Contacts of the helix formed by residues 492 - 500 (chain B) in PDB entry 5M64
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 ASN 492 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490B LYS* 3.8 3.2 - - - -
491B ILE* 1.3 82.3 + - - +
493B PHE* 1.3 79.2 + - - +
494B TYR* 3.2 29.6 + - - +
495B ARG* 3.2 22.1 + - + +
496B PHE* 3.1 18.9 + - - +
722B GLY 2.5 30.9 + - - -
723B LYS* 4.2 2.0 - - - +
725B THR* 2.7 30.2 + - - +
727B GLY* 4.7 4.6 + - - +
728B THR 5.1 0.7 - - - -
729B PRO* 5.4 3.1 - - - -
767B ASN* 4.7 8.5 - - - +
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Residues in contact with PHE 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.8 24.0 - - + -
188B ASP* 4.6 0.2 - - - -
190B ILE* 3.6 24.5 - - + -
490B LYS* 5.1 0.7 - - - +
492B ASN* 1.3 77.6 + - - +
494B TYR* 1.3 63.8 + - + +
496B PHE* 3.1 11.3 + + + +
497B ILE* 3.1 45.6 + - + +
727B GLY 5.7 0.2 - - - -
728B THR 4.3 9.8 + - - +
729B PRO* 4.6 8.7 - - - +
760B TYR 4.9 0.2 - - - -
762B MET* 3.6 37.2 - - + -
765B PHE* 3.5 59.9 - + + -
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Residues in contact with TYR 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B ASN* 3.2 26.8 + - - +
493B PHE* 1.3 77.9 - - + +
495B ARG* 1.3 56.9 + - - +
497B ILE* 3.5 5.0 + - - +
498B SER* 2.9 32.2 + - - -
699B ILE* 4.3 20.1 - - + +
700B LEU* 3.5 39.4 - - + +
703B LEU* 3.7 28.4 - - + +
722B GLY* 3.6 4.9 - - - +
723B LYS* 5.0 1.8 - - - -
757B TYR* 4.4 2.9 - - - -
762B MET* 3.5 49.4 - - + +
767B ASN* 3.3 34.7 + - - -
1034B GLN* 5.1 5.4 - - - -
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Residues in contact with ARG 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ALA* 4.8 2.2 - - - +
489B GLU* 2.9 39.9 + - - +
490B LYS 5.1 0.8 - - - +
491B ILE* 3.4 23.2 - - - +
492B ASN* 3.2 21.1 + - + +
494B TYR* 1.3 77.0 - - - +
496B PHE* 1.3 57.2 + - - +
498B SER* 3.2 7.4 + - - -
499B HIS* 2.9 70.2 + - + +
723B LYS* 3.1 43.7 + - + +
724B GLN* 4.6 5.0 - - - +
7R C 5.3 7.5 + - - -
8R U 5.8 5.3 - - - -
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Residues in contact with PHE 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLU* 5.7 0.9 - - - -
190B ILE* 3.7 32.5 - - + -
191B GLY 5.1 0.2 - - - -
193B TYR* 3.6 29.2 - + - -
200B GLU* 6.0 1.3 - - + -
488B ALA* 4.6 19.7 - - + -
490B LYS* 3.6 41.7 - - + +
492B ASN 3.1 12.2 + - - +
493B PHE* 3.1 18.3 + + + +
495B ARG* 1.3 75.1 - - - +
497B ILE* 1.3 66.4 + - + +
499B HIS* 3.9 4.1 - - + +
500B PHE* 3.3 68.3 + + - -
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Residues in contact with ILE 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 5.2 7.9 - - + -
41B ALA* 5.2 12.8 - - + -
190B ILE* 4.9 10.3 - - + -
493B PHE* 3.1 55.6 + - + +
494B TYR* 4.2 4.5 - - + +
496B PHE* 1.3 82.9 - - + +
498B SER* 1.3 67.1 + - - +
500B PHE* 3.1 17.9 + - + +
501B ARG* 3.3 32.0 + - - +
699B ILE* 3.9 29.2 - - + -
762B MET* 6.1 1.6 - - + -
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Residues in contact with SER 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B TYR 2.9 22.8 + - - -
495B ARG* 3.2 12.0 + - - -
497B ILE* 1.3 78.9 - - - +
499B HIS* 1.3 66.6 + - - +
501B ARG* 3.4 12.0 + - - +
502B MET* 3.3 29.9 + - - +
532B HIS* 4.2 26.5 - - - -
544B HIS* 4.2 8.3 - - - +
699B ILE* 6.4 0.2 - - - -
700B LEU* 5.3 2.2 - - - -
723B LYS* 3.8 11.6 - - - +
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Residues in contact with HIS 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B HIS* 4.6 0.7 - - - -
202B LEU* 3.3 27.6 - - + +
486B VAL* 5.1 15.5 - - + +
487B VAL 4.8 4.5 - - - -
488B ALA* 3.6 29.8 + - + +
495B ARG* 2.9 62.9 + - - +
496B PHE* 3.9 5.6 - - + +
497B ILE 3.2 0.2 - - - -
498B SER* 1.3 83.2 + - - +
500B PHE* 1.3 63.9 + - + +
501B ARG 3.2 1.5 + - - -
502B MET* 3.5 34.8 + - + +
723B LYS* 5.6 7.0 + - + +
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Residues in contact with PHE 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA 5.0 5.7 - - - +
42B VAL* 3.5 30.0 - - + +
44B PRO* 5.9 1.9 - - - +
45B HIS* 3.0 32.2 + - + -
190B ILE* 3.6 8.5 - - + -
191B GLY 3.2 24.9 - - - -
192B GLY 4.1 2.9 - - - -
193B TYR* 3.5 15.5 - + + -
202B LEU* 3.6 37.0 - - + -
496B PHE* 3.3 57.5 + + - -
497B ILE* 3.1 13.0 + - + +
499B HIS* 1.3 78.0 - - + +
501B ARG* 1.3 59.5 + - - +
502B MET 3.8 0.2 - - - -
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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