Contacts of the helix formed by residues 673 - 687 (chain X) in PDB entry 6AH0
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 GLN 673 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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671X VAL 3.5 2.8 - - - -
672X ASN* 1.3 78.3 + - - +
674X LYS* 1.3 60.1 + - - +
675X LYS 3.1 3.1 - - - -
676X GLY* 2.9 23.0 + - - +
677X CYS 3.1 8.7 + - - -
721X THR* 6.1 2.2 - - - -
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Residues in contact with LYS 674 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673X GLN* 1.3 70.5 - - - +
675X LYS* 1.3 60.3 + - - +
677X CYS* 3.5 5.3 + - - +
678X ASP* 3.2 17.0 + - - -
721X THR* 6.3 2.2 - - - +
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Residues in contact with LYS 675 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673X GLN 3.1 0.8 - - - -
674X LYS* 1.3 74.9 - - - +
676X GLY* 1.3 65.2 + - - +
678X ASP* 3.2 2.5 + - - +
679X VAL* 3.0 20.3 + - - -
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Residues in contact with GLY 676 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671X VAL* 6.2 2.0 - - - -
673X GLN 2.9 10.6 + - - -
675X LYS* 1.3 76.3 - - - +
677X CYS* 1.3 63.9 + - - +
679X VAL* 5.3 0.2 - - - -
680X LEU* 2.8 25.5 + - - -
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Residues in contact with CYS 677 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671X VAL* 5.7 5.4 - - - +
673X GLN 3.1 10.8 + - - -
674X LYS* 3.5 6.7 + - - +
675X LYS 3.2 0.4 - - - -
676X GLY* 1.3 75.2 - - - +
678X ASP* 1.3 61.3 + - - +
681X ALA* 3.1 18.2 + - - -
694X LEU 6.6 0.7 - - - -
719X VAL* 5.5 8.1 - - - +
720X ALA* 5.4 14.8 - - - +
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Residues in contact with ASP 678 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674X LYS 3.2 10.0 + - - -
675X LYS* 3.2 6.8 + - - +
677X CYS* 1.3 75.6 - - - +
679X VAL* 1.3 56.2 + - - +
681X ALA* 3.4 2.1 + - - -
682X LYS* 3.1 23.2 + - - -
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Residues in contact with VAL 679 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675X LYS 3.0 13.2 + - - -
676X GLY 3.8 0.9 - - - -
678X ASP* 1.3 72.8 - - - +
680X LEU* 1.3 67.0 + - - +
682X LYS* 3.4 2.3 + - - +
683X SER* 3.3 16.3 + - - -
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Residues in contact with LEU 680 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676X GLY 2.8 18.1 + - - -
677X CYS 4.2 0.2 - - - -
679X VAL* 1.3 70.2 - - - +
681X ALA* 1.3 63.3 + - - +
683X SER* 3.1 12.6 + - - +
684X LEU* 3.2 10.2 + - - -
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Residues in contact with ALA 681 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677X CYS 3.1 15.1 + - - -
678X ASP* 3.8 4.0 - - - +
679X VAL 3.2 0.2 - - - -
680X LEU* 1.3 77.4 - - - +
682X LYS* 1.3 59.9 + - - +
684X LEU* 3.4 2.0 + - - +
685X GLU* 3.2 17.3 + - - -
691X ALA* 5.4 12.5 - - - +
692X CYS 6.0 2.2 - - - -
719X VAL* 6.3 2.7 - - - +
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Residues in contact with LYS 682 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678X ASP 3.1 14.6 + - - -
679X VAL* 3.4 4.4 + - - +
680X LEU 3.2 0.6 - - - -
681X ALA* 1.3 75.9 - - - +
683X SER* 1.3 62.3 + - - +
685X GLU* 3.0 5.4 + - - +
686X LYS* 2.9 18.9 + - - -
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Residues in contact with SER 683 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679X VAL 3.3 9.4 + - - -
680X LEU* 3.1 8.6 + - - +
682X LYS* 1.3 75.4 - - - +
684X LEU* 1.3 56.8 + - - +
686X LYS* 3.1 4.0 + - - +
687X MET* 3.0 22.5 + - - -
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Residues in contact with LEU 684 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680X LEU 3.2 11.0 + - - -
681X ALA* 3.4 3.6 + - - +
682X LYS 3.1 1.0 - - - -
683X SER* 1.3 73.3 - - - +
685X GLU* 1.3 61.0 + - - +
686X LYS 3.1 1.6 - - - -
687X MET* 3.0 11.3 + - - +
688X GLY 3.2 0.3 + - - -
689X TYR* 2.8 27.1 + - - -
691X ALA* 6.5 0.2 - - - -
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Residues in contact with GLU 685 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681X ALA 3.2 9.8 + - - -
682X LYS* 3.0 8.0 + - - +
684X LEU* 1.3 75.7 - - - +
686X LYS* 1.3 59.7 + - - +
688X GLY* 3.3 11.8 + - - -
689X TYR 3.3 18.9 + - - +
691X ALA* 5.5 1.7 - - - +
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Residues in contact with LYS 686 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682X LYS 2.9 13.2 + - - -
683X SER* 3.1 7.1 + - - +
684X LEU 3.1 0.2 - - - -
685X GLU* 1.3 75.3 - - - +
687X MET* 1.3 56.2 + - - +
688X GLY* 3.0 9.3 + - - -
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Residues in contact with MET 687 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683X SER 3.0 12.9 + - - -
684X LEU* 3.0 7.7 + - - +
686X LYS* 1.3 73.0 - - - +
688X GLY* 1.3 61.8 + - - +
689X TYR 3.5 0.2 - - - -
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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