Contacts of the strand formed by residues 545 - 550 (chain M) in PDB entry 3RWR
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 TRP 545 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523M LEU* 5.7 2.2 - - + -
537M LEU* 3.2 17.2 - - - +
538M VAL* 3.0 37.4 + - + +
539M SER* 3.9 3.6 - - - -
540M ASP* 3.7 26.2 - - - -
543M GLN* 3.3 45.8 - - + -
544M VAL* 1.3 97.3 + - - +
546M HIS* 1.3 65.4 + - - +
599M CYS* 4.3 12.8 - - - -
602M ASP* 3.8 8.0 + - - -
603M ALA 3.5 9.9 + - - -
604M LEU* 3.4 48.3 - - + +
623M CYS* 3.4 31.4 - - - -
624M MET 3.8 8.3 - - - -
625M LEU* 4.6 3.9 - - + +
626M ALA* 3.4 7.1 - - - +
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Residues in contact with HIS 546 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505M GLU* 3.2 25.3 + - - -
508M LEU* 5.1 1.8 - - + +
535M ALA* 5.0 1.6 - - + -
536M LEU 3.2 19.1 + - - -
537M LEU* 3.5 10.5 - - + +
545M TRP* 1.3 79.7 - - - +
547M GLU* 1.3 77.1 + - - +
548M GLN* 3.4 38.2 + - + +
623M CYS* 3.6 4.1 - - - +
624M MET* 3.2 26.3 + - - +
626M ALA* 4.0 11.9 - - + -
627M SER* 5.1 7.6 - - - -
630M LEU* 3.4 23.1 - - + -
556Q GLN* 5.7 4.0 + - - -
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Residues in contact with GLU 547 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534M TYR* 2.8 29.7 + - - +
536M LEU* 3.3 29.0 + - + +
546M HIS* 1.3 76.4 + - - +
548M GLN* 1.3 63.2 + - - +
549M VAL* 3.1 22.2 - - + +
557M ARG* 2.9 28.8 + - - -
621M PHE* 3.2 18.2 - - - +
622M HIS 2.9 28.4 + - - +
623M CYS* 3.2 22.5 - - + +
624M MET* 6.3 0.9 - - + -
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Residues in contact with GLN 548 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501M MET* 2.9 62.9 - - + +
504M LEU* 3.2 27.9 - - + +
505M GLU* 2.9 25.7 + - - +
534M TYR 3.5 4.5 - - - +
535M ALA* 4.7 0.7 - - - -
546M HIS* 3.4 18.6 + - + +
547M GLU* 1.3 72.5 - - - +
549M VAL* 1.3 63.7 + - - +
559Q LYS* 4.8 12.6 + - - +
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Residues in contact with VAL 549 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504M LEU* 4.9 1.2 - - - +
533M GLY* 3.4 0.5 - - - -
534M TYR* 3.3 60.7 + - + +
547M GLU* 3.1 29.8 - - + +
548M GLN* 1.3 80.9 - - - +
550M ASP* 1.3 61.0 + - - +
553M VAL* 3.9 21.8 - - + -
554M VAL* 4.2 12.3 - - + +
557M ARG* 4.1 14.1 - - - +
619M TRP* 5.0 3.4 - - + -
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Residues in contact with ASP 550 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501M MET* 4.9 18.9 + - + +
504M LEU* 6.3 0.4 - - - -
532M GLN* 2.9 32.1 - - - +
533M GLY* 3.3 2.6 + - - -
549M VAL* 1.3 75.2 - - - +
551M THR* 1.3 88.8 + - - +
552M SER* 2.6 16.1 + - - +
553M VAL* 3.0 14.4 + - - +
554M VAL* 3.2 12.9 + - - +
11N VAL* 5.5 2.6 - - - +
87N ASN* 4.6 15.1 + - - +
96N PHE* 6.0 0.7 - - - -
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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