Contacts of the helix formed by residues 455 - 463 (chain A) in PDB entry 2IBI
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 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A LEU* 3.9 24.2 - - + -
454A THR* 1.3 70.9 - - - +
456A MET* 1.3 63.6 + - - +
458A CYS* 2.9 16.4 + - + +
459A MET* 3.0 19.0 + - + +
500A LEU* 4.0 10.5 - - + -
502A LEU* 4.3 10.8 - - + -
519A VAL* 3.6 9.9 - - + +
520A ASN 2.7 17.2 + - - +
521A PHE* 3.8 13.2 - - + -
522A PRO* 4.0 4.3 - - + -
526A LEU* 4.0 17.5 - - + -
594A LEU* 3.7 18.4 - - + -
596A TYR* 3.4 39.5 - - + +
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Residues in contact with MET 456 (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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454A THR* 3.2 8.1 + - - +
455A LEU* 1.3 76.3 - - - +
457A ASP* 1.3 56.7 + - - +
459A MET* 3.3 5.3 + - - +
460A ARG* 3.0 53.6 + - - +
526A LEU* 4.2 13.7 - - + -
527A ASP 3.6 25.1 - - - +
528A LEU* 4.1 9.6 - - - -
530A GLU* 3.4 27.8 - - + +
531A PHE* 3.6 23.7 - - + -
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Residues in contact with ASP 457 (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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446A ALA* 4.1 21.0 - - + +
448A ARG* 4.1 26.5 + - - +
452A GLU 3.9 5.4 - - - +
453A VAL* 3.7 8.0 - - - +
454A THR* 3.0 43.6 + - - +
456A MET* 1.3 75.1 - - - +
458A CYS* 1.3 57.8 + - - +
460A ARG* 3.1 26.9 + - - +
461A LEU* 3.2 25.8 + - - +
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Residues in contact with CYS 458 (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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443A LEU* 4.1 19.6 - - + +
444A PRO 3.4 25.2 - - - +
445A ILE* 4.0 8.3 - - - -
446A ALA 4.0 15.3 - - - +
453A VAL* 4.0 7.4 - - - -
454A THR 3.4 14.4 - - - -
455A LEU* 2.9 11.2 + - + +
457A ASP* 1.3 77.4 - - - +
459A MET* 1.3 60.0 + - - +
461A LEU* 3.4 4.5 + - - +
462A PHE* 3.1 27.5 + - - +
502A LEU* 5.6 2.5 - - + -
519A VAL* 4.0 21.5 - - - -
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Residues in contact with MET 459 (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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441A LEU* 4.6 10.5 - - + -
443A LEU* 4.1 25.7 - - + +
455A LEU* 3.0 34.5 + - + +
456A MET* 3.6 4.9 - - - +
458A CYS* 1.3 76.8 - - - +
460A ARG* 1.3 58.7 + - - +
462A PHE* 3.7 3.2 + - + +
463A THR* 2.8 33.8 + - + +
491A ILE* 5.5 3.6 - - + -
500A LEU* 4.0 21.5 - - + -
526A LEU* 5.0 1.3 - - + -
528A LEU* 3.7 27.8 - - + -
531A PHE* 3.5 35.7 - - + -
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Residues in contact with ARG 460 (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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448A ARG* 5.6 4.0 - - - +
454A THR* 4.5 1.2 + - - -
456A MET* 3.0 42.3 + - - +
457A ASP* 3.1 30.9 + - - +
459A MET* 1.3 73.0 - - - +
461A LEU* 1.3 60.1 + - - +
463A THR* 3.5 7.7 - - - -
464A LYS* 2.9 31.9 + - - +
530A GLU* 3.0 34.9 + - - +
531A PHE* 3.4 19.7 - - + -
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Residues in contact with LEU 461 (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 PRO* 3.9 16.8 - - + +
445A ILE 3.9 5.4 - - - +
446A ALA* 3.7 35.2 - - + +
447A LYS* 5.3 1.1 - - + +
448A ARG* 6.3 3.4 - - - -
457A ASP 3.2 17.0 + - - +
458A CYS 3.6 5.8 - - - +
459A MET 3.3 0.4 - - - -
460A ARG* 1.3 77.0 - - - +
462A PHE* 1.3 62.0 + - - +
464A LYS* 3.2 48.4 - - + +
6B LYS* 3.7 6.6 + - - -
9B THR 3.8 22.2 - - - +
10B GLY* 4.3 5.4 - - - +
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Residues in contact with PHE 462 (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 LEU* 3.9 20.4 - - + -
441A LEU* 3.8 27.1 - - + -
442A SER 3.7 25.8 - - - -
443A LEU* 3.6 18.8 - - + -
444A PRO* 4.0 9.0 - - + +
458A CYS 3.1 16.4 + - - +
459A MET* 3.7 4.5 - - + +
460A ARG 3.4 0.2 - - - -
461A LEU* 1.3 75.7 - - - +
463A THR* 1.3 69.5 + - + +
464A LYS 4.5 0.7 - - - +
489A PHE* 3.6 35.5 + + + -
491A ILE* 5.9 1.1 - - + -
6B LYS* 3.1 34.1 + - + +
68B HIS* 3.7 32.1 - + - -
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Residues in contact with THR 463 (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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459A MET* 2.8 26.9 + - + +
460A ARG* 3.5 6.6 - - - -
461A LEU 3.3 0.2 - - - -
462A PHE* 1.3 89.9 - - + +
464A LYS* 1.3 65.1 + - - +
488A LYS* 3.3 27.5 + - - +
489A PHE* 3.5 28.7 - - + +
490A SER* 4.8 3.6 - - - -
491A ILE* 5.3 5.8 - - + -
531A PHE* 3.3 35.1 - - + -
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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