Contacts of the strand formed by residues 458 - 463 (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 LEU 458 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449B ILE* 3.4 43.3 - - + +
452B GLN* 4.0 18.8 - - + +
454B LEU 3.8 12.8 - - - +
455B VAL* 3.1 28.3 + - + +
456B ASP 3.2 1.4 + - - -
457B GLY* 1.3 76.7 - - - +
459B PHE* 1.3 60.7 + - - +
474B THR 4.0 0.2 - - - +
475B LEU* 3.4 1.4 - - - +
476B CYS* 3.0 28.8 + - + +
529B HIS* 3.2 27.8 - - + +
530B HIS 4.2 3.1 - - - +
531B CYS* 3.6 25.1 - - - +
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Residues in contact with PHE 459 (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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435B TRP* 3.8 21.8 - + + -
449B ILE* 4.9 0.7 - - - -
457B GLY 3.5 9.0 - - - -
458B LEU* 1.3 78.1 - - - +
460B LEU* 1.3 63.3 + - - +
461B LEU* 3.7 21.8 - - + -
473B LEU* 3.9 7.4 - - + -
474B THR 3.2 13.9 - - - +
475B LEU* 4.1 2.9 - - + -
513B VAL* 4.1 15.0 - - + -
517B GLN* 4.5 9.0 - - - -
527B LEU* 3.7 44.2 - - + -
528B LYS 4.1 3.1 - - - -
529B HIS 2.8 46.3 + - - -
530B HIS* 3.1 19.5 - - + -
531B CYS* 2.7 36.2 + - - -
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Residues in contact with LEU 460 (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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435B TRP 3.5 7.9 - - - -
437B HIS* 3.6 35.4 - - + +
440B ILE* 4.3 4.5 - - + -
445B SER* 3.9 35.7 - - - +
448B ILE* 4.2 10.3 - - + -
449B ILE* 4.5 2.0 - - + -
459B PHE* 1.3 80.9 - - - +
461B LEU* 1.3 78.1 + - - +
462B ARG* 4.1 6.5 - - + -
473B LEU* 3.6 5.0 - - - +
474B THR* 3.0 46.8 + - - +
531B CYS* 4.0 19.1 - - + +
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Residues in contact with LEU 461 (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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435B TRP* 2.9 23.9 + - + +
436B PHE* 3.6 15.7 - - + -
437B HIS* 2.9 26.2 + - - -
459B PHE* 3.7 19.7 - - + -
460B LEU* 1.3 83.2 - - - +
462B ARG* 1.3 62.4 + - - +
471B PHE* 5.5 0.9 - - + -
472B VAL 3.3 10.3 - - - +
473B LEU* 3.6 22.0 - - + -
486B ILE* 3.8 24.2 - - + -
509B LEU* 4.1 16.2 - - + -
512B LEU* 4.7 3.8 - - + -
513B VAL* 3.9 26.5 - - + -
527B LEU* 5.1 0.4 - - + -
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Residues in contact with ARG 462 (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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436B PHE* 3.9 11.4 - - - -
438B GLY 3.3 15.7 - - - +
440B ILE* 3.6 24.0 + - + +
442B ARG* 3.6 31.9 - - - +
445B SER* 2.8 28.8 + - - -
460B LEU* 4.1 4.9 - - + -
461B LEU* 1.3 77.9 - - - +
463B ASP* 1.3 73.2 + - - +
465B GLN* 4.2 11.7 - - - +
471B PHE* 3.3 6.4 - - - +
472B VAL* 2.8 59.9 + - + +
474B THR* 3.3 10.9 + - - -
483B ASN* 3.2 24.9 - - - +
485B GLN* 5.3 1.0 - - - +
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Residues in contact with ASP 463 (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* 4.9 0.3 + - - -
436B PHE* 3.6 9.7 - - - -
438B GLY* 2.8 35.6 + - - +
439B ARG* 3.2 34.6 + - + +
440B ILE 4.5 4.2 - - - +
462B ARG* 1.3 89.1 + - - +
464B SER* 1.3 69.1 + - - +
465B GLN* 3.6 4.4 + - - +
470B ALA 4.2 3.7 - - - +
471B PHE* 3.5 22.8 - - - -
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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