Contacts of the strand formed by residues 543 - 550 (chain A) 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 ALA 543 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505A LEU* 3.9 2.8 - - - +
529A SER* 3.5 2.8 - - - -
530A VAL* 3.0 33.8 + - + +
542A GLY* 1.3 73.1 - - - -
544A VAL* 1.3 64.8 - - - +
558A VAL* 3.9 8.3 - - + -
559A ASN 3.3 8.5 - - - +
560A CYS* 3.9 6.1 - - + -
579A ILE* 3.3 43.8 - - + +
583A LEU* 4.3 6.0 - - + +
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Residues in contact with VAL 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A GLN* 3.1 37.5 - - + +
504A SER 4.2 0.7 - - - -
505A LEU* 3.7 21.1 - - + +
508A ILE* 3.4 39.5 - - + +
510A VAL* 3.1 26.0 - - + +
528A SER 3.9 3.6 - - - -
529A SER* 4.6 0.4 - - - +
543A ALA* 1.3 76.5 - - - +
545A GLY* 1.3 57.3 + - - +
558A VAL* 3.5 3.8 - - - +
559A ASN* 2.6 41.3 + - + +
583A LEU* 5.3 0.4 - - - -
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Residues in contact with GLY 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A GLN* 4.2 2.1 - - - +
510A VAL* 4.4 0.9 - - - -
527A THR* 3.4 4.7 - - - -
528A SER 2.9 35.1 + - - +
544A VAL* 1.3 77.2 - - - +
546A VAL* 1.3 66.3 + - - +
557A PHE 3.3 10.8 - - - -
558A VAL* 4.3 4.3 - - - -
583A LEU* 4.9 5.0 - - - +
585A LEU* 3.5 13.7 - - - -
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Residues in contact with VAL 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A ALA* 4.0 22.7 - - + +
503A GLN* 5.1 0.7 - - + -
510A VAL* 3.3 36.8 - - + +
512A VAL* 3.5 33.4 - - + -
526A SER 3.4 12.1 - - - +
527A THR* 4.3 4.0 - - + -
545A GLY* 1.3 74.1 - - - +
547A SER* 1.3 70.1 + - - +
548A PHE* 4.2 5.8 - - + -
557A PHE* 3.0 38.5 + - + +
585A LEU* 3.3 9.3 - - - +
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Residues in contact with SER 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A HIS 5.0 1.4 + - - -
525A VAL* 3.5 3.3 - - - +
526A SER* 3.0 38.5 + - - +
546A VAL* 1.3 79.6 - - - +
548A PHE* 1.3 72.6 + - - +
555A PHE 3.3 16.8 - - - -
556A GLY* 4.3 0.2 - - - -
557A PHE* 5.2 0.2 - - - -
585A LEU* 3.5 18.9 - - - +
586A GLY* 4.4 1.6 + - - -
599A PHE* 3.6 24.8 - - - -
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Residues in contact with PHE 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A ILE* 3.9 28.0 - - + -
500A ILE* 4.3 11.0 - - + -
512A VAL* 3.7 26.0 - - + -
514A VAL* 5.1 1.6 - - + -
522A ILE* 4.2 20.4 - - + -
523A SER 3.6 9.9 - - - +
524A HIS 3.6 11.9 - - - -
525A VAL* 3.8 14.4 - - + -
546A VAL* 4.2 6.7 - - + -
547A SER* 1.3 83.2 - - - +
549A MET* 1.3 75.8 + - - +
550A PHE* 4.4 2.9 - - + -
554A SER* 3.7 2.5 - - - -
555A PHE* 2.8 42.6 + + + +
557A PHE* 3.7 29.4 - + - -
599A PHE* 5.8 0.2 - - - -
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Residues in contact with MET 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ARG 3.5 0.2 - - - +
522A ILE* 3.5 3.1 - - - -
523A SER* 2.9 46.6 + - - +
524A HIS* 4.1 25.7 + - + -
548A PHE* 1.3 83.5 - - - +
550A PHE* 1.3 60.1 + - - +
551A ASN 4.0 8.3 - - - +
552A GLY* 3.7 17.5 - - - +
553A THR 3.3 13.5 - - - +
554A SER* 3.7 22.4 - - - +
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Residues in contact with PHE 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A ILE* 4.0 33.4 - - + -
466A ILE* 4.2 12.6 - - + -
518A HIS* 3.6 51.1 - + + -
521A ARG* 3.4 16.6 - - + -
522A ILE* 3.4 22.0 - - + -
548A PHE* 4.3 2.6 + + + -
549A MET* 1.3 71.3 - - - +
551A ASN* 1.3 93.1 + - - +
552A GLY 3.1 2.8 + - - -
553A THR* 3.0 12.8 + - - +
555A PHE* 3.8 21.7 - - + -
729A VAL* 3.2 24.6 - - + +
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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