Contacts of the helix formed by residues 489 - 494 (chain I) in PDB entry 2VKZ
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 LYS 489 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346I GLN* 5.9 3.8 - - - +
371I VAL* 4.0 22.7 - - + -
462I THR 3.3 10.7 + - - +
463I PHE* 3.4 43.2 - - + +
487I PRO* 3.9 11.1 + - + -
488I VAL* 1.3 69.4 - - - +
490I TRP* 1.3 64.0 + - - +
491I GLU 3.3 2.5 - - - -
492I THR* 3.0 30.0 + - + +
493I THR* 3.0 21.8 + - - +
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Residues in contact with TRP 490 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159I ILE* 3.5 14.8 - - + -
271I THR* 4.0 18.8 - - + -
272I GLY 3.6 20.6 - - - -
273I HIS* 3.6 25.4 - + + -
371I VAL 3.5 14.2 + - - +
372I ASN* 3.8 16.2 - - - +
488I VAL* 3.0 18.9 + - + +
489I LYS* 1.3 71.2 - - - +
491I GLU* 1.3 60.4 + - - +
493I THR* 3.0 31.0 - - + +
494I THR* 2.9 34.4 + - + +
496I PHE* 6.6 0.2 - + - -
512I LEU* 3.3 23.3 - - + +
515I LEU* 4.4 6.7 - - + -
516I THR* 2.7 40.7 - - + +
519I ASN* 3.6 23.8 - - - -
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Residues in contact with GLU 491 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371I VAL 4.3 3.6 + - - +
373I GLY* 3.5 22.9 - - - -
374I ALA* 3.8 6.7 + - - +
489I LYS 3.3 0.6 - - - -
490I TRP* 1.3 78.7 - - - +
492I THR* 1.3 64.4 + - + +
494I THR* 3.0 30.4 + - + +
495I GLN* 3.6 5.4 + - - +
519I ASN* 3.8 49.9 - - + +
520I LYS* 6.1 1.1 - - - -
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Residues in contact with THR 492 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463I PHE 3.7 13.7 + - - -
464I ASP 4.1 6.4 + - - +
465I GLY* 3.4 12.9 - - - -
489I LYS* 3.0 35.7 + - + +
491I GLU* 1.3 77.1 - - + +
493I THR* 1.3 60.0 + - - +
494I THR 3.2 0.7 - - - -
495I GLN* 3.5 33.7 + - - +
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Residues in contact with THR 493 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271I THR* 3.9 13.7 - - - +
460I TYR* 3.6 28.8 + - - +
461I ASP 3.0 23.2 + - - -
462I THR* 3.5 24.1 - - - +
465I GLY* 3.7 10.3 - - - -
488I VAL* 4.5 2.2 - - + -
489I LYS 3.0 13.4 + - - +
490I TRP* 3.0 42.0 - - + +
492I THR* 1.3 75.8 + - - +
494I THR* 1.3 56.4 + - - +
495I GLN* 3.3 4.8 + - - -
496I PHE* 4.3 1.0 - - - -
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Residues in contact with THR 494 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271I THR* 6.3 0.4 - - - -
490I TRP* 2.9 46.3 + - + +
491I GLU* 3.0 23.9 - - + +
493I THR* 1.3 76.7 - - - +
495I GLN* 1.3 60.7 + - - +
496I PHE* 3.3 26.5 + - - -
501I ILE* 4.7 1.9 - - - +
516I THR* 5.5 2.1 - - - -
519I ASN* 5.7 0.7 - - - +
520I LYS* 2.9 44.4 + - - -
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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