Contacts of the helix formed by residues 490 - 499 (chain A) in PDB entry 4I2C
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 SER 490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A ALA* 3.6 16.6 - - - +
488A ALA* 3.5 1.1 - - - +
489A GLU* 1.3 80.9 - - - +
491A GLU* 1.3 64.3 + - - +
492A GLU* 3.5 18.5 + - - +
493A GLU* 3.4 33.8 + - - +
494A ILE* 3.5 9.5 + - - +
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Residues in contact with GLU 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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335A ARG* 3.1 35.9 + - - -
444A ALA* 4.1 16.5 - - - +
447A LEU* 3.7 14.3 - - + +
448A LEU* 3.2 24.1 + - + +
490A SER* 1.3 70.3 - - - +
492A GLU* 1.4 61.9 + - - +
494A ILE* 2.9 26.8 + - - +
495A PHE* 3.0 22.9 + - + -
502A TYR* 3.3 16.8 + - + +
508A ARG* 2.8 37.7 + - - +
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Residues in contact with GLU 492 (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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490A SER* 3.5 21.3 - - - +
491A GLU* 1.4 79.5 + - - +
493A GLU* 1.4 57.0 + - + +
495A PHE* 3.3 3.6 + - - +
496A ALA* 2.9 28.7 + - - +
502A TYR* 3.7 51.6 + - + +
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Residues in contact with GLU 493 (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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487A GLU 4.4 2.7 - - - +
488A ALA* 3.4 12.6 - - + -
489A GLU* 2.8 39.8 + - - +
490A SER* 3.4 21.1 + - - +
491A GLU 3.3 0.4 - - - -
492A GLU* 1.4 74.4 - - + +
494A ILE* 1.4 59.4 + - - +
496A ALA* 3.4 7.9 + - - +
497A HIS* 2.9 39.3 + - + +
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Residues in contact with ILE 494 (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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444A ALA* 3.4 41.1 - - + +
445A PHE* 3.6 20.6 - - + +
448A LEU* 3.7 30.5 - - + -
472A LEU* 4.1 17.9 - - + -
477A LEU* 4.5 7.9 - - + -
488A ALA* 3.5 19.1 - - + -
490A SER 3.5 4.2 + - - +
491A GLU* 2.9 10.5 + - - +
493A GLU* 1.4 71.7 - - - +
495A PHE* 1.3 66.7 + - + +
497A HIS* 3.2 9.9 + - - +
498A LEU* 3.1 32.8 + - + +
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Residues in contact with PHE 495 (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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155A CYS 4.6 0.4 - - - -
448A LEU* 3.7 25.4 - - + -
456A PHE* 3.8 28.9 - + - -
460A LEU* 4.7 4.9 - - + -
491A GLU* 3.0 25.1 + - + -
492A GLU 3.6 6.7 - - - +
494A ILE* 1.3 77.7 - - + +
496A ALA* 1.4 60.3 + - - +
498A LEU* 3.1 8.1 + - - +
499A GLY 3.1 4.5 + - - -
500A LEU* 3.0 57.1 + - + +
501A ASP 3.5 16.2 - - - -
502A TYR* 3.5 30.3 - + + -
503A ILE* 3.7 33.7 - - + -
508A ARG* 3.9 5.2 - - - -
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Residues in contact with ALA 496 (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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492A GLU 2.9 17.8 + - - +
493A GLU* 3.7 9.0 - - - +
495A PHE* 1.4 75.8 - - - +
497A HIS* 1.4 61.5 + - - +
499A GLY* 3.2 13.5 + - - +
500A LEU 4.2 4.4 + - - +
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Residues in contact with HIS 497 (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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445A PHE* 5.9 0.2 - + - -
468A ARG* 5.2 0.5 - - - -
470A MET* 3.4 22.0 - - - +
477A LEU* 3.6 19.7 - - + -
486A LEU* 3.9 39.3 - - + +
487A GLU 2.7 31.5 + - - -
488A ALA* 4.6 2.5 - - + -
493A GLU* 2.9 30.9 + - - +
494A ILE* 3.2 9.4 + - - +
496A ALA* 1.4 75.6 - - - +
498A LEU* 1.3 58.6 + - - +
499A GLY 3.3 0.7 + - - -
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Residues in contact with LEU 498 (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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460A LEU* 4.0 19.1 - - + +
463A TYR* 3.3 12.8 - - + -
464A ALA* 3.7 31.6 - - + +
468A ARG* 3.3 27.3 + - + -
470A MET* 4.0 18.2 - - - -
472A LEU* 4.2 9.0 - - + -
477A LEU* 4.1 13.9 - - + -
494A ILE* 3.1 30.4 + - + +
495A PHE* 3.1 10.4 + - - +
497A HIS* 1.3 74.6 - - - +
499A GLY* 1.3 61.0 + - - +
500A LEU* 4.0 26.0 - - + -
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Residues in contact with GLY 499 (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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156A GLN* 5.6 1.2 + - - -
463A TYR* 3.9 8.7 + - - -
468A ARG* 4.8 12.4 + - - -
495A PHE 3.1 2.4 + - - -
496A ALA* 3.2 13.5 + - - -
497A HIS 3.3 1.4 + - - -
498A LEU* 1.3 80.4 - - - +
500A LEU* 1.3 58.6 + - - +
501A ASP 4.3 0.5 + - - -
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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