Contacts of the helix formed by residues 653 - 662 (chain A) in PDB entry 5VOT
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 GLY 653 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A TYR* 3.6 16.4 - - - -
451A GLY 5.7 0.9 - - - -
485A ARG* 4.4 1.1 - - - -
650A LEU* 4.1 9.9 + - - -
651A ASP 3.1 5.9 - - - -
652A SER* 1.3 80.5 - - - +
654A SER* 1.3 66.6 + - - -
655A THR* 3.1 5.9 + - - -
656A LYS* 3.2 14.9 + - - +
657A GLU* 3.4 8.5 + - - +
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Residues in contact with SER 654 (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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450A TYR* 3.9 6.4 - - - -
480A THR* 3.1 35.8 + - - +
482A THR* 4.2 12.2 - - - +
485A ARG* 3.3 32.7 + - - +
653A GLY* 1.3 69.8 - - - -
655A THR* 1.3 62.4 + - - +
657A GLU* 3.2 10.8 + - - +
658A PHE* 2.9 28.1 + - - +
705A GLU* 4.3 3.5 + - - -
730A LYS* 5.2 3.8 + - - +
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Residues in contact with THR 655 (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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450A TYR* 5.7 3.7 - - - -
500A ILE* 5.4 11.8 - - + +
649A THR* 3.7 22.7 - - + -
650A LEU* 5.4 2.9 - - - -
653A GLY* 3.1 3.3 - - - -
654A SER* 1.3 80.8 + - - +
656A LYS* 1.3 63.7 + - - +
658A PHE* 3.0 8.5 + - - +
659A PHE* 3.0 50.8 + - + -
703A LEU* 5.1 8.5 - - + +
704A LEU* 5.4 5.4 - - - +
705A GLU* 4.9 13.9 + - - +
730A LYS* 6.0 0.7 - - - +
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Residues in contact with LYS 656 (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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649A THR* 4.2 7.5 + - - +
650A LEU 4.1 12.7 + - - +
651A ASP* 3.0 29.5 + - - +
652A SER 4.9 3.8 - - - +
653A GLY 3.2 11.6 + - - +
655A THR* 1.3 78.9 - - - +
657A GLU* 1.3 58.4 + - - +
659A PHE* 3.4 3.9 + - - +
660A ARG* 2.9 40.3 + - - +
671A TRP* 3.7 27.8 - - + -
682A PHE* 3.5 35.1 - - + -
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Residues in contact with GLU 657 (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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482A THR* 5.7 4.9 - - + +
484A VAL* 4.7 29.1 - - + +
653A GLY 3.4 5.2 + - - +
654A SER* 3.2 19.0 + - - +
655A THR 3.1 0.4 - - - -
656A LYS* 1.3 77.5 - - - +
658A PHE* 1.3 64.5 + - - +
660A ARG* 2.3 36.1 + - - +
661A ARG* 2.8 61.5 + - + +
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Residues in contact with PHE 658 (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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500A ILE* 3.6 26.7 - - + -
654A SER 2.9 16.3 + - - +
655A THR* 3.0 10.5 + - - +
657A GLU* 1.3 74.5 - - - +
659A PHE* 1.3 71.6 + + - +
661A ARG* 3.2 4.4 + - - +
662A SER* 2.8 35.6 + - - -
667A PHE* 4.4 28.7 - + - -
727A LEU* 5.3 2.2 - - + -
728A ASP* 3.3 24.7 - - + -
730A LYS* 3.5 24.7 - - - +
754D ASN 6.0 0.2 - - - -
755D GLU* 4.7 20.4 - - + -
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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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500A ILE* 4.6 17.9 - - + -
649A THR* 4.2 5.8 - - + -
655A THR* 3.0 49.4 + - + -
656A LYS* 3.9 4.3 - - - +
658A PHE* 1.3 88.0 - + - +
660A ARG* 1.3 64.3 + - - +
662A SER* 3.1 20.2 + - - +
667A PHE* 4.5 27.8 - + + +
668A ASP* 5.7 0.7 - - - -
670A MET* 4.4 18.4 - - + -
671A TRP* 3.7 31.1 - - + +
674A MET* 3.8 20.6 - - + -
703A LEU* 3.5 28.9 - - + -
727A LEU* 5.0 5.4 - - + -
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Residues in contact with ARG 660 (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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656A LYS* 2.9 41.9 + - - +
657A GLU* 2.3 37.6 + - - +
659A PHE* 1.3 76.9 - - - +
661A ARG* 1.3 84.9 + - - +
662A SER 4.4 3.3 - - - +
671A TRP* 3.6 40.2 + - + +
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Residues in contact with ARG 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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657A GLU* 2.8 47.2 + - + +
658A PHE* 3.5 4.0 - - - +
660A ARG* 1.3 111.1 - - - +
662A SER* 1.3 65.7 + - - +
663A LYS* 3.6 7.8 + - - +
755D GLU* 6.1 1.8 - - - +
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Residues in contact with SER 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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658A PHE* 2.8 24.8 + - - -
659A PHE* 3.1 17.1 + - - +
660A ARG 4.4 3.1 - - - +
661A ARG* 1.3 79.7 - - - +
663A LYS* 1.3 62.7 + - - +
664A ILE* 3.2 12.9 + - - +
667A PHE* 3.2 35.3 - - - +
668A ASP* 5.0 10.2 - - - +
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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