Contacts of the helix formed by residues 653 - 665 (chain A) in PDB entry 3SHW
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 ILE 653 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651A GLY 3.2 0.2 - - - -
652A PRO* 1.3 84.8 - - + +
654A ALA* 1.3 58.6 + - - +
655A ASP* 3.3 7.6 - - - -
656A VAL* 3.2 13.6 + - + -
657A ALA* 2.9 26.7 + - - +
728A LEU* 4.0 8.5 - - + -
736A VAL* 5.3 0.9 - - + -
739A MET* 4.2 19.1 - - + -
740A ARG* 4.3 20.6 - - + +
743A LEU* 4.2 15.7 - - + -
775A LEU* 3.8 30.7 - - + -
782A TRP* 3.7 44.4 - - + +
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Residues in contact with ALA 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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649A ILE* 3.2 41.0 - - + +
650A PHE* 4.0 4.0 - - - -
651A GLY 3.1 18.0 + - - +
652A PRO 3.6 0.6 - - - -
653A ILE* 1.3 77.7 - - - +
655A ASP* 1.3 62.7 + - - +
657A ALA* 3.0 9.9 + - - +
658A ARG* 3.0 35.4 + - - +
728A LEU* 4.4 1.2 - - - +
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Residues in contact with ASP 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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652A PRO 4.0 0.5 - - - +
653A ILE 3.6 8.5 - - - -
654A ALA* 1.3 74.6 - - - +
656A VAL* 1.3 73.3 + - - +
658A ARG* 3.6 25.0 + - - +
659A GLU* 3.1 38.0 + - - +
740A ARG* 2.8 37.7 + - - -
744A CYS* 5.3 0.2 - - - -
747A SER* 5.0 1.4 + - - -
749A LYS* 3.1 24.7 + - - +
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Residues in contact with VAL 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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653A ILE* 3.2 18.8 + - + +
655A ASP* 1.3 90.6 + - - +
657A ALA* 1.3 66.2 + - - +
659A GLU* 3.3 10.0 + - + +
660A LYS* 3.1 27.8 + - + +
740A ARG* 4.7 0.4 - - - +
743A LEU* 4.0 35.7 - - + +
744A CYS* 3.5 35.7 - - + -
782A TRP* 4.5 9.6 - - + -
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Residues in contact with ALA 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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649A ILE* 4.0 9.4 - - + -
653A ILE 2.9 13.6 + - - +
654A ALA* 3.0 13.2 + - - +
656A VAL* 1.3 77.1 - - - +
658A ARG* 1.3 61.9 + - - +
660A LYS* 3.5 3.0 + - - +
661A LEU* 3.0 29.7 + - - +
728A LEU* 4.1 6.3 - - + -
782A TRP* 4.0 18.8 - - + -
783A TYR* 4.8 0.7 - - - -
786A LEU* 3.8 24.5 - - + -
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Residues in contact with ARG 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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649A ILE* 3.6 37.5 + - + +
654A ALA* 3.0 19.8 + - - +
655A ASP* 3.6 30.8 - - - +
657A ALA* 1.3 75.9 - - - +
659A GLU* 1.3 54.2 + - + +
661A LEU* 3.1 6.2 + - - +
662A ALA* 2.7 36.8 + - - +
671A ILE* 4.6 14.7 - - + +
705A LEU* 3.7 43.0 - - + +
706A LEU 4.3 6.9 + - - +
707A ASP* 3.4 45.8 + - - +
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Residues in contact with GLU 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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655A ASP* 3.1 32.5 + - - +
656A VAL* 3.3 9.2 + - - +
658A ARG* 1.3 77.4 - - + +
660A LYS* 1.3 58.2 + - - +
662A ALA* 4.0 5.7 - - - +
663A ARG* 3.1 53.5 + - - +
671A ILE* 4.9 9.0 - - + -
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Residues in contact with LYS 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 VAL* 3.1 21.2 + - + +
657A ALA* 3.8 4.0 - - - +
659A GLU* 1.3 73.2 - - - +
661A LEU* 1.3 61.2 + - - +
663A ARG* 3.5 16.4 - - - +
664A GLU* 2.8 65.1 + - + +
743A LEU* 5.4 8.2 - - + +
780A ASP* 6.5 1.3 - - - -
782A TRP* 4.5 13.2 - - + -
783A TYR* 3.5 41.8 + - + -
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Residues in contact with LEU 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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649A ILE* 3.8 17.0 - - + -
657A ALA 3.0 21.3 + - - +
658A ARG 3.5 3.6 - - - +
660A LYS* 1.3 75.8 - - - +
662A ALA* 1.3 61.0 + - - +
665A GLU* 3.1 33.2 + - + +
669A TYR* 3.7 35.8 - - + +
705A LEU* 4.1 20.6 - - + -
783A TYR* 4.0 15.3 - - + +
786A LEU* 3.8 22.0 - - + -
787A LYS* 3.9 23.1 - - + -
790A ILE* 4.2 10.5 - - + -
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Residues in contact with ALA 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 ARG 2.7 19.5 + - - +
659A GLU* 4.0 4.5 - - - +
661A LEU* 1.3 72.2 - - - +
663A ARG* 1.3 59.5 + - - +
665A GLU 4.6 2.5 - - - -
666A PRO* 3.8 18.2 - - - +
669A TYR* 5.0 5.8 - - - -
670A GLN* 5.2 2.0 - - - -
671A ILE* 3.7 34.1 - - + +
705A LEU* 4.1 6.0 - - + +
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Residues in contact with ARG 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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659A GLU* 3.1 60.3 + - - +
660A LYS* 3.5 24.3 - - - +
662A ALA* 1.3 76.9 - - - +
664A GLU* 1.3 71.8 + - + +
666A PRO* 3.4 17.3 - - - +
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Residues in contact with GLU 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 LYS* 2.8 58.2 + - + +
663A ARG* 1.3 84.0 - - + +
665A GLU* 1.3 68.4 + - + +
666A PRO* 3.4 7.2 - - - +
783A TYR* 3.4 20.1 - - + +
787A LYS* 5.8 0.9 + - - +
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Residues in contact with GLU 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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661A LEU* 3.1 21.1 + - + +
664A GLU* 1.3 86.4 - - - +
666A PRO* 1.3 65.5 - - - +
667A ASP* 3.3 5.3 - - - +
668A ILE* 3.6 24.4 - - + +
669A TYR* 3.2 40.8 + - + +
783A TYR* 3.9 14.6 - - - +
787A LYS* 3.2 32.0 + - + -
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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