Contacts of the helix formed by residues 604 - 612 (chain A) in PDB entry 3RTR
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 SER 604 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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583A TYR 6.0 0.2 - - - -
584A GLN 6.5 0.7 - - - -
586A SER 3.8 9.0 - - - -
587A LYS* 4.0 1.1 - - - +
588A GLY 4.5 0.2 - - - -
603A ALA* 1.3 74.4 - - - +
605A THR* 1.3 60.1 + - - +
606A PHE* 3.3 10.5 + - - +
607A GLN* 3.1 34.3 + - - +
608A MET* 2.9 31.4 + - - +
685A ASN* 3.4 27.6 - - - +
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Residues in contact with THR 605 (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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553A PHE* 3.4 31.9 - - + -
556A PRO* 5.8 0.2 - - - +
559A LEU* 4.8 5.6 - - + +
583A TYR* 3.6 25.5 + - + +
586A SER* 2.9 31.1 + - - -
604A SER* 1.3 68.8 - - - +
606A PHE* 1.3 69.2 + - - +
607A GLN 3.0 0.9 + - - -
608A MET* 3.1 20.0 + - - +
609A ALA* 3.2 11.6 + - - +
27B TRP* 2.8 33.5 + - + +
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Residues in contact with PHE 606 (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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551A CYS* 4.3 24.9 - - + -
553A PHE* 3.3 44.4 - + + -
583A TYR* 4.0 20.1 + - + -
584A GLN* 3.7 28.9 - - + -
604A SER* 3.3 8.6 + - - +
605A THR* 1.3 76.7 - - - +
607A GLN* 1.3 64.2 + - - +
609A ALA* 3.3 8.5 + - - +
610A ILE* 3.3 19.9 + - - +
631A ILE* 3.7 20.9 - - + +
635A ILE* 4.3 22.2 - - + -
639A VAL* 4.4 19.5 - - + -
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Residues in contact with GLN 607 (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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603A ALA* 3.3 24.2 - - + +
604A SER* 3.1 25.9 + - - +
606A PHE* 1.3 71.9 - - - +
608A MET* 1.3 56.1 + - - +
609A ALA 2.7 15.7 + - - -
610A ILE* 2.8 14.9 + - - +
611A LEU* 3.0 17.1 + - + +
639A VAL* 3.8 10.3 - - + +
642A ILE* 3.3 38.4 - - - +
643A LEU* 3.4 31.9 - - + +
684A ILE* 3.3 23.3 + - - +
685A ASN* 4.1 3.0 + - - +
686A VAL 5.0 0.4 + - - +
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Residues in contact with MET 608 (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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559A LEU* 4.3 18.8 - - + -
588A GLY* 3.3 37.2 - - - -
589A GLU 4.0 1.1 - - - +
590A LEU* 3.5 38.4 - - + +
603A ALA* 4.0 8.7 - - + +
604A SER 2.9 24.8 + - - +
605A THR* 3.5 8.3 - - - +
607A GLN* 1.3 75.4 - - - +
609A ALA* 1.3 56.2 + - - +
611A LEU 4.0 0.7 - - - -
612A LEU* 2.9 37.9 + - + +
24B VAL* 3.5 36.6 - - + -
26B LYS 4.3 2.7 - - - +
27B TRP* 4.5 7.4 - - + -
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Residues in contact with ALA 609 (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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553A PHE* 3.7 22.9 - - + -
554A ALA 5.5 1.1 - - - +
556A PRO* 3.7 30.3 - - + +
605A THR 3.2 3.5 + - - +
606A PHE 3.6 9.9 - - - +
607A GLN 2.7 3.2 + - - -
608A MET* 1.3 74.9 - - - +
610A ILE* 1.3 63.7 + - - +
612A LEU* 4.0 3.8 - - - +
613A GLN* 3.2 24.8 + - - +
629A THR* 3.9 14.6 - - + +
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Residues in contact with ILE 610 (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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606A PHE 3.3 15.9 - - - +
607A GLN* 2.8 7.5 + - - +
609A ALA* 1.3 78.6 - - - +
611A LEU* 1.3 66.3 + - + +
613A GLN* 3.1 22.8 - - - +
614A TYR* 3.2 27.3 - - + -
625A LEU* 4.1 18.6 - - + -
629A THR* 4.5 10.5 - - + -
631A ILE* 4.8 4.0 - - + -
636A LEU* 3.6 29.8 - - + -
639A VAL* 4.1 22.2 - - + -
640A LEU* 4.3 18.4 - - + -
643A LEU* 5.3 3.8 - - + -
649A LEU* 4.4 7.6 - - + -
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Residues in contact with LEU 611 (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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590A LEU* 3.4 31.4 - - + -
601A LEU* 3.9 20.2 - - + -
603A ALA* 4.7 1.6 - - + -
607A GLN 3.0 16.7 + - - +
608A MET 4.5 0.2 - - - +
610A ILE* 1.3 72.9 - - - +
612A LEU* 1.3 54.0 + - - +
613A GLN 2.9 4.9 - - - -
614A TYR* 2.6 36.6 + - - +
643A LEU* 3.7 23.3 - - + -
648A LEU* 4.5 9.2 - - + -
649A LEU* 4.5 20.9 - - + -
671A LEU* 5.9 0.2 - - + -
684A ILE* 4.3 14.6 - - + -
22B PHE* 3.3 30.1 - - + -
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Residues in contact with LEU 612 (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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556A PRO* 3.9 20.4 - - + -
558A GLU* 3.3 41.8 - - + +
559A LEU* 5.5 1.6 - - + -
590A LEU* 4.0 5.4 - - + -
608A MET* 2.9 28.9 + - + +
609A ALA* 4.3 4.5 - - - +
610A ILE 3.3 0.2 - - - -
611A LEU* 1.3 77.5 - - - +
613A GLN* 1.3 61.6 + - - +
614A TYR 3.1 0.2 - - - -
615A ASN* 3.2 27.6 + - - +
616A THR* 5.6 1.2 - - - +
22B PHE* 3.5 36.3 - - + +
24B VAL* 4.0 19.3 - - + -
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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