Contacts of the helix formed by residues 112 - 124 (chain R) in PDB entry 6MZL
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 112 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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895E HIS* 4.9 3.4 - - + -
898E VAL* 3.3 20.6 - - - +
106R ARG* 2.4 44.9 + - - +
108R SER* 5.4 3.7 + - - -
110R THR* 3.7 16.8 + - + +
111R LEU* 1.3 92.2 - - - +
113R VAL* 1.3 67.7 + - + +
114R LYS* 3.1 20.6 + - - +
115R ASP 3.9 4.4 + - - -
116R VAL* 3.6 5.2 + - - +
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Residues in contact with VAL 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895E HIS* 5.8 1.1 - - + -
898E VAL* 3.7 28.5 - - + -
901E TYR* 6.0 5.8 - - + -
112R GLU* 1.3 76.9 - - + +
114R LYS* 1.3 69.2 + - + +
116R VAL* 3.2 6.6 + - + +
117R GLN* 2.9 43.9 + - + +
128R ILE* 5.9 7.2 - - + -
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Residues in contact with LYS 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M HIS* 4.7 24.6 + - + +
62M LYS* 5.4 14.0 - - - +
106R ARG* 3.4 15.7 - - - +
112R GLU* 3.1 36.2 + - - +
113R VAL* 1.3 90.4 - - + +
115R ASP* 1.3 61.2 + - - +
117R GLN* 3.4 9.8 + - - +
118R LEU* 2.9 31.2 + - - +
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Residues in contact with ASP 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M HIS* 6.1 0.5 - - - +
99R ALA* 4.7 6.4 - - - +
102R LEU* 2.9 55.7 - - + +
103R ALA* 3.4 7.0 - - - +
105R HIS* 5.3 2.3 + - - -
106R ARG* 3.0 31.3 + - - -
111R LEU* 3.3 31.0 - - + +
112R GLU 3.9 1.3 + - - +
113R VAL 3.3 0.2 - - - -
114R LYS* 1.3 75.3 - - - +
116R VAL* 1.3 66.6 + - - +
118R LEU* 3.4 0.4 + - - -
119R HIS* 3.0 22.2 + - - +
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Residues in contact with VAL 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898E VAL* 3.7 17.5 - - + +
901E TYR* 4.2 24.0 - - + +
902E VAL* 3.7 29.6 - - + -
905E ALA* 5.7 1.6 - - + -
99R ALA* 5.8 4.7 - - + -
111R LEU* 3.8 9.9 - - + -
112R GLU 3.6 16.2 - - - +
113R VAL* 3.2 8.9 + - + +
115R ASP* 1.3 75.9 - - + +
117R GLN* 1.3 58.0 + - - +
119R HIS* 3.2 7.4 + - - +
120R LEU* 2.8 40.7 + - + +
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Residues in contact with GLN 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113R VAL* 2.9 32.1 + - + +
114R LYS* 3.9 10.7 - - - +
116R VAL* 1.3 76.4 - - - +
118R LEU* 1.3 56.9 + - - +
120R LEU* 3.2 21.0 + - + +
121R GLU* 2.9 39.4 + - + +
126R MET* 5.7 2.6 + - + -
128R ILE* 6.4 0.2 - - - +
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Residues in contact with LEU 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56M ILE* 3.9 21.8 - - + -
57M TYR* 3.6 36.6 - - + +
60M HIS* 3.8 33.7 - - + +
102R LEU* 3.8 16.4 - - + -
105R HIS* 5.7 0.4 - - - +
114R LYS 2.9 19.4 + - - +
115R ASP* 5.7 0.2 - - - -
116R VAL 3.3 0.2 - - - -
117R GLN* 1.3 74.3 - - - +
119R HIS* 1.3 61.9 + - - +
121R GLU* 3.1 29.2 + - + +
122R ARG* 2.9 28.7 + - + +
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Residues in contact with HIS 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91R PHE* 4.6 11.9 - + - -
94R SER* 5.6 2.6 + - - -
95R VAL* 4.6 21.5 + - + +
98R ALA* 3.9 18.9 - - + +
99R ALA 6.2 0.2 - - - +
102R LEU* 4.3 3.9 - - + +
115R ASP 3.0 16.5 + - - +
116R VAL* 3.8 4.7 - - - +
118R LEU* 1.3 73.3 - - - +
120R LEU* 1.3 62.4 + - + +
122R ARG* 3.1 39.6 + - - +
123R GLN* 2.9 61.9 + - + +
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Residues in contact with LEU 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901E TYR* 3.7 28.9 - - + +
905E ALA* 4.2 18.2 - - + -
116R VAL* 2.8 20.6 + - + +
117R GLN* 3.3 27.4 - - + +
118R LEU 3.2 0.4 - - - -
119R HIS* 1.3 77.8 - - + +
121R GLU* 1.3 54.0 + - + +
123R GLN* 2.9 2.2 + - + +
124R TRP* 2.3 58.3 + - + +
125R ASN 2.7 9.8 + - - -
126R MET* 3.7 33.0 - - + +
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Residues in contact with GLU 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56M ILE* 6.0 1.0 - - - +
60M HIS* 5.1 4.4 + - - -
117R GLN* 2.9 29.8 + - + +
118R LEU* 3.1 28.6 + - + +
120R LEU* 1.3 76.5 - - + +
122R ARG* 1.3 60.9 - - - +
123R GLN 3.5 1.4 + - - -
125R ASN* 4.1 29.0 + - - +
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Residues in contact with ARG 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M TYR* 2.3 31.8 + - - -
77M CYS* 2.8 35.9 - - - +
81M GLN* 5.6 10.1 - - - +
98R ALA* 3.8 17.0 - - - +
101R GLN* 5.4 0.4 + - - -
102R LEU* 3.4 20.0 - - - +
118R LEU* 2.9 19.1 + - + +
119R HIS* 3.1 45.0 + - + +
121R GLU* 1.3 78.4 - - - +
123R GLN* 1.3 66.6 + - - +
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Residues in contact with GLN 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909E ARG* 5.7 2.6 - - - -
91R PHE* 4.5 19.5 - - + -
119R HIS* 2.9 52.1 + - + +
120R LEU* 2.9 2.7 + - + -
121R GLU 4.8 1.1 - - - -
122R ARG* 1.3 90.2 + - - +
124R TRP* 1.3 82.2 + - + +
125R ASN 4.0 0.2 - - - -
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Residues in contact with TRP 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905E ALA* 4.4 10.0 + - + +
908E GLN* 3.1 39.2 - - + +
909E ARG* 3.5 27.7 - - + +
912E ASN* 3.6 28.0 - - + -
915E GLU* 5.9 2.2 - - - -
91R PHE* 5.6 4.0 - - - -
120R LEU* 2.3 41.9 + - + +
123R GLN* 1.3 89.2 - - + +
125R ASN* 1.3 66.8 + - - +
126R MET* 3.6 32.5 - - + +
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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