Contacts of the helix formed by residues 604 - 619 (chain A) in PDB entry 5VLR
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 THR 604 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A LYS 3.4 6.3 + - - +
603A LEU* 1.3 74.1 - - - +
605A ASP* 1.3 67.4 + - - +
606A ASP* 2.9 11.7 + - - +
607A GLU* 3.0 34.3 + - - +
608A LEU* 3.0 10.0 + - - +
636A ARG* 4.1 0.4 - - - -
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Residues in contact with ASP 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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603A LEU 3.7 0.8 + - - -
604A THR* 1.3 70.6 - - - +
606A ASP* 1.3 59.1 + - - +
608A LEU* 3.4 2.4 + - - +
609A PHE* 3.0 30.5 + - - +
636A ARG* 3.1 27.0 + - - +
639A ALA* 5.1 4.5 - - - +
640A ASN* 2.8 35.5 + - - +
643A ILE* 3.8 23.5 - - + +
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Residues in contact with ASP 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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169A LEU 4.8 12.0 - - - +
171A LEU* 5.0 17.2 + - - +
604A THR* 2.9 11.3 + - - +
605A ASP* 1.3 81.0 - - - +
607A GLU* 1.4 59.6 + - - +
609A PHE* 3.5 16.7 + - - +
610A GLN* 3.6 15.0 + - - +
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Residues in contact with GLU 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A VAL* 3.9 14.9 - - - +
603A LEU* 3.6 20.5 - - + +
604A THR* 3.0 24.0 + - - +
606A ASP* 1.4 72.2 - - - +
608A LEU* 1.3 64.7 + - - +
610A GLN* 3.2 23.1 + - + +
611A TYR* 3.1 40.9 + - + +
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Residues in contact with LEU 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A LEU* 4.1 19.9 - - + +
604A THR 3.0 11.2 + - - +
605A ASP* 3.5 6.7 - - - +
607A GLU* 1.3 74.0 - - - +
609A PHE* 1.3 59.5 + - - +
611A TYR* 2.9 21.3 + - - +
612A LEU* 2.9 20.3 + - + -
615A LEU* 3.7 27.4 - - + -
632A PHE* 4.0 20.2 - - + -
633A LEU* 5.3 2.5 - - + -
636A ARG* 3.6 39.9 - - + +
643A ILE* 3.6 28.9 - - + -
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Residues in contact with PHE 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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605A ASP 3.0 12.8 + - - +
606A ASP* 3.6 12.8 - - - +
607A GLU 3.4 0.2 - - - -
608A LEU* 1.3 77.4 - - - +
610A GLN* 1.3 72.6 + - - +
611A TYR 3.4 0.9 + - - -
612A LEU* 3.6 30.2 + - + +
613A LEU 5.1 0.3 + - - -
642A LYS* 4.5 13.0 - - + -
643A ILE* 4.7 9.6 - - + -
646A PHE* 3.2 52.5 - + + -
650A HIS* 6.0 1.1 - - - -
792A GLN* 5.9 0.9 - - - +
795A GLN* 5.5 9.0 - - - -
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Residues in contact with GLN 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 ASP 3.6 14.2 + - - +
607A GLU* 3.2 17.4 + - + +
608A LEU 3.1 0.8 - - - -
609A PHE* 1.3 89.1 - - - +
611A TYR* 1.4 68.8 + - + +
792A GLN* 3.7 34.0 + - + +
795A GLN* 3.4 34.8 + - - +
796A LEU* 3.6 29.8 - - + +
799A VAL* 4.0 26.8 - - - +
977A LEU* 4.9 0.7 - - - +
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Residues in contact with TYR 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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576A VAL* 4.0 10.2 - - + +
580A LEU* 4.2 16.6 - - + -
603A LEU* 3.9 18.6 - - + -
607A GLU* 3.1 50.5 + - + +
608A LEU 2.9 6.0 + - - +
610A GLN* 1.4 91.7 - - + +
612A LEU* 1.4 65.2 + - - +
613A LEU 3.3 2.9 - - - -
614A GLN* 2.9 22.5 + - + +
615A LEU* 3.0 24.7 + - + +
796A LEU* 4.8 5.8 - - + +
973A LEU* 3.7 29.9 - - + +
977A LEU* 3.6 37.5 - - + -
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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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608A LEU* 2.9 18.4 + - + +
609A PHE* 3.6 29.2 + - + +
611A TYR* 1.4 74.5 - - - +
613A LEU* 1.4 57.6 + - - +
615A LEU* 3.2 6.2 + - - +
616A VAL* 2.9 39.5 + - + +
633A LEU* 3.9 28.3 - - + -
643A ILE* 3.9 39.9 - - + +
646A PHE* 4.2 13.0 - - + -
647A LEU* 4.1 15.7 - - + +
650A HIS* 4.1 13.7 - - + +
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Residues in contact with LEU 613 (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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609A PHE 5.1 0.6 + - - -
611A TYR 3.3 0.8 - - - -
612A LEU* 1.4 77.5 - - - +
614A GLN* 1.3 64.4 + - - +
616A VAL* 3.6 2.4 + - + +
617A GLN* 3.2 41.2 + - + +
650A HIS* 3.6 35.2 + - + +
785A ARG 5.3 0.7 - - - +
788A MET* 3.6 26.7 - - + -
789A LEU* 4.3 16.4 - - + +
792A GLN* 3.4 25.7 + - - +
981A MET* 4.0 24.9 - - + -
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Residues in contact with GLN 614 (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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580A LEU* 6.3 0.2 - - + -
610A GLN 3.9 0.2 - - - +
611A TYR* 2.9 21.6 + - + +
613A LEU* 1.3 74.8 - - - +
615A LEU* 1.3 64.4 + - + +
617A GLN* 3.0 18.4 + - - +
618A VAL* 3.1 18.4 + - - +
789A LEU* 3.6 8.3 - - - +
792A GLN* 3.2 39.7 + - - +
793A MET* 4.0 3.0 - - - +
977A LEU* 3.3 41.8 - - + +
980A LEU* 4.1 20.4 - - + +
981A MET* 3.5 28.3 - - + +
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Residues in contact with LEU 615 (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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580A LEU* 4.7 5.2 - - + -
583A LEU* 3.4 33.7 - - + -
600A LEU* 3.9 15.5 - - + -
603A LEU* 5.0 2.0 - - + -
608A LEU* 3.7 30.1 - - + -
611A TYR* 3.0 32.1 + - + +
612A LEU* 3.2 8.0 + - - +
614A GLN* 1.3 75.4 - - + +
616A VAL* 1.3 62.7 + - - +
618A VAL* 3.4 9.8 + - - +
619A LEU* 4.1 0.9 - - - +
629A LEU* 3.6 32.8 - - + +
632A PHE* 4.6 9.2 - - + -
633A LEU* 4.1 18.6 - - + +
980A LEU* 5.2 0.9 - - + -
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Residues in contact with VAL 616 (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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612A LEU* 2.9 26.1 + - + +
613A LEU 3.9 4.7 - - - +
615A LEU* 1.3 70.6 - - - +
617A GLN* 1.4 68.0 + - - +
619A LEU* 3.0 35.1 + - - +
633A LEU* 4.4 5.6 - - + -
647A LEU* 3.7 29.2 - - + -
650A HIS* 3.9 31.0 - - + +
651A LEU* 3.8 22.2 - - + -
664A PHE* 4.0 17.1 - - + -
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Residues in contact with GLN 617 (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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613A LEU* 3.2 27.9 + - + +
614A GLN* 3.0 11.7 + - - +
616A VAL* 1.4 84.8 - - - +
618A VAL* 1.3 55.9 + - - +
620A LYS* 3.1 47.5 + - - +
650A HIS* 5.7 1.6 + - - -
654A GLU* 3.3 20.2 + - - -
785A ARG* 6.0 2.6 - - - +
980A LEU 4.4 4.3 - - - +
981A MET* 3.7 23.3 - - - -
983A ALA* 3.3 19.0 - - + +
984A ALA* 3.1 31.4 + - + +
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Residues in contact with VAL 618 (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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583A LEU* 3.3 35.7 - - + +
614A GLN 3.1 12.2 + - - +
615A LEU* 3.6 10.8 - - - +
616A VAL 3.3 0.4 - - - -
617A GLN* 1.3 70.0 - - - +
619A LEU* 1.4 64.7 + - - +
620A LYS 3.0 2.0 - - - -
621A TYR* 3.0 30.7 + - + +
622A GLU* 3.7 10.7 - - - +
629A LEU* 3.8 16.2 - - + -
980A LEU* 3.7 46.4 - - + +
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Residues in contact with LEU 619 (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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615A LEU 3.6 2.3 + - - +
616A VAL* 3.0 23.4 + - - +
618A VAL* 1.4 76.5 - - - +
620A LYS* 1.3 59.2 + - - +
621A TYR 3.2 0.4 - - - -
622A GLU* 3.2 17.9 + - + +
627A CYS* 4.5 5.6 - - - -
629A LEU* 3.8 22.2 - - + +
630A THR* 3.3 36.3 - - - +
633A LEU* 3.8 17.9 - - + -
647A LEU* 5.7 0.2 - - + -
651A LEU* 4.0 7.9 - - + -
663A ARG* 3.2 32.8 + - - -
664A PHE* 4.0 13.7 - - + -
667A ILE* 3.8 22.9 - - + -
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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