Contacts of the helix formed by residues 612 - 624 (chain A) in PDB entry 3BWT
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 PHE 612 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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573A LYS 3.5 18.8 - - - +
574A ASP* 5.4 0.2 - - - -
575A GLN* 3.4 57.0 - - + -
578A CYS* 3.7 24.4 - - + +
582A GLN* 4.3 0.2 + - - -
610A ASP* 3.1 5.3 + - - +
611A SER* 1.3 98.9 + - - +
613A GLY* 1.3 67.1 + - - +
614A ASN 3.2 1.8 - - - -
615A TYR* 3.2 25.1 + + - +
616A LEU 3.7 3.6 + - - -
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Residues in contact with GLY 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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572A CYS 4.1 5.2 - - - -
578A CYS* 3.8 13.9 - - - -
607A LEU* 2.8 21.4 - - - +
610A ASP* 2.8 16.2 + - - -
612A PHE* 1.3 75.9 - - - +
614A ASN* 1.3 65.4 + - - +
616A LEU* 3.1 7.6 + - - +
617A ILE* 3.0 22.5 + - - +
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Residues in contact with ASN 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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607A LEU 2.7 10.8 + - - -
608A MET* 3.1 28.5 - - - +
610A ASP 2.8 22.1 + - - +
611A SER 3.0 20.6 + - - -
612A PHE 3.2 0.2 - - - -
613A GLY* 1.3 76.8 - - - +
615A TYR* 1.3 68.0 + - - +
617A ILE* 3.4 3.3 + - - +
618A GLN* 3.0 50.1 + - - +
648A HIS* 3.5 23.8 + - + +
651A ARG* 3.0 20.1 + - - -
652A ALA* 4.2 5.3 - - + +
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Residues in contact with TYR 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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579A ARG* 6.2 2.2 - - - -
582A GLN* 3.8 19.9 - - - +
611A SER 3.4 20.4 - - - -
612A PHE* 3.2 14.0 + + - +
613A GLY 3.1 0.8 - - - -
614A ASN* 1.3 93.4 - - - +
616A LEU* 1.3 59.7 + - - +
618A GLN* 3.4 20.3 - - + +
619A LYS* 3.0 27.0 + - - +
648A HIS* 5.5 0.4 - + - -
651A ARG* 3.3 35.2 + - - -
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Residues in contact with LEU 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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572A CYS* 3.3 39.5 - - + -
578A CYS* 4.0 13.2 - - - +
581A LEU* 3.5 34.1 - - + -
582A GLN* 3.7 26.4 - - + +
585A LEU* 4.0 13.9 - - + -
596A ILE* 4.8 11.7 - - + -
600A THR* 5.1 1.6 - - + -
607A LEU* 5.0 7.0 - - + -
612A PHE 3.7 1.0 + - - -
613A GLY* 3.1 12.3 + - - +
615A TYR* 1.3 75.9 - - - +
617A ILE* 1.3 57.3 + - + +
619A LYS* 2.9 4.9 + - - +
620A LEU* 2.6 35.4 + - + +
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Residues in contact with ILE 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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600A THR* 4.2 13.0 - - - +
604A THR* 4.6 13.9 - - + +
607A LEU* 3.8 42.4 - - + -
608A MET* 4.0 27.1 - - + +
613A GLY 3.0 13.5 + - - +
614A ASN 3.8 5.4 - - - +
616A LEU* 1.3 80.6 - - + +
618A GLN* 1.3 53.1 + - - +
620A LEU* 3.4 12.9 - - + +
621A LEU* 2.7 59.1 + - + +
632A LEU* 5.0 9.4 - - + -
652A ALA* 5.0 1.6 - - + -
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Residues in contact with GLN 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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614A ASN* 3.0 38.7 + - - +
615A TYR* 3.4 27.8 - - - +
617A ILE* 1.3 76.5 - - - +
619A LYS* 1.3 62.5 + - - +
621A LEU* 3.5 7.2 + - - +
622A GLU* 3.4 25.8 + - - +
651A ARG* 3.8 29.2 - - - +
652A ALA* 3.8 15.9 - - - -
655A LYS* 3.8 31.1 - - + +
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Residues in contact with LYS 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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582A GLN* 4.0 22.4 - - + +
585A LEU* 3.7 21.3 - - + -
586A ASP* 3.1 45.5 + - - +
615A TYR 3.0 13.6 + - - +
616A LEU 2.9 7.9 + - - +
618A GLN* 1.3 73.6 - - - +
620A LEU* 1.3 67.0 + - - +
622A GLU* 3.2 37.4 + - - +
623A GLU* 3.3 35.0 + - - +
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Residues in contact with LEU 620 (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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585A LEU* 3.7 25.3 - - + +
593A ALA* 4.0 17.7 - - - +
596A ILE* 3.6 26.5 - - + -
597A PHE* 4.3 9.0 - - + -
600A THR* 3.8 22.0 - - - +
616A LEU* 2.6 20.7 + - + +
617A ILE* 3.4 17.9 - - + +
619A LYS* 1.3 73.4 - - - +
621A LEU* 1.3 62.4 + - - +
623A GLU 3.1 1.2 + - - -
624A VAL* 3.0 35.9 + - + +
632A LEU* 3.9 26.7 - - + -
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Residues in contact with LEU 621 (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 MET* 4.5 2.5 - - + -
617A ILE* 2.7 45.7 + - + +
618A GLN* 3.7 9.4 - - - +
619A LYS 3.2 0.2 - - - -
620A LEU* 1.3 74.7 - - - +
622A GLU* 1.3 62.6 + - - +
624A VAL* 3.9 14.9 + - - +
629A ARG* 4.3 28.8 + - + +
632A LEU* 4.1 22.7 - - + -
652A ALA 3.8 22.4 - - - +
655A LYS* 4.4 1.3 - - + -
656A LEU* 3.8 37.0 - - + +
659A CYS* 3.9 19.2 - - - +
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Residues in contact with GLU 622 (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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618A GLN* 3.4 14.1 + - - +
619A LYS* 3.2 32.3 + - - +
621A LEU* 1.3 78.8 - - - +
623A GLU* 1.3 69.0 + - - +
624A VAL 3.7 4.0 + - - +
629A ARG* 6.0 0.2 + - - -
655A LYS* 2.8 36.6 + - - -
659A CYS* 4.1 13.0 - - - -
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Residues in contact with GLU 623 (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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585A LEU* 3.4 41.1 - - + +
586A ASP* 5.0 2.9 - - - +
589A GLY* 4.7 12.6 - - - -
590A SER* 5.3 3.3 - - - +
593A ALA* 3.8 11.4 - - + +
619A LYS* 3.3 33.4 + - - +
620A LEU 3.1 4.2 + - - +
622A GLU* 1.3 82.2 - - - +
624A VAL* 1.3 64.4 + - - +
625A THR* 4.2 0.9 + - - +
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Residues in contact with VAL 624 (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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593A ALA* 4.2 11.2 - - + +
597A PHE* 4.1 18.6 - - + -
620A LEU* 3.0 23.7 + - + +
621A LEU* 4.0 11.8 - - - +
622A GLU 3.5 5.4 - - - +
623A GLU* 1.3 81.5 - - - +
625A THR* 1.3 73.8 + - - +
628A GLN* 3.0 33.7 - - + +
629A ARG* 3.4 30.9 + - + +
632A LEU* 5.0 4.7 - - + -
661A LYS* 5.4 1.6 + - - -
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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