Contacts of the helix formed by residues 658 - 667 (chain A) in PDB entry 3SXS
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 658 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A GLU* 3.5 19.7 - - - +
592A LYS* 3.7 22.4 - - - +
595A VAL* 4.4 0.9 - - - -
657A PRO* 1.3 76.2 - - - +
659A PHE* 1.4 58.9 + - - +
660A GLN* 3.4 6.9 + - - +
661A GLN* 3.1 36.1 + - - +
662A LEU* 3.0 28.2 + - - +
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Residues in contact with PHE 659 (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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521A CYS* 3.7 13.2 - - - +
524A MET* 3.5 43.5 - - + -
525A ALA* 3.5 22.6 - - - +
528A GLU* 2.8 29.6 + - + +
537A LEU* 4.1 0.2 - - + -
594A ASP* 3.4 53.8 - - - -
595A VAL* 3.7 9.4 - - + +
598A PHE* 3.5 29.8 - + + -
658A THR* 1.4 68.5 - - - +
660A GLN* 1.3 56.7 + - - +
662A LEU* 3.6 15.1 - - + +
663A LEU* 2.8 36.2 + - - +
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Residues in contact with GLN 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ALA* 4.0 20.7 - - - +
528A GLU* 3.1 12.1 + - - +
529A SER* 5.3 5.9 - - - -
658A THR* 3.2 8.9 - - - +
659A PHE* 1.3 76.0 - - - +
661A GLN* 1.4 63.2 + - + +
663A LEU* 3.5 15.7 + - - +
664A SER* 3.3 22.2 + - - -
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Residues in contact with GLN 661 (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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592A LYS* 5.8 0.2 + - - -
656A ARG 4.8 0.5 - - - +
657A PRO* 3.4 16.7 - - + +
658A THR* 3.1 42.4 + - - +
660A GLN* 1.4 73.7 - - + +
662A LEU* 1.4 65.5 + - - +
664A SER* 3.2 9.6 + - - -
665A SER* 3.0 27.9 + - - +
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Residues in contact with LEU 662 (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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521A CYS* 3.6 15.3 - - - -
595A VAL* 3.9 27.1 - - + -
598A PHE* 3.9 22.4 - - + -
644A ILE* 3.6 31.4 - - + +
647A SER* 4.4 1.1 - - - +
648A CYS* 4.0 9.6 - - - -
657A PRO* 3.7 20.2 - - + -
658A THR 3.0 18.1 + - - +
659A PHE* 3.3 15.5 + - + +
661A GLN* 1.4 75.6 - - - +
663A LEU* 1.3 63.2 + - - +
665A SER* 3.1 9.3 + - - -
666A ILE* 3.0 26.6 + - + +
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Residues in contact with LEU 663 (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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518A TYR* 3.6 33.4 - - + +
521A CYS* 3.5 10.0 - - + -
522A GLU* 3.6 41.7 - - + +
525A ALA* 4.0 20.4 - - + -
659A PHE 2.8 20.8 + - - +
660A GLN* 3.6 17.0 - - - +
661A GLN 3.3 0.2 - - - -
662A LEU* 1.3 73.0 - - - +
664A SER* 1.3 57.6 + - - +
666A ILE* 3.2 4.4 + - - +
667A GLU* 3.0 31.5 + - - +
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Residues in contact with SER 664 (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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660A GLN* 3.3 10.8 + - - -
661A GLN* 3.2 13.5 + - - -
663A LEU* 1.3 77.0 - - - +
665A SER* 1.4 63.2 + - - +
667A GLU* 3.8 8.6 - - - +
668A PRO* 3.2 20.1 - - - +
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Residues in contact with SER 665 (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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644A ILE* 4.2 21.1 - - - +
661A GLN* 3.0 18.1 + - - +
662A LEU* 3.1 13.7 + - - +
664A SER* 1.4 78.0 + - - +
666A ILE* 1.4 62.2 + - - +
668A PRO* 3.4 10.5 - - - +
669A LEU* 4.0 14.4 - - - +
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Residues in contact with ILE 666 (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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514A LEU* 3.9 26.7 - - + -
517A CYS* 4.8 4.9 - - + +
518A TYR* 3.8 32.3 - - + -
521A CYS* 4.0 25.4 - - + -
598A PHE* 4.1 21.5 - - + -
602A MET* 4.9 5.8 - - + -
644A ILE* 4.3 22.2 - - + -
662A LEU* 3.0 21.7 + - + +
663A LEU* 3.8 3.6 - - - +
665A SER* 1.4 78.0 - - - +
667A GLU* 1.3 66.4 + - - +
669A LEU* 2.9 23.2 + - - +
670A ARG* 3.6 5.0 + - + +
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Residues in contact with GLU 667 (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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518A TYR* 2.6 32.1 + - - -
663A LEU* 3.0 18.8 + - - +
664A SER* 3.8 9.2 - - - +
666A ILE* 1.3 76.1 - - - +
668A PRO* 1.4 67.2 - - + +
669A LEU 3.2 1.0 + - - -
670A ARG* 2.7 54.6 + - - +
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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