Contacts of the strand formed by residues 480 - 488 (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 LYS 480 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475B LEU 3.7 0.7 - - - +
476B CYS* 3.5 1.2 - - - -
477B HIS 2.9 31.8 + - - +
478B HIS* 3.3 16.2 - - + +
479B GLN* 1.3 90.4 - - - +
481B ILE* 1.3 66.5 + - - +
482B LYS* 3.3 26.8 + - - +
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Residues in contact with ILE 481 (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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442B ARG* 5.7 2.1 + - - -
446B HIS* 3.5 39.6 + - + +
449B ILE* 3.4 24.5 - - + -
450B LYS* 4.2 14.6 - - + +
454B LEU* 3.4 31.4 - - + -
474B THR* 3.5 30.7 - - + -
475B LEU 3.6 3.4 - - - +
476B CYS* 3.8 9.4 - - + -
479B GLN 4.2 1.3 + - - +
480B LYS* 1.3 72.8 - - - +
482B LYS* 1.3 69.6 + - - +
483B ASN* 4.4 3.0 - - - +
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Residues in contact with LYS 482 (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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473B LEU 3.6 1.0 - - - +
474B THR* 3.5 3.5 - - - +
475B LEU 2.8 39.9 + - - +
477B HIS* 4.8 4.4 + - + +
480B LYS* 3.3 36.9 - - - +
481B ILE* 1.3 78.4 + - - +
483B ASN* 1.3 63.2 + - - +
484B PHE* 3.6 26.0 - - + -
524B PRO* 4.5 21.1 - - + -
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Residues in contact with ASN 483 (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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442B ARG* 3.5 18.2 + - - +
446B HIS* 3.1 29.9 + - - -
462B ARG* 3.2 20.5 - - - +
472B VAL* 3.8 8.8 - - + +
473B LEU 3.4 1.6 - - - -
474B THR* 2.9 34.2 + - - +
481B ILE 4.7 0.9 - - - +
482B LYS* 1.3 77.8 - - - +
484B PHE* 1.3 66.9 + - - +
485B GLN* 4.2 9.9 + - - +
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Residues in contact with PHE 484 (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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472B VAL* 3.5 0.7 - - - +
473B LEU* 2.8 58.7 + - + +
475B LEU* 4.5 6.3 - - + -
482B LYS* 3.6 31.4 - - + -
483B ASN* 1.3 78.3 - - - +
485B GLN* 1.3 67.1 + - - +
486B ILE* 3.5 2.8 + - - +
499B LEU* 4.3 24.7 - - + +
522B VAL* 4.4 16.4 - - + -
523B LEU* 3.7 26.7 - - + -
524B PRO* 3.6 27.8 - - + -
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Residues in contact with GLN 485 (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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462B ARG* 5.3 1.2 - - - +
464B SER* 4.1 11.3 + - - -
466B SER* 4.8 5.6 + - - -
470B ALA* 5.3 2.6 - - - +
471B PHE 3.7 3.3 - - - +
472B VAL* 3.5 37.5 - - - +
483B ASN* 4.7 10.0 + - - +
484B PHE* 1.3 71.9 - - - +
486B ILE* 1.3 61.7 + - - +
487B LEU* 3.7 25.3 + - + +
498B SER 3.7 1.4 - - - +
499B LEU* 3.4 21.7 + - - +
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Residues in contact with ILE 486 (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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461B LEU* 3.8 29.4 - - + -
470B ALA* 3.4 6.1 - - - +
471B PHE* 2.8 43.7 + - + +
472B VAL 4.4 0.2 - - - -
473B LEU* 4.1 18.6 - - + +
484B PHE 3.9 7.9 - - - +
485B GLN* 1.3 73.0 - - - +
487B LEU* 1.3 60.9 + - - +
488B PRO* 4.3 0.2 - - - +
497B PHE* 3.8 30.1 - - + -
498B SER 3.5 7.0 - - - +
499B LEU* 4.1 15.0 - - + -
509B LEU* 3.9 15.5 - - + -
512B LEU* 3.9 21.8 - - + -
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Residues in contact with LEU 487 (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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467B ASN* 4.4 12.6 - - + +
470B ALA* 3.8 21.5 - - + -
485B GLN* 4.3 24.0 - - + +
486B ILE* 1.3 75.5 - - - +
488B PRO* 1.3 74.4 - - + +
489B CYS* 3.8 7.4 - - - -
497B PHE* 3.5 5.6 - - - -
498B SER 3.0 32.2 + - - +
501B ASP* 6.6 0.4 - - - -
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Residues in contact with PRO 488 (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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467B ASN* 5.1 4.7 - - - +
469B LYS* 3.5 45.1 - - + +
470B ALA* 4.3 4.5 - - + -
486B ILE 4.3 1.3 - - - +
487B LEU* 1.3 94.2 - - + +
489B CYS* 1.3 63.4 + - - +
495B THR* 3.9 19.7 - - + -
496B PHE 3.2 7.0 - - - +
497B PHE* 4.0 7.8 - - + -
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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