Contacts of the helix formed by residues 480 - 491 (chain A) 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 LEU 480 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A LEU* 3.4 13.7 - - + +
477A THR 2.9 10.0 + - - +
479A LEU* 1.3 79.8 - - - +
481A GLY* 1.3 57.3 + - - +
482A GLY 3.3 3.4 - - - -
483A ARG* 3.4 12.3 + - + +
484A ALA* 2.9 28.4 + - - +
500A ASP* 4.8 4.3 - - + +
501A ILE* 4.9 16.2 - - + -
504A ALA* 4.0 21.8 - - + -
561A VAL* 3.6 24.9 - - + +
564A CYS* 3.9 7.0 - - + -
565A TYR* 3.4 49.9 - - + +
568A ALA* 4.5 2.0 - - + -
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Residues in contact with GLY 481 (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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426A GLY* 3.9 10.9 - - - -
430A VAL* 3.9 25.4 - - - -
477A THR 3.3 2.7 + - - -
478A ALA 3.0 12.5 + - - -
480A LEU* 1.3 76.8 - - - +
482A GLY* 1.3 66.4 + - - +
484A ALA* 3.4 7.3 - - - +
485A ALA* 2.8 27.0 + - - +
568A ALA* 4.4 0.4 - - - -
572A ILE* 4.5 0.9 - - - +
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Residues in contact with GLY 482 (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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423A HIS* 3.1 52.6 + - - -
427A HIS* 3.8 11.4 + - - +
480A LEU 3.3 0.8 - - - -
481A GLY* 1.3 77.9 - - - +
483A ARG* 1.3 60.4 + - - +
485A ALA* 3.2 3.6 + - - +
486A GLU* 3.2 22.5 + - - +
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Residues in contact with ARG 483 (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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423A HIS* 3.9 3.4 - - - -
479A LEU 5.4 0.2 + - - -
480A LEU* 3.4 15.0 + - + +
481A GLY 3.2 0.4 - - - -
482A GLY* 1.3 76.3 - - - +
484A ALA* 1.3 62.4 + - - +
486A GLU* 3.2 11.8 + - - +
487A GLU* 3.0 21.3 + - - +
493A VAL* 2.8 45.1 - - + +
494A THR 3.0 15.5 + - - -
495A SER* 5.1 1.0 - - - +
497A ALA* 3.8 23.9 - - + +
498A ALA 5.3 0.2 - - - +
500A ASP* 5.3 0.8 + - + -
501A ILE* 3.9 28.6 - - + +
565A TYR* 3.8 21.0 + - + +
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Residues in contact with ALA 484 (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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480A LEU 2.9 17.8 + - - +
481A GLY* 3.0 6.3 + - - +
483A ARG* 1.3 78.4 - - - +
485A ALA* 1.3 61.0 + - - +
487A GLU* 3.5 1.4 + - - +
488A VAL* 3.2 31.0 + - - +
565A TYR* 3.8 13.9 - - + -
568A ALA* 3.7 26.5 - - + -
569A LYS* 3.8 18.8 - - + +
572A ILE* 4.2 4.7 - - + -
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Residues in contact with ALA 485 (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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422A TYR* 3.6 29.0 - - + +
426A GLY* 4.1 2.2 - - - -
481A GLY 2.8 16.2 + - - +
482A GLY 3.7 2.9 - - - +
483A ARG 3.1 0.2 - - - -
484A ALA* 1.3 76.7 - - - +
486A GLU* 1.3 62.6 + - - +
489A VAL* 3.1 29.8 + - - +
490A PHE* 4.5 0.3 - - - -
572A ILE* 4.0 24.5 - - + -
579A LEU* 4.2 10.8 - - + -
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Residues in contact with GLU 486 (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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419A ILE* 3.7 21.9 - - + +
422A TYR* 5.7 0.4 - - + -
423A HIS* 2.7 36.3 + - + +
482A GLY 3.2 10.2 + - - +
483A ARG* 3.2 11.0 + - - +
485A ALA* 1.3 75.4 - - - +
487A GLU* 1.3 60.9 + - - +
490A PHE* 2.8 39.4 + - + +
492A ASP 3.2 17.8 - - - +
493A VAL* 4.0 5.8 - - + -
494A THR* 2.4 48.9 + - - +
496A GLY* 4.7 0.7 - - - -
497A ALA* 4.6 4.9 + - - +
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Residues in contact with GLU 487 (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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483A ARG 3.0 9.4 + - - +
484A ALA 3.9 3.4 - - - +
486A GLU* 1.3 78.0 - - - +
488A VAL* 1.3 57.7 + - - +
491A GLY* 2.7 38.8 + - - +
492A ASP 4.0 7.6 - - - -
493A VAL* 4.0 13.5 - - + +
565A TYR* 2.0 50.1 + - + +
569A LYS* 3.2 26.8 + - + +
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Residues in contact with VAL 488 (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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484A ALA 3.2 19.4 + - - +
485A ALA 4.2 0.4 - - - +
487A GLU* 1.3 79.1 - - - +
489A VAL* 1.3 63.9 + - + +
491A GLY 4.4 1.2 + - - -
569A LYS* 4.1 27.1 - - + +
572A ILE* 4.0 19.3 - - + -
573A ARG* 3.9 36.6 - - + +
576A ARG* 3.9 19.8 + - - +
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Residues in contact with VAL 489 (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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418A ARG* 5.1 4.9 - - - +
422A TYR* 3.6 35.0 - - + +
485A ALA 3.1 18.7 + - - +
488A VAL* 1.3 85.2 - - + +
490A PHE* 1.3 86.7 + - + +
576A ARG* 3.7 42.0 + - - +
579A LEU* 4.3 6.7 - - + -
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Residues in contact with PHE 490 (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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418A ARG* 4.2 27.1 - - + -
419A ILE* 3.9 39.5 - - + -
422A TYR* 4.0 35.7 - + + -
486A GLU* 2.8 30.7 + - + +
489A VAL* 1.3 91.9 - - + +
491A GLY* 1.3 53.7 + - - +
492A ASP* 2.7 28.0 + - + +
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Residues in contact with GLY 491 (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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486A GLU 3.4 0.4 + - - -
487A GLU* 2.7 37.5 + - - +
488A VAL 4.4 1.0 + - - -
489A VAL 3.7 1.0 - - - -
490A PHE* 1.3 69.1 - - - +
492A ASP* 1.3 59.8 + - - -
493A VAL* 4.1 1.6 + - - +
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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