Contacts of the strand formed by residues 542 - 550 (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 GLY 542 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505B LEU* 4.3 2.2 - - - -
508B ILE* 3.6 11.7 - - - +
530B VAL 3.2 12.1 - - - -
532B THR* 3.9 14.1 - - - +
541B LYS* 1.3 73.3 - - - +
543B ALA* 1.3 60.0 + - - -
560B CYS* 3.2 5.0 - - - +
561B HIS 2.8 40.4 + - - +
579B ILE* 4.2 3.4 - - - -
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Residues in contact with ALA 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B LEU* 3.8 3.6 - - - +
508B ILE* 5.0 0.2 - - - -
529B SER* 3.4 3.4 - - - -
530B VAL 2.9 32.0 + - - +
542B GLY* 1.3 71.7 - - - +
544B VAL* 1.3 68.8 + - - +
558B VAL* 4.2 8.1 - - + -
559B ASN 3.3 8.3 - - - +
560B CYS* 3.8 4.7 - - + -
579B ILE* 3.3 43.3 - - + +
583B LEU* 4.8 7.9 - - + -
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Residues in contact with VAL 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B GLN* 3.0 38.6 - - + +
504B SER 3.9 1.3 - - - -
505B LEU* 3.4 28.5 - - + +
508B ILE* 3.3 33.2 - - + +
510B VAL* 3.2 21.3 - - + +
528B SER 3.7 4.3 - - - -
529B SER* 4.7 0.7 - - - -
543B ALA* 1.3 73.9 - - - +
545B GLY* 1.3 59.3 + - - +
557B PHE 4.0 0.2 - - - +
558B VAL* 3.7 0.8 - - - -
559B ASN* 2.6 47.9 + - - +
583B LEU* 5.2 0.9 - - - -
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Residues in contact with GLY 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B GLN* 4.2 1.4 - - - +
510B VAL* 4.6 0.4 - - - -
527B THR* 3.3 5.4 - - - +
528B SER 2.9 34.8 + - - -
544B VAL* 1.3 77.8 - - - +
546B VAL* 1.3 68.5 + - - +
557B PHE 3.2 10.5 - - - -
558B VAL* 4.3 2.7 - - - -
583B LEU* 4.7 4.2 - - - +
585B LEU* 3.9 15.7 - - - -
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Residues in contact with VAL 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B ALA* 4.4 17.0 - - + +
502B MET 4.9 0.2 - - - +
503B GLN* 4.9 1.1 - - + -
510B VAL* 3.7 23.3 - - + +
512B VAL* 3.4 34.3 - - + -
526B SER 3.3 10.3 - - - +
527B THR* 3.9 15.5 - - + -
545B GLY* 1.3 79.3 - - - +
547B SER* 1.3 58.7 + - - +
548B PHE* 4.4 9.0 - - + -
556B GLY* 3.7 0.3 - - - -
557B PHE* 2.8 48.7 + - + +
585B LEU* 3.8 5.2 - - - +
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Residues in contact with SER 547 (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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524B HIS 4.6 2.4 + - - -
525B VAL* 3.4 2.6 - - - +
526B SER* 2.8 48.6 + - - +
546B VAL* 1.3 73.9 - - - +
548B PHE* 1.3 70.1 + - - +
555B PHE 3.2 16.6 - - - -
585B LEU* 3.5 13.0 + - - +
599B PHE* 3.3 31.3 - - - -
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Residues in contact with PHE 548 (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* 4.2 23.6 - - + -
500B ILE* 4.7 4.3 - - + -
512B VAL* 3.8 28.3 - - + -
514B VAL* 5.5 0.7 - - + -
522B ILE* 3.6 33.7 - - + -
524B HIS 3.6 10.8 - - - -
525B VAL* 3.7 24.5 - - + -
546B VAL* 4.4 6.3 - - + -
547B SER* 1.3 84.0 - - - +
549B MET* 1.3 69.0 + - - +
550B PHE* 4.2 8.7 + - + -
554B SER* 3.6 2.3 - - - -
555B PHE* 2.9 36.6 + + + +
557B PHE* 3.4 34.8 - + - -
599B PHE* 5.7 0.2 - - - -
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Residues in contact with MET 549 (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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521B ARG 3.2 2.1 - - - +
522B ILE* 3.2 8.5 - - - +
523B SER* 2.9 48.3 + - - +
524B HIS* 4.2 27.4 - - + -
548B PHE* 1.3 75.0 - - - +
550B PHE* 1.3 59.8 + - - +
551B ASN 3.9 8.7 - - - +
552B GLY 4.1 14.6 - - - +
553B THR 3.3 11.4 - - - +
554B SER* 3.9 20.4 - - - -
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Residues in contact with PHE 550 (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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421B PRO* 4.6 4.9 - - + -
424B ILE* 3.7 38.8 - - + -
466B ILE* 4.5 11.7 - - + -
514B VAL* 5.5 0.4 - - + -
518B HIS* 3.8 44.9 - + + -
521B ARG* 3.7 23.8 - - + -
522B ILE* 3.3 24.9 - - + -
548B PHE* 4.2 3.9 + - + -
549B MET* 1.3 70.3 - - - +
551B ASN* 1.3 74.9 + - - +
552B GLY 3.1 2.9 + - - -
553B THR 2.8 13.0 + - - +
555B PHE* 3.7 22.4 - - + -
729B VAL* 3.1 29.0 - - + +
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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