Contacts of the helix formed by residues 483 - 492 (chain I) in PDB entry 6NZD
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 PRO 483 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181H TYR* 4.6 15.3 - - + -
268H ARG* 5.1 11.7 - - - +
482I ASN* 1.3 83.3 - - + +
484I LEU* 1.3 62.5 + - + +
486I ALA* 3.5 8.3 - - + +
487I GLN* 2.9 28.2 + - - +
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Residues in contact with LEU 484 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184H ASN* 3.4 29.8 - - - +
335I SER 5.3 4.7 - - - +
482I ASN* 3.3 3.3 - - + -
483I PRO* 1.3 79.3 - - + +
485I TRP* 1.3 60.1 + - + +
487I GLN* 3.4 6.5 + - - +
488I LEU* 2.9 28.8 + - - +
943I PHE* 4.4 16.4 - - + -
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Residues in contact with TRP 485 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178H ASP* 5.6 6.1 + - - -
180H ILE* 3.4 50.8 - - + +
181H TYR 5.6 1.3 - - - -
184H ASN* 6.0 0.7 - - - -
337I PHE* 6.0 3.6 - + + -
482I ASN* 3.4 26.9 + - + +
484I LEU* 1.3 77.6 - - + +
486I ALA* 1.3 60.5 + - - +
488I LEU* 3.8 18.5 - - + +
489I GLY* 2.9 26.0 + - - -
986I VAL 3.6 19.1 - - - -
987I LEU* 3.6 30.1 - - + -
988I ASP* 4.2 18.4 - - + +
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Residues in contact with ALA 486 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482I ASN 2.9 18.0 + - - +
483I PRO* 3.5 10.3 - - + +
484I LEU 3.2 0.2 - - - -
485I TRP* 1.3 77.4 - - - +
487I GLN* 1.3 57.7 + - - +
489I GLY* 3.4 1.1 + - - -
490I ASP* 2.9 29.8 + - - +
527I CYS 5.1 0.9 - - - -
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Residues in contact with GLN 487 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483I PRO 2.9 17.3 + - - +
484I LEU* 3.8 6.1 - - - +
486I ALA* 1.3 75.7 - - - +
488I LEU* 1.3 57.8 + - - +
490I ASP* 3.8 1.0 - - - +
491I LEU* 2.9 30.5 + - - +
527I CYS* 4.1 25.8 - - + +
528I SER 5.9 2.0 - - - -
943I PHE* 4.5 21.3 - - + -
944I GLY* 5.3 3.4 - - - +
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Residues in contact with LEU 488 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484I LEU 2.9 17.0 + - - +
485I TRP* 3.8 24.0 - - + +
487I GLN* 1.3 77.3 - - - +
489I GLY* 1.3 55.8 + - - +
491I LEU* 3.3 3.8 + - - +
492I TYR* 2.9 42.1 + - + +
943I PHE* 3.6 27.3 - - + -
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Residues in contact with GLY 489 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447I ALA* 5.2 0.7 - - - +
485I TRP* 2.9 17.1 + - - -
486I ALA 3.8 1.8 - - - -
488I LEU* 1.3 76.7 - - - +
490I ASP* 1.3 58.0 + - - +
492I TYR* 3.1 18.3 - - - +
494I ALA* 3.5 32.2 + - - +
495I ILE* 4.4 4.9 + - - +
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Residues in contact with ASP 490 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445I HIS* 5.9 1.6 - - - +
447I ALA* 3.3 21.1 - - + +
486I ALA 2.9 17.7 + - - +
487I GLN 3.8 0.9 - - - +
489I GLY* 1.3 77.3 - - - +
491I LEU* 1.3 63.7 + - - +
492I TYR 3.2 6.8 - - - +
526I ARG 2.9 26.3 + - - +
527I CYS* 3.7 20.0 - - - +
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Residues in contact with LEU 491 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445I HIS* 4.3 22.2 + - - -
487I GLN 2.9 18.7 + - - +
488I LEU* 3.3 5.4 + - - +
490I ASP* 1.3 76.7 - - - +
492I TYR* 1.3 71.3 + - + +
502I THR 4.5 0.7 - - - +
525I LEU* 6.0 2.9 - - - -
526I ARG 3.7 7.1 + - - +
527I CYS* 4.7 7.6 - - + +
943I PHE* 5.7 7.0 - - + +
944I GLY* 6.2 2.2 - - - -
947I LEU* 6.4 2.2 - - + -
960I VAL* 4.6 14.9 - - + +
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Residues in contact with TYR 492 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338I PRO* 5.8 1.6 - - - +
445I HIS* 5.1 5.9 - - - -
446I LEU 5.4 0.3 - - - +
447I ALA* 4.7 4.5 - - - +
488I LEU* 2.9 24.9 + - + +
489I GLY* 3.1 13.2 - - - +
490I ASP 3.2 10.6 - - - +
491I LEU* 1.3 86.6 - - + +
493I GLY* 1.3 59.0 + - - +
494I ALA* 3.3 9.4 + - + +
500I ARG 4.6 3.6 - - - +
501I LEU* 3.3 31.2 - - + +
502I THR* 4.6 6.7 - - - -
503I ARG* 5.5 4.0 - - + -
943I PHE* 6.5 0.9 - + - -
958I ASP* 4.4 24.4 - - - +
959I LEU* 4.6 2.7 + - - -
960I VAL* 4.9 20.2 - - + -
986I VAL* 6.0 5.4 - - + -
987I LEU* 5.8 8.5 - - + -
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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