Contacts of the strand formed by residues 508 - 514 (chain B) in PDB entry 3NR8
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 ILE 508 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471B THR 3.5 6.3 - - - +
472B GLN* 3.8 10.1 - - - +
505B LEU* 2.7 48.5 + - + +
507B ASN* 1.3 75.7 - - - +
509B LYS* 1.3 64.2 + - - +
540B ASN 3.6 25.1 - - - +
541B LYS 4.1 0.7 - - - -
542B GLY* 3.6 29.8 - - - +
544B VAL* 3.3 19.0 - - + +
559B ASN* 3.6 28.5 - - - +
560B CYS* 4.4 7.6 - - - -
561B HIS* 3.7 21.3 - - + +
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Residues in contact with LYS 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B PHE 3.9 0.7 - - - +
470B GLY* 3.6 0.3 - - - -
471B THR* 2.9 42.2 + - - +
474B ASN* 3.5 32.3 + - + +
475B SER 5.0 0.6 - - - -
476B VAL 2.6 27.1 + - - +
477B GLY* 3.8 2.0 - - - -
478B ASP* 2.5 32.8 + - - +
481B TRP* 4.2 17.6 - - + -
502B MET* 6.1 1.3 - - + -
503B GLN 3.5 8.3 - - - +
504B SER* 4.0 7.9 - - - -
506B TRP 3.4 20.0 - - - -
507B ASN* 3.8 7.2 - - - +
508B ILE* 1.3 80.8 - - - +
510B VAL* 1.3 60.2 + - - +
544B VAL* 4.6 0.9 - - - -
559B ASN* 3.1 4.2 - - - +
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Residues in contact with VAL 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B VAL* 4.4 5.8 - - + -
469B PHE 3.1 19.1 - - - +
470B GLY* 4.1 4.3 - - - -
481B TRP* 4.0 2.5 - - - -
502B MET* 3.4 8.5 - - - +
503B GLN 3.1 26.2 + - - +
509B LYS* 1.3 74.8 - - - +
511B ALA* 1.3 69.6 + - - +
512B VAL* 5.3 0.2 - - + -
544B VAL* 3.2 30.7 - - + +
545B GLY* 4.6 0.7 - - - -
546B VAL* 3.7 27.1 - - + -
557B PHE* 5.3 3.4 - - + +
559B ASN* 3.9 17.7 - - + +
605B PHE* 4.3 12.1 - - + -
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Residues in contact with ALA 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B TYR 3.7 1.0 - - - +
468B VAL* 3.3 4.5 - - - +
469B PHE* 2.8 38.2 + - - +
481B TRP* 3.5 25.8 - - + -
482B LEU* 4.1 15.9 - - + -
485B LEU* 3.7 16.2 - - + -
501B ALA 3.7 7.2 - - - +
502B MET* 4.5 2.7 - - + -
510B VAL* 1.3 76.1 - - - +
512B VAL* 1.3 64.4 + - - +
513B LEU* 4.1 3.1 - - + +
546B VAL* 5.7 0.7 - - - -
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Residues in contact with VAL 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ILE* 4.4 5.8 - - + -
467B TYR 3.4 2.2 - - - -
468B VAL* 3.7 27.8 - - + -
482B LEU* 5.9 0.2 - - - +
499B PRO* 3.6 2.6 - - - +
500B ILE* 2.8 49.7 + - + -
501B ALA* 3.0 16.1 + - + +
510B VAL* 5.3 0.7 - - + -
511B ALA* 1.3 74.9 - - - +
513B LEU* 1.3 63.0 + - - +
514B VAL* 4.7 1.1 - - + -
546B VAL* 3.4 31.4 - - + -
548B PHE* 3.8 24.9 - - + -
557B PHE* 4.4 4.3 - - + -
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Residues in contact with LEU 513 (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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466B ILE* 3.4 2.6 - - - +
467B TYR* 2.7 36.4 + - + +
469B PHE* 3.9 29.6 - - + -
482B LEU* 4.4 9.0 - - + -
485B LEU* 4.1 13.9 - - + -
486B ARG* 4.1 25.4 - - + +
489B LEU* 3.7 24.2 - - + -
497B TYR* 4.1 21.5 - - + +
498B ARG 3.6 5.2 - - - +
499B PRO* 4.2 13.2 - - + -
511B ALA* 4.1 9.2 - - + -
512B VAL* 1.3 78.3 - - - +
514B VAL* 1.3 71.7 + - - +
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Residues in contact with VAL 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ASP 3.7 4.3 - - - +
466B ILE* 3.7 25.4 - - + -
497B TYR* 3.3 9.6 - - - -
498B ARG* 3.0 31.5 + - + +
500B ILE* 3.9 25.8 - - + -
512B VAL* 4.7 3.4 - - + -
513B LEU* 1.3 84.0 - - - +
515B LYS* 1.3 80.8 + - - +
518B HIS* 3.4 28.3 - - + +
519B GLU* 4.0 4.9 - - - +
522B ILE* 4.5 11.2 - - + -
548B PHE* 5.5 1.1 - - + -
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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
------------------------------------------------------------
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