Contacts of the helix formed by residues 574 - 588 (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 ASP 574 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A PHE* 4.4 13.5 - - - -
570A SER 5.3 3.8 - - - +
571A LEU* 3.5 9.9 + - - +
573A LYS* 1.3 91.2 - - - +
575A GLN* 1.3 59.6 + - - +
576A HIS* 3.8 5.6 - - + +
577A GLY* 3.4 17.7 - - - +
578A CYS* 3.0 29.5 + - - -
612A PHE* 4.2 0.9 - - - -
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Residues in contact with GLN 575 (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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573A LYS 3.7 0.8 + - - -
574A ASP* 1.3 74.6 - - - +
576A HIS* 1.3 77.0 + - + +
578A CYS* 3.5 2.4 + - - +
579A ARG* 3.0 61.3 + - - +
612A PHE* 3.4 51.8 - - + -
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Residues in contact with HIS 576 (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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554A SER* 3.9 24.0 + - - +
555A ARG* 6.2 0.2 - - + -
556A PHE* 3.6 25.3 - - + -
574A ASP* 3.2 6.6 - - + +
575A GLN* 1.3 98.9 + - + +
577A GLY* 1.3 60.3 - - - +
579A ARG* 3.3 9.5 + - - +
580A PHE* 2.9 29.6 + - - +
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Residues in contact with GLY 577 (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 PHE* 3.5 24.0 - - - -
571A LEU* 3.4 22.7 - - - -
574A ASP* 3.4 9.9 - - - +
576A HIS* 1.3 78.6 - - - +
578A CYS* 1.3 61.0 + - - +
580A PHE* 3.3 3.5 - - - +
581A LEU* 3.0 29.1 + - - +
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Residues in contact with CYS 578 (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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571A LEU 3.4 2.2 + - - -
572A CYS* 3.4 31.2 - - - -
574A ASP 3.0 24.4 + - - +
575A GLN 3.7 5.4 - - - +
577A GLY* 1.3 75.9 - - - +
579A ARG* 1.3 56.2 + - - +
581A LEU* 3.2 7.9 + - - +
582A GLN* 2.8 48.1 + - - +
612A PHE* 3.7 28.7 - - + +
613A GLY* 3.8 5.6 - - - -
616A LEU* 4.0 9.8 - - + +
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Residues in contact with ARG 579 (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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575A GLN* 3.0 51.2 + - + +
576A HIS* 3.9 11.7 - - - +
577A GLY 3.3 0.2 - - - -
578A CYS* 1.3 74.4 - - + +
580A PHE* 1.3 66.8 + - - +
582A GLN* 3.3 19.9 + - - +
583A LYS* 2.9 23.7 + - - +
615A TYR* 6.2 2.2 - - - -
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Residues in contact with PHE 580 (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 PHE* 3.3 48.0 - + + -
559A ALA* 3.9 12.6 - - + -
560A VAL 3.9 8.5 - - - -
561A LEU* 3.9 25.6 - - + -
564A TYR* 3.7 23.6 - + + -
571A LEU* 4.1 9.9 - - + -
576A HIS 2.9 14.7 + - - +
577A GLY 3.3 7.6 - - - +
579A ARG* 1.3 75.0 - - - +
581A LEU* 1.3 80.7 + - + +
583A LYS* 3.1 16.6 - - - +
584A GLN* 3.0 52.3 + - + +
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Residues in contact with LEU 581 (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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561A LEU* 5.0 5.8 - - + -
568A ILE* 3.9 24.0 - - + +
571A LEU* 3.9 16.6 - - + -
572A CYS* 3.6 31.2 - - - -
577A GLY 3.0 19.7 + - - +
578A CYS 3.5 3.1 - - - +
580A PHE* 1.3 96.0 - - + +
582A GLN* 1.3 57.3 + - - +
584A GLN* 3.2 7.8 + - + +
585A LEU* 2.8 31.0 + - - +
596A ILE* 4.0 21.2 - - + +
616A LEU* 3.5 23.8 - - + -
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Residues in contact with GLN 582 (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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578A CYS* 2.8 43.0 + - - +
579A ARG* 3.3 19.3 + - - +
581A LEU* 1.3 74.8 - - - +
583A LYS* 1.3 62.0 + - - +
585A LEU* 3.4 5.8 + - - +
586A ASP* 3.0 22.2 + - - +
612A PHE 4.3 0.6 + - - -
615A TYR* 3.8 20.1 - - - +
616A LEU* 3.7 36.7 - - + +
619A LYS* 4.0 24.3 - - + +
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Residues in contact with LYS 583 (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 PHE 3.7 21.8 + - - -
557A ALA* 4.5 10.1 + - - +
559A ALA 5.4 1.8 + - - -
579A ARG 2.9 13.0 + - - +
580A PHE* 3.1 20.5 - - - +
582A GLN* 1.3 76.2 - - - +
584A GLN* 1.3 82.8 + - - +
586A ASP* 2.7 29.6 + - - +
587A ILE* 3.1 27.4 + - + +
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Residues in contact with GLN 584 (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 ALA 5.1 2.4 + - - -
560A VAL* 5.6 0.6 - - - -
561A LEU* 4.4 21.6 + - + +
580A PHE* 3.0 43.6 + - + +
581A LEU* 3.4 9.0 - - + +
583A LYS* 1.3 111.6 - - - +
585A LEU* 1.3 61.1 + - - +
587A ILE* 4.2 11.6 - - - +
588A LEU* 2.9 49.2 + - + +
592A ALA* 3.4 12.3 - - + +
596A ILE* 5.0 2.0 - - + -
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Residues in contact with LEU 585 (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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581A LEU 2.8 20.8 + - - +
582A GLN* 3.5 8.1 - - - +
584A GLN* 1.3 74.2 - - - +
586A ASP* 1.3 62.1 + - - +
587A ILE 3.3 0.7 + - - -
589A GLY* 3.6 9.0 - - - -
592A ALA* 3.9 8.3 - - - +
593A ALA* 3.6 36.8 - - + +
596A ILE* 3.8 9.0 - - + -
616A LEU* 4.0 18.6 - - + -
619A LYS* 3.7 27.8 - - + -
620A LEU* 3.7 31.9 - - + +
623A GLU* 3.4 31.4 - - + +
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Residues in contact with ASP 586 (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 3.0 12.1 + - - +
583A LYS* 2.7 21.4 + - + +
585A LEU* 1.3 73.0 - - - +
587A ILE* 1.3 64.5 + - + +
589A GLY* 5.3 0.2 - - - -
619A LYS* 3.1 27.1 + - - +
623A GLU* 5.0 3.2 - - - +
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Residues in contact with ILE 587 (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 LYS* 3.1 34.4 + - + +
584A GLN* 4.0 17.0 - - - +
586A ASP* 1.3 94.0 - - + +
588A LEU* 1.3 82.0 + - + +
589A GLY 3.8 0.9 - - - -
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Residues in contact with LEU 588 (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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561A LEU* 3.6 35.4 - - + -
584A GLN* 2.9 34.5 + - - +
587A ILE* 1.3 93.7 - - + +
589A GLY* 1.3 59.8 + - - +
590A SER* 3.7 1.4 + - - -
591A LYS* 4.9 9.6 + - + +
592A ALA* 3.6 12.8 - - + +
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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