Contacts of the helix formed by residues 508 - 517 (chain B) in PDB entry 1NRV
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 ASP 508 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429B ILE* 3.3 36.4 - - + +
430B HIS* 5.9 0.7 - - - +
497B PHE* 4.0 14.1 - - + -
506B PHE* 3.2 9.8 - - - +
507B SER* 1.3 97.7 + - - +
509B LEU* 1.3 65.2 + - - +
510B ILE* 3.0 14.4 + - - +
511B GLN* 2.9 30.5 + - - +
512B LEU* 3.2 16.8 + - - +
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Residues in contact with LEU 509 (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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430B HIS* 3.6 39.2 + - + +
435B TRP* 3.8 15.0 - - + -
436B PHE* 4.1 8.7 - - + -
461B LEU* 4.1 10.1 - - + -
471B PHE* 3.7 35.9 - - + -
486B ILE* 3.9 40.2 - - + -
497B PHE* 4.9 5.8 - - + -
508B ASP* 1.3 74.2 - - - +
510B ILE* 1.3 59.5 + - - +
512B LEU* 3.3 8.0 + - + +
513B VAL* 2.9 35.0 + - - +
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Residues in contact with ILE 510 (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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429B ILE* 3.7 35.7 - - + +
430B HIS* 4.5 5.8 - - + -
433B GLN* 3.7 24.5 - - + +
435B TRP* 3.9 24.5 - - + -
508B ASP* 3.0 8.9 + - - +
509B LEU* 1.3 73.9 - - - +
511B GLN* 1.3 66.9 + - - +
513B VAL* 3.3 1.6 + - - +
514B ASP* 2.9 45.5 + - - +
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Residues in contact with GLN 511 (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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511A GLN* 5.1 6.4 + - + -
514A ASP* 3.2 44.9 + - + +
515A PHE* 3.7 9.5 - - + +
518A LEU* 3.5 8.4 - - - +
505B LYS 5.2 0.2 + - - -
506B PHE* 3.5 18.2 - - + -
507B SER* 2.8 42.2 + - - +
508B ASP* 2.9 18.1 + - - +
510B ILE* 1.3 78.3 - - - +
512B LEU* 1.3 63.1 + - - +
514B ASP* 3.4 7.3 + - - +
515B PHE* 3.0 23.3 + - + +
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B LEU* 4.7 3.8 - - + -
473B LEU* 5.4 2.5 - - + -
486B ILE* 3.9 42.6 - - + -
497B PHE* 4.7 6.5 - - + +
498B SER* 4.9 0.7 - - - -
499B LEU* 4.3 14.6 - - + -
506B PHE* 3.7 36.3 - - + -
508B ASP 3.2 11.5 + - - +
509B LEU* 3.5 11.2 - - + +
510B ILE 3.2 0.6 - - - -
511B GLN* 1.3 79.1 - - - +
513B VAL* 1.3 73.9 + - + +
515B PHE* 3.2 2.4 + - - +
516B TYR* 3.0 49.6 + - + -
527B LEU* 5.3 3.8 - - + -
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Residues in contact with VAL 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B TRP* 3.7 41.3 - - + +
459B PHE* 4.1 17.5 - - + -
461B LEU* 3.9 27.6 - - + -
509B LEU 2.9 23.7 + - - +
510B ILE 3.9 3.4 - - - +
512B LEU* 1.3 74.2 - - + +
514B ASP* 1.3 65.9 + - - +
515B PHE 3.2 0.2 + - - -
516B TYR 3.3 1.6 + - - -
517B GLN* 3.0 47.1 + - + +
527B LEU* 4.1 9.9 - - + +
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Residues in contact with ASP 514 (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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511A GLN* 3.2 25.2 + - + +
435B TRP* 5.6 2.1 + - - -
510B ILE* 2.9 36.3 + - - +
511B GLN* 3.7 6.5 - - - +
513B VAL* 1.3 78.8 - - - +
515B PHE* 1.3 64.3 + - - +
517B GLN* 3.6 22.9 + - - +
518B LEU* 3.7 12.8 - - - +
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Residues in contact with PHE 515 (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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504A THR* 3.8 17.9 - - + -
506A PHE* 4.1 10.5 - + - -
511A GLN* 3.7 7.4 - - + +
515A PHE* 3.3 37.9 - + - -
504B THR* 4.2 7.0 - - + -
506B PHE* 3.4 35.4 - + + -
511B GLN* 3.0 7.9 + - + +
512B LEU 3.5 3.8 - - - +
513B VAL 3.1 0.2 - - - -
514B ASP* 1.3 78.6 - - - +
516B TYR* 1.3 83.5 + + - +
517B GLN 3.1 0.2 - - - -
518B LEU 3.0 5.2 + - - -
519B ASN* 2.9 67.8 + - + +
521B GLY* 5.4 3.4 - - - -
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Residues in contact with TYR 516 (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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499B LEU* 3.5 34.6 + - + +
500B ASP* 4.1 5.4 + - - -
504B THR* 3.9 21.3 + - - -
506B PHE* 3.7 21.2 - + - -
512B LEU* 3.0 40.8 + - + +
513B VAL 3.3 0.4 + - - -
515B PHE* 1.3 92.7 - + - +
517B GLN* 1.3 62.3 + - - +
518B LEU 3.2 0.4 - - - -
519B ASN 3.2 23.9 - - - +
520B LYS 3.7 11.7 - - - -
521B GLY* 4.2 8.6 - - - -
522B VAL* 4.7 1.9 + - - +
523B LEU* 3.5 21.8 - - + -
526B LYS* 3.5 4.3 - - - -
527B LEU* 2.9 44.7 + - + -
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Residues in contact with GLN 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B TRP* 5.7 2.6 - - - -
459B PHE* 4.5 10.3 - - - -
513B VAL* 3.0 35.3 + - + +
514B ASP* 3.6 26.8 - - - +
515B PHE 3.1 0.4 - - - -
516B TYR* 1.3 79.0 - - - +
518B LEU* 1.3 68.5 + - + +
526B LYS* 3.7 15.2 + - - +
527B LEU* 3.4 32.4 + - + +
528B LYS 4.8 8.1 + - - -
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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