 - - - -
544F ASN* 3.4 47.2 + - - +
545F TYR* 5.1 0.2 - - - +
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Residues in contact with ASN 510 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472E LEU* 6.3 0.4 - - + -
506E GLU 3.1 12.0 + - - +
507E ILE* 2.9 15.7 + - - +
508E ALA 2.9 0.2 - - - -
509E ARG* 1.3 76.5 - - - +
511E MET* 1.3 64.0 + - - +
512E VAL 3.0 1.1 - - - -
513E CYS 4.5 0.2 - - - +
514E GLN* 3.0 57.0 + - - +
515E LEU* 3.1 32.4 + - + +
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Residues in contact with MET 511 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469E ARG* 3.4 48.2 - - + +
472E LEU* 3.8 30.5 - - + -
473E LEU* 3.9 16.2 - - + -
476E LEU* 3.9 27.6 - - - -
507E ILE* 3.0 17.1 + - - +
508E ALA* 3.7 7.9 - - - +
510E ASN* 1.3 79.7 - - - +
512E VAL* 1.3 66.2 + - + +
515E LEU* 3.5 9.0 + - - -
516E GLY 3.3 5.9 + - - -
517E MET* 2.9 36.4 + - + +
560E ILE* 4.6 10.3 - - + -
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Residues in contact with VAL 512 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508E ALA 3.3 18.1 + - - +
509E ARG 3.9 2.7 - - - +
510E ASN 3.0 0.4 - - - -
511E MET* 1.3 82.6 - - + +
513E CYS* 1.3 67.4 + - - +
514E GLN 3.6 0.2 - - - -
516E GLY* 4.4 6.8 + - - -
518E SER* 3.8 22.6 + - - -
521E LEU* 3.3 32.9 - - + +
522E GLY 4.9 1.2 - - - +
524E LEU 4.4 3.3 - - - +
526E TRP* 3.9 12.1 + - - -
553E ILE* 4.4 6.5 - - + +
556E GLU* 4.2 13.2 - - + -
557E VAL* 4.4 6.3 - - + -
560E ILE* 3.5 27.6 - - + -
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Residues in contact with CYS 513 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509E ARG* 2.8 28.1 + - - +
512E VAL* 1.3 79.3 - - - +
514E GLN* 1.3 71.0 + - - +
524E LEU 4.2 2.7 - - - -
525E ALA* 3.4 6.2 - - - +
526E TRP* 3.0 46.6 + - + +
545E TYR* 5.3 1.8 - - - -
553E ILE* 3.7 44.2 - - - -
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Residues in contact with GLN 514 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498D ALA* 3.9 22.1 - - + +
501D ILE* 4.0 14.2 - - - +
509E ARG 5.5 0.2 - - - -
510E ASN* 3.0 45.3 + - - +
513E CYS* 1.3 90.1 - - + +
515E LEU* 1.3 65.0 + - + +
516E GLY 3.3 4.8 + - - -
524E LEU 5.0 0.2 - - - -
525E ALA* 5.1 4.8 - - + +
526E TRP 5.6 0.4 - - - +
527E GLY 6.5 0.2 - - - -
528E LYS* 4.7 27.2 - - + +
542E LEU* 6.1 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