Contacts of the helix formed by residues 646 - 653 (chain I) in PDB entry 3AOI
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 LYS 646 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188G GLN 4.0 9.7 + - - -
190G THR* 4.5 9.9 - - - +
644I LEU 3.3 3.8 + - - -
645I PRO* 1.3 68.2 - - - +
647I ARG* 1.3 87.8 + - + +
649I ALA* 2.8 11.2 + - - +
650I LEU* 2.6 36.1 + - - +
688I TRP* 3.6 44.3 - - + +
691I LEU* 3.9 5.1 - - + +
720I LEU* 4.0 27.8 - - + -
721I VAL 3.2 16.7 + - - +
722I GLU* 3.6 28.0 + - - +
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Residues in contact with ARG 647 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834H GLN* 5.4 1.4 + - - -
1005H MET* 5.6 3.8 - - + -
1007H ALA* 4.9 1.1 - - - +
645I PRO* 3.1 2.0 + - + +
646I LYS* 1.3 106.3 - - + +
648I MET* 1.3 62.5 + - + +
650I LEU* 3.2 24.7 - - - +
651I GLU* 3.4 7.8 + - - +
680I GLN* 5.1 13.8 - - - +
688I TRP* 5.1 7.0 - - + -
722I GLU* 4.2 7.1 + - - +
723I GLY* 3.0 53.3 + - - +
724I GLN* 3.1 23.5 - - - +
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Residues in contact with MET 648 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005H MET* 3.2 33.7 - - + -
1006H HIS 3.8 13.0 - - - +
1007H ALA* 3.9 16.4 - - + -
627I GLY* 3.8 8.7 - - - -
628I ARG 3.6 32.8 - - - +
629I SER* 3.9 15.9 - - - -
644I LEU* 4.7 2.9 - - + -
645I PRO* 2.7 26.9 + - + +
647I ARG* 1.3 72.3 - - - +
649I ALA* 1.3 52.4 + - - +
651I GLU* 3.3 2.9 + - - +
652I LEU* 2.7 48.3 + - + +
726I ILE* 4.1 11.4 - - - -
747I VAL* 4.3 9.4 - - + -
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Residues in contact with ALA 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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644I LEU* 4.4 13.0 - - + +
645I PRO 2.9 9.5 + - - +
646I LYS* 2.8 17.4 + - - +
648I MET* 1.3 69.5 - - - +
650I LEU* 1.3 61.1 + - - +
652I LEU* 2.9 11.1 + - - -
653I PHE* 2.5 49.9 + - + +
691I LEU* 4.1 13.9 - - + -
695I ILE* 4.7 3.6 - - + -
720I LEU* 4.6 9.9 - - + -
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Residues in contact with LEU 650 (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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646I LYS 2.6 15.7 + - - +
647I ARG* 3.2 15.5 - - - +
649I ALA* 1.3 75.9 - - - +
651I GLU* 1.3 57.4 + - + +
653I PHE 3.3 1.4 - - - -
654I LYS* 2.9 28.3 + - + +
657I LEU* 3.7 27.5 - - + +
677I LEU* 4.6 18.4 - - + +
683I ILE* 5.4 7.2 - - + -
687I VAL* 4.5 3.8 - - + -
688I TRP* 3.2 41.3 - - + -
691I LEU* 3.6 16.9 - - + +
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Residues in contact with GLU 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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1007H ALA* 3.1 32.0 - - + +
1008H ARG* 3.6 1.4 - - - -
1009H SER* 2.7 71.8 + - - -
1010H THR 4.5 2.4 + - - +
1027H PHE* 4.0 12.2 - - + -
647I ARG 3.4 4.6 + - - +
648I MET 3.3 6.8 + - - +
649I ALA 3.2 0.4 - - - -
650I LEU* 1.3 79.1 - - + +
652I LEU* 1.3 61.9 + - - +
654I LYS* 3.2 27.4 + - - +
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Residues in contact with LEU 652 (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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1007H ALA* 4.3 7.4 - - + -
1008H ARG 4.0 15.7 - - - +
625I TYR* 3.4 27.2 - - - -
626I SER 3.1 32.1 - - - +
627I GLY* 4.4 1.3 - - - -
644I LEU* 4.5 14.4 - - + -
648I MET* 2.7 33.1 + - + +
649I ALA* 3.4 8.5 - - - +
651I GLU* 1.3 76.1 - - - +
653I PHE* 1.3 68.1 + - + +
654I LYS 3.5 1.7 + - - -
700I VAL* 5.8 0.2 - - + -
747I VAL* 4.2 32.8 - - + +
749I VAL* 4.5 17.8 - - + +
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Residues in contact with PHE 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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625I TYR* 5.8 0.2 - - - -
644I LEU* 4.5 8.3 - - + -
649I ALA* 2.5 29.8 + - + +
650I LEU 3.3 4.0 - - - -
652I LEU* 1.3 80.3 - - + +
654I LYS* 1.3 61.4 + - - +
655I PRO* 3.5 2.7 - - - -
656I PHE* 3.5 27.2 + + + -
657I LEU* 3.0 22.7 + - - +
691I LEU* 4.1 12.3 - - + -
694I VAL* 5.2 8.3 - - + -
695I ILE* 3.9 35.9 - - + -
698I LYS* 4.6 20.9 - - + -
699I VAL 5.1 0.9 - - - -
700I VAL* 3.5 20.0 - - + -
718I PRO* 5.0 0.2 - - + -
749I VAL* 3.2 33.4 - - + -
756I GLN* 5.9 0.4 - - - -
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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