Contacts of the helix formed by residues 654 - 668 (chain A) in PDB entry 1XMJ
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 SER 654 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652A GLN 4.0 0.6 + - - -
653A PHE* 1.3 78.2 - - - +
655A ALA* 1.3 60.8 + - - +
656A GLU* 3.6 8.0 + - - +
657A ARG* 3.2 21.9 + - - +
658A ARG* 2.9 30.0 + - - +
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Residues in contact with ALA 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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576A GLY* 5.4 9.2 - - - +
605A SER* 5.0 0.4 - - - +
654A SER* 1.3 73.1 - - - +
656A GLU* 1.3 61.8 + - + +
658A ARG* 3.8 26.9 - - - +
659A ASN* 2.7 40.5 + - - +
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Residues in contact with GLU 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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654A SER* 3.2 8.4 + - - +
655A ALA* 1.3 81.0 - - + +
657A ARG* 1.3 57.9 + - - +
659A ASN* 3.5 5.4 + - - +
660A SER* 3.0 31.5 + - - -
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Residues in contact with ARG 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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653A PHE* 3.9 35.7 - - + -
654A SER* 3.2 18.3 + - - +
656A GLU* 1.3 77.2 - - - +
658A ARG* 1.3 61.8 + - - +
660A SER* 3.2 17.7 + - - -
661A ILE* 2.8 56.7 + - + +
664A GLU* 3.5 25.3 + - - -
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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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583A GLU* 5.1 2.8 + - - -
605A SER* 2.7 47.4 + - - +
606A LYS* 3.3 34.4 - - - +
650A PHE* 3.4 54.9 - - + +
651A ASP* 4.0 9.6 - - - +
653A PHE* 3.1 23.2 + - + +
654A SER 2.9 15.4 + - - +
655A ALA* 3.8 28.2 - - - +
657A ARG* 1.3 75.7 - - - +
659A ASN* 1.3 57.3 + - - +
661A ILE* 3.3 2.9 + - - +
662A LEU* 2.8 30.4 + - - +
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Residues in contact with ASN 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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1A ATP 5.4 2.0 + - - -
458A GLY 4.3 13.2 - - - +
459A SER* 5.2 0.2 - - - -
460A THR* 5.6 12.1 + - + +
464A LYS* 5.0 6.6 + - - -
605A SER* 3.7 25.6 + - - -
655A ALA* 2.7 35.2 + - - +
656A GLU* 3.9 5.3 - - - +
658A ARG* 1.3 74.9 - - - +
660A SER* 1.3 54.1 + - - +
662A LEU* 3.8 6.3 - - - +
663A THR* 2.7 38.7 + - - +
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Residues in contact with SER 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A THR* 6.3 0.2 - - - -
656A GLU* 3.0 17.7 + - - -
657A ARG* 3.2 26.7 + - - -
659A ASN* 1.3 75.6 - - - +
661A ILE* 1.3 64.0 + - - +
663A THR* 3.4 4.5 + - - -
664A GLU* 3.0 36.4 + - - +
667A ARG* 5.2 0.7 + - - +
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Residues in contact with ILE 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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643A LYS* 4.7 9.2 - - + +
644A LEU* 4.2 5.6 - - + -
650A PHE* 3.8 23.6 - - + -
653A PHE* 3.8 35.9 - - + -
657A ARG* 2.8 51.5 + - - +
658A ARG 3.7 4.3 - - - +
660A SER* 1.3 70.8 - - - +
662A LEU* 1.3 64.2 + - - +
664A GLU* 3.3 9.1 + - - +
665A THR* 2.8 38.5 + - - +
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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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457A ALA* 4.2 12.3 - - + -
458A GLY* 3.5 39.7 - - - +
605A SER* 5.1 9.4 - - - -
607A MET* 5.2 6.3 - - + -
618A ILE* 5.3 4.0 - - + -
640A PHE* 4.3 15.7 - - + -
644A LEU* 4.2 25.1 - - + -
650A PHE* 4.7 5.6 - - + -
658A ARG 2.8 20.9 + - - +
659A ASN* 3.8 12.8 - - - +
661A ILE* 1.3 72.9 - - - +
663A THR* 1.3 58.7 + - - +
665A THR* 3.3 1.0 + - - -
666A LEU* 2.9 56.1 + - + +
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Residues in contact with THR 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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459A SER* 3.5 19.9 - - - -
460A THR* 3.2 38.6 + - + +
620A HIS* 5.5 1.1 - - + -
659A ASN 2.7 21.3 + - - -
660A SER* 3.7 6.3 - - - -
662A LEU* 1.3 77.8 - - - +
664A GLU* 1.3 55.7 + - - +
666A LEU* 3.2 2.6 + - - +
667A ARG* 2.9 63.6 + - + +
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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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657A ARG* 3.5 28.3 + - - -
660A SER* 3.0 26.8 + - - +
661A ILE* 3.7 7.8 + - - +
663A THR* 1.3 72.7 - - - +
665A THR* 1.3 68.3 + - - +
667A ARG* 3.5 36.4 + - - +
668A ARG* 3.5 15.5 + - - +
674A ASP* 5.0 0.5 - - - +
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Residues in contact with THR 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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640A PHE* 3.6 31.6 - - + +
643A LYS* 4.0 35.3 - - + +
644A LEU* 4.4 3.9 - - + +
661A ILE* 2.8 28.2 + - - +
662A LEU* 3.8 4.7 - - - -
664A GLU* 1.3 76.5 - - - +
666A LEU* 1.3 64.8 + - - +
668A ARG* 3.0 33.1 + - - +
669A PHE* 4.2 5.9 - - - -
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Residues in contact with LEU 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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458A GLY* 4.1 2.5 - - - -
459A SER* 3.7 24.9 - - - +
618A ILE* 4.1 12.1 - - + -
619A LEU 3.8 7.0 - - - +
620A HIS* 3.6 37.3 - - + +
625A TYR* 5.2 3.4 - - + -
640A PHE* 3.4 30.1 - - + -
662A LEU* 2.9 39.7 + - + +
663A THR 3.7 3.8 - - - +
665A THR* 1.3 77.4 - - - +
667A ARG* 1.3 58.6 + - - +
669A PHE* 2.9 45.8 + - + +
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Residues in contact with ARG 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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620A HIS* 4.0 20.6 + - + +
660A SER 5.2 0.2 + - - -
663A THR* 2.9 43.7 + - + +
664A GLU* 3.7 33.2 - - - +
665A THR 3.2 0.2 - - - -
666A LEU* 1.3 77.3 - - - +
668A ARG* 1.3 59.8 + - - +
669A PHE 3.0 4.8 + - - +
670A SER* 4.0 13.5 + - - -
674A ASP* 4.2 7.9 - - - +
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Residues in contact with ARG 668 (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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639A ASP* 4.8 11.0 + - - -
643A LYS* 4.1 24.6 - - - +
664A GLU 3.5 11.4 - - - +
665A THR* 3.2 30.3 - - - +
666A LEU 3.0 1.2 - - - -
667A ARG* 1.3 77.4 - - - +
669A PHE* 1.3 59.0 + - + +
670A SER* 2.9 14.6 + - - +
672A GLU 5.7 0.5 - - - +
674A ASP* 3.5 36.5 + - + +
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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