Contacts of the helix formed by residues 647 - 658 (chain i) in PDB entry 5M32
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 HIS 647 (chain i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612i ASP* 2.5 51.1 - - + +
616i ARG* 5.3 2.9 - - - +
645i ASN 2.4 12.2 + - - +
646i PRO* 1.3 73.6 - - - +
648i VAL* 1.3 60.3 + - - +
649i ARG 3.2 1.3 - - - -
650i TYR* 3.3 11.2 + - - +
651i GLY* 3.2 17.5 + - - -
682i TYR* 5.2 6.2 - - + +
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Residues in contact with VAL 648 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612i ASP* 4.3 3.0 + - - +
615i ARG* 4.0 30.6 - - + +
619i VAL* 5.0 0.9 - - - +
640i LEU 5.0 2.6 - - - +
641i SER 4.5 0.2 - - - +
643i SER* 6.4 1.6 - - - -
644i TYR 4.9 5.4 - - - +
645i ASN* 3.2 9.9 + - + +
647i HIS* 1.3 78.2 - - - +
649i ARG* 1.3 63.4 + - - +
651i GLY* 3.2 3.3 + - - +
652i ALA* 3.0 23.0 + - - +
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Residues in contact with ARG 649 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641i SER* 3.1 22.1 - - - +
642i GLU* 4.6 9.4 - - + -
643i SER 4.9 6.1 - - - +
644i TYR 5.1 3.0 + - - +
645i ASN 4.6 0.4 + - - -
646i PRO* 4.6 18.2 - - + -
647i HIS 4.0 0.4 - - - +
648i VAL* 1.3 79.5 - - - +
650i TYR* 1.3 61.9 + - - +
652i ALA* 3.2 18.4 + - - +
653i ALA* 3.5 5.4 + - - +
680i VAL* 5.8 0.4 - - + -
683i VAL* 5.1 10.3 - - + -
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Residues in contact with TYR 650 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646i PRO 5.5 0.4 - - - +
647i HIS* 3.3 11.0 + - - +
648i VAL 3.3 0.4 - - - -
649i ARG* 1.3 76.8 - - - +
651i GLY* 1.3 67.1 + - - +
653i ALA* 2.9 25.0 + - - +
654i MET* 3.4 4.5 + - - +
682i TYR* 3.9 15.7 - - + +
683i VAL* 3.7 34.2 - - + +
686i GLY* 5.0 6.8 - - - -
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Residues in contact with GLY 651 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616i ARG* 4.4 15.5 - - - -
619i VAL* 2.7 29.6 - - - +
647i HIS 3.2 11.4 + - - -
648i VAL* 3.2 5.1 + - - -
650i TYR* 1.3 77.4 - - - +
652i ALA* 1.3 60.5 + - - +
653i ALA 3.0 0.9 + - - -
654i MET* 3.1 9.5 + - - +
655i ALA 3.0 12.1 + - - -
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Residues in contact with ALA 652 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619i VAL* 3.3 8.8 - - - +
637i VAL* 5.0 7.9 - - + +
640i LEU* 4.1 7.2 - - + +
641i SER* 3.8 28.7 - - - +
648i VAL 3.0 12.2 + - - +
649i ARG 3.3 11.2 - - - +
650i TYR 3.2 0.2 - - - -
651i GLY* 1.3 75.3 - - - +
653i ALA* 1.3 62.1 + - - +
655i ALA* 3.2 5.1 + - - +
656i LEU* 2.9 27.0 + - - +
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Residues in contact with ALA 653 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649i ARG 3.5 4.7 + - - +
650i TYR* 2.9 20.1 + - - +
652i ALA* 1.3 79.8 - - - +
654i MET* 1.3 49.9 + - - +
656i LEU* 3.4 3.1 - - - +
657i GLY* 2.4 38.3 + - - -
686i GLY* 4.6 23.1 - - - +
687i ALA* 5.0 1.8 - - - +
690i ALA* 5.3 9.2 - - + +
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Residues in contact with MET 654 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616i ARG 6.2 0.2 - - - +
620i GLU* 5.3 8.7 - - - -
623i GLY* 4.2 0.7 - - - -
650i TYR 3.4 4.4 + - - +
651i GLY* 3.1 9.7 + - - +
653i ALA* 1.3 78.5 - - - +
655i ALA* 1.3 62.8 + - - +
657i GLY* 3.1 11.5 + - - +
658i ILE* 3.3 15.8 + - - +
686i GLY* 6.1 0.2 - - - -
767i THR* 5.4 10.5 - - - -
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Residues in contact with ALA 655 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619i VAL* 2.1 49.2 + - + +
620i GLU* 4.6 0.4 - - - +
622i LEU* 3.6 10.3 - - + +
623i GLY* 2.0 41.0 + - - +
637i VAL* 6.3 0.9 - - + -
651i GLY 3.0 4.8 + - - -
652i ALA* 3.4 10.8 - - - +
654i MET* 1.3 75.1 - - - +
656i LEU* 1.3 58.4 + - + +
658i ILE 4.4 0.7 + - - -
659i CYS* 4.5 3.1 + - - +
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Residues in contact with LEU 656 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633i CYS* 5.5 4.5 - - + +
634i PRO* 5.7 3.6 - - + -
637i VAL* 3.8 25.8 - - + -
652i ALA 2.9 15.4 + - - +
653i ALA* 3.9 3.1 - - - +
655i ALA* 1.3 72.9 - - - +
657i GLY* 1.3 67.8 + - - +
658i ILE 3.2 2.2 - - - -
659i CYS* 3.1 24.0 + - + +
660i CYS* 3.9 3.8 + - - +
668i ALA* 5.8 3.2 - - - +
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Residues in contact with GLY 657 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653i ALA 2.4 27.7 + - - -
654i MET* 3.1 4.2 + - - -
656i LEU* 1.3 71.0 - - - +
658i ILE* 1.3 62.4 + - - +
660i CYS* 3.3 20.6 + - - +
661i ALA* 3.9 1.9 + - - -
668i ALA* 6.3 2.7 - - - -
690i ALA* 5.0 15.7 - - - -
693i LEU* 5.0 9.0 - - - +
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Residues in contact with ILE 658 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623i GLY 3.4 26.9 - - - +
624i PHE* 5.1 2.5 - - - -
654i MET 3.3 9.9 + - - +
656i LEU 3.2 0.4 - - - -
657i GLY* 1.3 75.8 - - - +
659i CYS* 1.3 62.9 + - - +
660i CYS 2.9 1.6 + - - -
661i ALA* 3.1 21.4 + - - +
763i VAL* 5.8 8.3 - - + -
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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