Contacts of the helix formed by residues 113 - 125 (chain F) in PDB entry 1Z6Z
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 ASP 113 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106F LYS* 6.0 4.0 - - - +
110F ASP 4.7 1.2 + - - +
111F LEU* 3.5 2.8 - - - +
112F SER* 1.3 76.1 + - - +
114F SER* 1.3 57.7 + - - +
115F THR* 3.2 13.1 + - - +
116F GLN* 2.9 48.8 + - + +
117F VAL* 3.0 31.4 + - + +
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Residues in contact with SER 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E GLU* 2.5 39.2 + - - -
73E LEU* 3.6 24.7 - - - -
74E GLN* 3.7 9.1 + - - +
126E THR* 3.7 10.5 - - - +
130E CYS* 3.8 12.1 - - - -
112F SER 3.4 5.0 + - - -
113F ASP* 1.3 73.2 + - - +
115F THR* 1.3 58.0 + - - +
117F VAL* 3.3 0.6 + - - -
118F ASN* 2.8 35.4 + - - -
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Residues in contact with THR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E GLU* 3.8 28.5 - - + +
113F ASP* 3.2 9.8 + - - +
114F SER* 1.3 73.0 - - - +
116F GLN* 1.3 62.5 + - - +
118F ASN* 3.4 7.8 + - - +
119F ASN* 2.9 43.0 + - - +
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Residues in contact with GLN 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ASP* 4.7 18.2 + - - +
106F LYS* 4.5 26.6 - - - +
111F LEU* 4.6 10.7 - - - +
113F ASP* 2.9 34.4 + - - +
115F THR* 1.3 79.6 + - - +
117F VAL* 1.3 61.9 + - - +
119F ASN* 3.5 10.2 + - - +
120F TYR* 3.2 20.1 + - - +
166F LEU* 4.9 8.4 - - - +
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Residues in contact with VAL 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E THR* 3.5 17.9 - - + +
129E LEU* 4.0 28.3 - - + -
130E CYS* 4.6 7.2 - - - -
111F LEU* 4.7 15.0 - - + +
113F ASP 3.0 23.2 + - - +
114F SER 3.7 3.8 - - - +
116F GLN* 1.3 77.3 - - - +
118F ASN* 1.3 64.8 + - - +
120F TYR* 3.1 17.4 + - - +
121F TRP* 3.2 37.2 + - + +
166F LEU* 4.2 14.8 - - + -
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Residues in contact with ASN 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E GLU* 3.4 19.6 + - - +
118E ASN* 4.8 5.2 - - + +
122E ALA* 3.4 26.3 + - - +
126E THR* 2.7 30.8 + - - +
114F SER 2.8 24.8 + - - +
115F THR* 3.8 6.7 - - - +
117F VAL* 1.3 72.0 - - - +
119F ASN* 1.3 61.2 + - - +
121F TRP* 3.3 9.4 + - - +
122F ALA* 3.0 27.1 + - - +
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Residues in contact with ASN 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F GLY* 4.8 9.1 - - - +
115F THR* 2.9 33.4 + - - +
116F GLN* 3.7 9.0 - - + +
118F ASN* 1.3 74.1 - - - +
120F TYR* 1.3 66.9 + - - +
122F ALA* 3.4 8.4 + - - +
123F LEU* 3.2 23.6 + - - +
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Residues in contact with TYR 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F SER* 2.7 33.4 + - - -
101F LEU 3.8 0.7 + - - -
102F GLY* 3.6 24.0 - - - -
116F GLN 3.2 12.8 + - - +
117F VAL 3.1 11.4 + - - +
119F ASN* 1.3 77.7 - - - +
121F TRP* 1.3 76.5 + + - +
123F LEU* 5.1 0.9 - - - -
124F ASN* 3.0 66.6 + - + +
166F LEU* 3.3 45.5 - - + -
167F TYR* 3.3 23.7 + - - -
170F GLY* 4.8 3.2 - - - -
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Residues in contact with TRP 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E TRP* 3.7 35.4 - - + -
125E LEU* 3.6 31.0 - - + +
126E THR* 3.0 28.0 + - - -
129E LEU* 4.5 7.2 - - + -
177E LEU* 4.8 5.6 - - + -
117F VAL* 3.2 23.4 + - + +
118F ASN* 3.7 8.1 - - - +
120F TYR* 1.3 86.1 - + - +
122F ALA* 1.3 61.6 + - - +
124F ASN* 5.7 0.2 - - + -
125F LEU* 2.7 47.4 + - + +
126F THR* 3.0 8.9 + - - -
166F LEU* 3.7 40.4 - - + -
169F ALA* 3.9 20.9 - - + -
170F GLY* 4.0 13.9 - - - -
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Residues in contact with ALA 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E ASN* 3.5 31.3 + - - +
67F LEU 3.8 4.4 - - - +
68F GLY 3.7 19.5 - - - +
73F LEU* 6.0 0.2 - - - +
118F ASN 3.0 13.8 + - - +
119F ASN* 3.6 12.1 - - - +
120F TYR 3.3 0.4 - - - -
121F TRP* 1.3 75.6 - - - +
123F LEU* 1.3 57.3 + - - +
126F THR* 3.4 3.3 - - + -
127F SER* 3.1 30.7 + - - -
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Residues in contact with LEU 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F LEU* 4.0 18.6 - - + -
68F GLY* 3.9 9.6 - - - +
98F ALA* 5.0 12.1 - - + +
99F GLY* 5.0 3.4 - - - -
100F SER* 3.5 35.0 - - - +
119F ASN 3.2 12.6 + - - +
120F TYR* 5.1 0.9 - - - -
122F ALA* 1.3 79.7 - - - +
124F ASN* 1.3 69.8 + - - +
127F SER* 2.7 23.0 + - - +
128F MET* 5.5 0.2 - - - +
174F ARG* 5.1 1.6 + - - -
806F NAP 3.6 49.8 - - + +
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Residues in contact with ASN 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F ALA 5.5 0.7 - - - -
99F GLY* 3.3 9.2 - - - -
100F SER* 2.9 48.8 + - - +
120F TYR* 3.0 55.8 + - + +
123F LEU* 1.3 83.8 - - - +
125F LEU* 1.3 63.4 + - + +
128F MET* 3.6 2.3 - - - +
167F TYR* 5.9 0.3 - - - -
170F GLY* 5.3 3.6 - - - -
171F LYS* 5.6 2.9 + - - -
174F ARG* 2.8 43.6 + - - +
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Residues in contact with LEU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E TRP* 3.6 44.2 - - + +
125E LEU* 4.0 9.9 - - + -
121F TRP* 2.7 45.4 + - + +
123F LEU 3.5 0.2 - - - -
124F ASN* 1.3 79.9 - - + +
126F THR* 1.3 67.4 + - - +
127F SER 3.4 1.1 - - - -
128F MET* 3.3 8.3 - - - +
129F LEU* 3.0 24.2 + - - +
170F GLY* 3.5 28.7 - - - +
173F ALA* 3.5 20.0 - - + -
174F ARG* 3.9 8.3 - - + +
177F LEU* 4.6 5.7 - - + +
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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