Contacts of the helix formed by residues 871 - 878 (chain M) in PDB entry 6D6Q
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 GLU 871 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63H VAL* 5.6 7.6 - - + +
862M GLY* 3.3 24.9 - - - +
863M PHE 4.0 4.2 + - - -
864M ALA 4.1 5.8 - - - +
865M THR* 3.9 22.0 - - + +
870M ILE* 1.3 83.8 - - - +
872M MET* 1.3 71.6 + - + +
873M LYS* 3.2 2.7 - - + +
874M GLY* 2.5 33.3 + - - -
875M ARG* 3.4 5.6 + - - -
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Residues in contact with MET 872 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H GLY* 6.3 0.9 - - - -
43H HIS* 5.7 11.9 - - - +
63H VAL* 6.0 5.8 - - + -
66H LEU* 3.4 34.3 - - + -
68H CYS* 6.0 3.1 - - - -
871M GLU* 1.3 85.9 - - + +
873M LYS* 1.3 64.7 + - - +
875M ARG* 2.9 23.8 + - + +
876M VAL* 2.9 21.0 + - + +
893M PHE* 4.5 5.4 - - + -
1014M ILE* 3.4 46.0 - - + +
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Residues in contact with LYS 873 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H VAL* 4.1 12.6 - - + -
64H ASN* 2.3 32.1 + - - +
861M LEU 2.4 37.3 + - - +
862M GLY* 3.6 20.6 + - - +
863M PHE* 3.6 24.3 - - + -
871M GLU* 3.0 1.9 + - + +
872M MET* 1.3 78.1 - - + +
874M GLY* 1.3 57.4 + - - +
876M VAL* 3.2 4.1 + - - +
877M ALA* 2.9 29.6 + - - +
889M THR* 4.3 1.6 - - - +
890M GLU* 2.9 20.5 + - - +
893M PHE* 3.4 40.6 - - + -
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Residues in contact with GLY 874 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571M LEU* 4.4 11.9 - - - -
863M PHE* 4.1 14.6 - - - +
870M ILE* 3.6 17.5 - - - -
871M GLU 2.5 18.8 + - - -
873M LYS* 1.3 74.1 - - - +
875M ARG* 1.3 54.8 + - - -
877M ALA* 3.9 1.2 - - - +
878M CYS* 2.9 35.9 + - - -
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Residues in contact with ARG 875 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H GLU* 3.3 22.6 + - - -
80H VAL* 3.6 33.2 - - + +
81H GLY* 3.7 12.9 - - - +
82H ASP* 4.0 7.9 + - - +
181H ARG* 3.0 30.7 - - - +
575M ARG* 4.3 25.9 + - - +
870M ILE* 3.5 38.9 - - + +
871M GLU 3.4 3.0 + - - +
872M MET* 2.9 16.4 + - + +
874M GLY* 1.3 74.3 - - - +
876M VAL* 1.3 61.4 + - + +
878M CYS* 4.4 6.1 - - - -
879M GLU* 3.9 16.5 - - - +
1013M ALA* 4.6 7.9 - - + +
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Residues in contact with VAL 876 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872M MET* 2.9 18.0 + - + +
873M LYS* 3.6 9.2 - - - +
874M GLY 3.1 0.2 - - - -
875M ARG* 1.3 82.2 - - + +
877M ALA* 1.3 62.0 + - - +
878M CYS 3.5 0.2 - - - -
879M GLU* 3.8 8.9 + - - +
880M ILE* 4.2 5.2 - - + +
889M THR* 4.1 10.5 - - + -
892M MET* 4.0 20.4 - - + -
893M PHE* 3.9 12.6 - - + -
1010M ALA* 3.9 33.4 - - + +
1013M ALA* 5.0 4.0 - - + -
1014M ILE* 3.2 33.2 - - + +
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Residues in contact with ALA 877 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568M ASN* 4.1 0.9 - - - +
571M LEU* 3.8 17.0 - - + -
863M PHE* 4.3 7.0 - - + -
873M LYS 2.9 16.2 + - - +
874M GLY 3.9 0.4 - - - +
876M VAL* 1.3 74.7 - - - +
878M CYS* 1.3 55.6 + - - +
879M GLU 3.1 2.2 - - - -
880M ILE* 2.6 37.5 + - - +
885M GLU* 3.8 25.6 - - + +
889M THR* 3.8 17.0 - - + -
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Residues in contact with CYS 878 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568M ASN* 5.0 2.5 - - - +
571M LEU* 3.4 32.1 - - - -
572M ASN* 3.1 41.0 + - - +
575M ARG* 3.2 34.5 + - - +
870M ILE* 4.6 1.8 - - - -
874M GLY 2.9 28.2 + - - +
875M ARG* 4.7 0.4 - - - -
876M VAL 3.5 0.2 - - - -
877M ALA* 1.3 76.7 - - - +
879M GLU* 1.3 60.8 + - - +
880M ILE 3.0 8.7 + - - +
881M SER* 5.3 1.9 - - - -
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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