Contacts of the helix formed by residues 500 - 508 (chain J) in PDB entry 1HVU
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 GLN 500 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499J SER* 1.3 71.3 - - - +
501J TYR* 1.3 56.2 + - - +
503J LEU* 3.5 9.3 - - - +
504J GLY* 2.7 29.8 + - - -
535J TRP* 5.9 2.9 - - - +
420K PRO* 6.5 0.9 - - + -
421K PRO* 6.5 1.1 - - + -
6L A 5.0 9.7 + - - +
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Residues in contact with TYR 501 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475J GLN* 5.2 16.8 - - + -
478J GLU* 6.3 0.7 - - + -
499J SER* 4.9 6.5 - - - -
500J GLN* 1.3 74.6 - - - +
502J ALA* 1.3 67.5 + - - +
504J GLY* 3.1 3.8 + - - -
505J ILE* 3.0 21.5 + - - +
6L A 5.1 17.1 + - - +
7L U 5.6 2.7 - - - +
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Residues in contact with ALA 502 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475J GLN 5.6 0.9 - - - +
478J GLU* 4.3 25.1 - - + +
479J LEU* 4.7 11.0 - - + -
482J ILE* 5.4 6.5 - - + -
497J THR* 5.6 4.9 - - - -
499J SER* 3.8 12.1 + - - +
501J TYR* 1.3 77.2 - - - +
503J LEU* 1.3 67.2 + - - +
505J ILE* 3.3 8.1 + - - +
506J ILE* 3.1 23.8 + - - +
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Residues in contact with LEU 503 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497J THR* 5.7 3.7 - - - -
499J SER 3.3 17.9 + - - +
500J GLN* 3.5 9.9 - - - +
501J TYR 3.2 0.6 - - - -
502J ALA* 1.3 79.4 - - - +
504J GLY* 1.3 52.5 + - - +
506J ILE* 3.3 4.7 + - - +
507J GLN* 2.7 37.6 + - - +
533J LEU* 6.0 5.6 - - + -
534J ALA 5.9 1.3 - - - +
535J TRP* 5.0 13.7 - - + -
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Residues in contact with GLY 504 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500J GLN 2.7 21.9 + - - -
501J TYR 3.1 1.5 + - - -
503J LEU* 1.3 70.6 - - - +
505J ILE* 1.3 68.0 + - - +
507J GLN* 3.0 8.0 + - - +
508J ALA* 3.0 22.4 + - - +
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Residues in contact with ILE 505 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361J HIS* 5.5 10.2 - - + +
501J TYR 3.0 12.5 + - - +
502J ALA* 3.3 10.3 + - - +
504J GLY* 1.3 76.4 - - - +
506J ILE* 1.3 63.1 + - - +
508J ALA* 3.2 17.6 + - - +
509J GLN 3.9 2.3 + - - -
510J PRO* 4.3 11.7 - - - +
518J VAL* 6.0 6.1 - - + -
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Residues in contact with ILE 506 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502J ALA 3.1 13.6 + - - +
503J LEU* 3.7 4.0 - - - +
505J ILE* 1.3 75.6 - - - +
507J GLN* 1.3 56.1 + - - +
508J ALA 3.0 2.2 - - - -
509J GLN* 2.8 27.7 + - - -
510J PRO* 5.5 2.5 - - - -
533J LEU* 5.6 10.1 - - + -
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Residues in contact with GLN 507 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503J LEU* 2.7 22.5 + - + +
504J GLY* 3.0 10.5 + - - +
506J ILE* 1.3 72.2 - - - +
508J ALA* 1.3 57.7 + - - +
509J GLN* 3.1 7.5 + - - +
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Residues in contact with ALA 508 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361J HIS* 5.8 5.6 - - + +
362J THR 5.9 0.2 - - - -
363J ASN* 5.0 6.4 - - - +
504J GLY 3.0 10.3 + - - +
505J ILE* 3.4 13.5 - - - +
506J ILE 3.0 1.2 + - - -
507J GLN* 1.3 74.9 - - - +
509J GLN* 1.3 69.1 + - - +
510J PRO* 3.4 4.0 - - + +
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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