Contacts of the helix formed by residues 612 - 626 (chain B) in PDB entry 5B2R
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 ASN 612 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B PHE* 3.0 68.4 + - + +
609B ASN* 3.0 30.7 + - - +
611B GLU* 1.3 78.6 - - - +
613B GLU* 1.3 63.3 + - - +
614B ASP 3.4 2.0 - - - -
615B ILE* 3.3 18.3 + - + +
616B LEU* 3.0 28.3 + - + +
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Residues in contact with GLU 613 (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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514B LEU* 3.5 33.1 - - + +
609B ASN 4.1 1.0 + - - -
610B GLU* 3.0 37.0 + - - +
611B GLU 3.3 0.6 - - - -
612B ASN* 1.3 77.0 - - - +
614B ASP* 1.3 64.2 + - - +
616B LEU* 3.4 6.6 + - - +
617B GLU* 3.0 30.0 + - - +
664B ARG* 3.0 20.9 + - - +
668B ASN* 3.8 21.6 + - - -
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Residues in contact with ASP 614 (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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611B GLU 4.7 4.9 + - - +
612B ASN 3.4 0.6 - - - -
613B GLU* 1.3 75.9 - - - +
615B ILE* 1.3 67.0 + - + +
617B GLU* 3.4 1.7 + - - +
618B ASP* 3.0 24.1 + - - +
664B ARG* 2.7 39.8 + - - +
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Residues in contact with ILE 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B PHE* 4.4 14.6 - - + -
611B GLU 5.3 3.1 + - - +
612B ASN* 3.3 27.2 + - - +
614B ASP* 1.3 78.7 - - + +
616B LEU* 1.3 59.8 + - + +
618B ASP* 3.2 4.2 + - - +
619B ILE* 2.9 45.7 + - + +
639B TYR* 3.9 34.5 - - + -
642B LEU* 3.9 24.0 - - + -
643B PHE* 5.4 0.2 - - + -
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Residues in contact with LEU 616 (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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513B LEU* 3.7 21.1 - - + -
597B LEU* 4.2 14.1 - - + -
601B ILE* 5.4 3.4 - - + -
606B PHE* 3.7 29.8 - - + -
607B LEU* 3.8 42.6 - - + +
609B ASN 5.5 0.2 - - - +
612B ASN* 3.0 28.2 + - + +
613B GLU* 4.1 4.7 - - - +
615B ILE* 1.3 74.1 - - - +
617B GLU* 1.3 68.2 + - - +
619B ILE* 3.4 17.2 + - + +
620B VAL* 3.2 29.3 + - - +
643B PHE* 5.5 1.1 - - + -
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Residues in contact with GLU 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B LEU* 3.7 14.9 - - + +
509B PRO* 5.4 1.7 - - - +
512B SER* 2.6 29.0 + - - -
513B LEU* 3.5 12.4 + - - +
514B LEU* 3.0 40.6 + - + +
613B GLU* 3.0 22.4 + - - +
614B ASP 3.8 3.6 - - - +
616B LEU* 1.3 78.6 - - - +
618B ASP* 1.3 56.4 + - - +
620B VAL* 3.5 3.5 + - - +
621B LEU* 3.0 29.6 + - - +
664B ARG* 3.9 31.9 - - - +
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Residues in contact with ASP 618 (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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614B ASP 3.0 16.5 + - - +
615B ILE 3.2 1.3 + - - +
617B GLU* 1.3 77.3 - - - +
619B ILE* 1.3 58.2 + - - +
621B LEU* 3.3 17.4 + - - +
622B THR* 3.0 36.1 + - - -
635B ARG* 5.0 11.6 + - - +
638B THR* 5.6 0.2 + - - -
639B TYR* 2.4 38.5 + - - +
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Residues in contact with ILE 619 (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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597B LEU* 5.4 4.5 - - + -
615B ILE* 2.9 37.1 + - + +
616B LEU* 3.8 19.5 - - + +
617B GLU 3.3 0.2 - - - -
618B ASP* 1.3 76.6 - - - +
620B VAL* 1.3 59.7 + - + +
622B THR* 3.2 4.7 + - - -
623B LEU* 3.0 47.8 + - + +
636B LEU* 4.0 19.5 - - + +
639B TYR* 3.8 22.4 - - + -
643B PHE* 4.3 20.2 - - + -
651B LEU* 4.2 21.3 - - + -
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Residues in contact with VAL 620 (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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509B PRO* 4.3 3.6 - - + -
511B HIS* 3.6 29.2 - - + +
512B SER* 3.9 11.4 - - - +
513B LEU* 4.9 4.3 - - + +
593B THR* 4.0 22.4 - - + -
597B LEU* 4.4 12.1 - - + -
616B LEU 3.2 16.6 + - - +
617B GLU* 4.1 3.8 - - - +
619B ILE* 1.3 74.8 - - + +
621B LEU* 1.3 61.3 + - - +
623B LEU* 3.2 10.4 + - + +
624B THR* 2.8 42.9 + - - +
656B TYR* 4.2 14.6 - - + -
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Residues in contact with LEU 621 (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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509B PRO* 3.9 21.2 - - + +
617B GLU 3.0 18.4 + - - +
618B ASP* 3.6 17.7 - - - +
620B VAL* 1.3 76.9 - - - +
622B THR* 1.3 52.8 + - - +
624B THR* 3.1 1.0 + - - -
625B LEU* 2.7 52.4 + - + +
635B ARG* 4.8 11.2 - - - +
659B TRP* 3.6 30.3 - - + -
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Residues in contact with THR 622 (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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618B ASP* 3.0 21.1 + - - -
619B ILE 3.2 8.0 + - - -
621B LEU* 1.3 77.0 - - - +
623B LEU* 1.3 61.9 + - - +
625B LEU* 4.6 2.7 - - - -
626B PHE* 3.1 27.2 + - + +
632B ILE* 4.0 24.9 - - + +
635B ARG* 3.0 56.4 + - + +
636B LEU* 4.2 14.6 - - + +
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Residues in contact with LEU 623 (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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597B LEU* 4.9 3.6 - - + -
619B ILE* 3.0 36.6 + - + +
620B VAL* 3.2 9.4 + - + +
622B THR* 1.3 75.5 - - - +
624B THR* 1.3 59.5 + - - +
626B PHE 3.5 10.4 - - - +
632B ILE* 3.7 30.1 - - + -
636B LEU* 4.5 5.2 - - + -
651B LEU* 3.3 24.9 - - + +
652B LYS* 4.7 0.4 - - - -
654B ARG* 3.1 42.2 - - + +
655B ARG* 4.0 4.7 - - - +
656B TYR* 3.2 35.3 + - + +
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Residues in contact with THR 624 (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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492B ILE* 5.5 1.9 - - - +
509B PRO* 3.5 20.8 - - + +
511B HIS* 5.2 0.9 - - - +
620B VAL* 2.8 22.7 + - - +
621B LEU 3.1 3.1 + - - -
623B LEU* 1.3 78.2 - - - +
625B LEU* 1.3 67.0 + - - +
626B PHE 3.4 3.4 + - - +
656B TYR* 3.4 30.7 - - + +
657B THR* 4.5 3.0 - - - +
658B GLY 3.6 28.7 - - - +
659B TRP* 3.8 25.8 + - + +
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Residues in contact with LEU 625 (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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488B ALA* 4.8 1.9 - - - +
489B GLN* 3.9 34.8 - - + +
492B ILE* 3.7 51.9 - - + +
493B GLU* 4.7 7.2 - - + +
621B LEU* 2.7 32.3 + - + +
622B THR* 4.2 3.1 - - - +
624B THR* 1.3 76.3 - - - +
626B PHE* 1.3 73.8 + - + +
627B GLU 4.1 0.7 + - - -
635B ARG* 3.8 31.0 - - - +
659B TRP* 4.0 14.6 - - + -
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Residues in contact with PHE 626 (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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485B GLY* 3.9 19.7 - - - -
488B ALA* 3.7 26.5 - - + -
489B GLN* 4.1 7.0 - - + -
622B THR* 3.1 8.9 + - + +
623B LEU 3.5 12.1 - - - +
624B THR 4.2 2.3 - - - +
625B LEU* 1.3 96.6 - - + +
627B GLU* 1.3 59.5 + - - +
628B ASP 4.5 4.7 - - - +
631B MET* 3.8 47.6 - - + -
632B ILE* 3.4 32.3 - - + +
635B ARG* 3.5 43.1 - - + -
655B ARG* 4.5 2.1 - - - +
656B TYR 5.3 0.2 - - - +
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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