Contacts of the helix formed by residues 110 - 128 (chain E) in PDB entry 1NZB
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 110 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E PRO* 2.9 38.5 - - - +
106E ARG 4.2 0.6 + - - -
107E PRO* 3.0 12.6 + - - +
109E ASP* 1.3 79.8 - - - +
111E ASN* 1.3 66.2 + - - +
112E ALA* 3.8 2.8 + - - -
113E VAL* 3.5 10.6 + - - +
114E SER* 3.2 22.5 + - - -
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Residues in contact with ASN 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASN* 4.8 17.8 + - - +
29B ASP* 4.2 20.8 + - - +
30B MET* 5.7 1.6 - - - +
101B ARG* 4.8 15.1 + - - +
109E ASP 3.9 1.6 + - - -
110E SER* 1.3 72.6 - - - +
112E ALA* 1.3 67.7 + - - +
114E SER* 3.3 7.8 + - - -
115E LEU* 3.0 49.1 + - - +
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Residues in contact with ALA 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 5.4 8.4 + - - +
32B ARG* 4.3 21.3 - - - +
33B ASP* 4.0 2.1 - - - +
68E PRO* 4.4 16.4 - - + +
69E GLU* 4.3 10.3 - - - +
72E ARG* 4.0 7.0 - - + -
110E SER* 3.3 8.2 - - - +
111E ASN* 1.3 83.7 - - - +
113E VAL* 1.3 54.5 + - - +
115E LEU* 3.3 8.9 + - - +
116E VAL* 2.8 28.5 + - - +
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Residues in contact with VAL 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E PRO* 3.4 26.9 - - + +
71E VAL* 4.1 16.8 - - + -
72E ARG* 4.2 2.7 - - - +
75E LEU* 3.7 11.4 - - + -
92E LEU* 3.5 32.3 - - + -
107E PRO* 3.4 29.2 - - + +
108E SER* 4.5 2.5 - - - -
110E SER* 3.3 8.1 + - - +
112E ALA* 1.3 70.0 - - - +
114E SER* 1.3 58.1 + - - +
115E LEU 3.0 4.9 - - - -
116E VAL* 2.9 28.7 + - - +
117E MET* 3.2 9.5 + - - +
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Residues in contact with SER 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E SER* 3.9 15.9 + - - +
109E ASP 5.5 0.2 - - - -
110E SER 3.2 16.4 + - - -
111E ASN* 3.3 12.0 + - - -
113E VAL* 1.3 79.7 - - - +
115E LEU* 1.3 60.1 + - - +
116E VAL 3.4 0.2 - - - -
117E MET* 4.3 7.9 - - - +
118E ARG* 3.8 19.9 + - - +
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Residues in contact with LEU 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 4.1 20.0 - - + +
30B MET* 4.2 15.9 - - + +
33B ASP* 3.7 16.4 - - - +
36B ALA* 3.4 42.4 - - + +
37B PHE* 4.1 22.7 - - + -
101B ARG* 4.4 12.6 - - - +
111E ASN* 3.0 44.9 + - - +
112E ALA* 3.5 5.6 - - - +
113E VAL 3.0 1.2 - - - -
114E SER* 1.3 79.6 - - - +
116E VAL* 1.3 60.6 + - - +
118E ARG* 3.9 4.4 + - - -
119E ARG* 3.4 4.7 + - - +
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Residues in contact with VAL 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP* 4.0 8.5 - - - +
72E ARG* 3.0 45.1 - - + +
75E LEU* 5.2 3.1 - - + -
76E LEU* 3.9 24.0 - - + +
112E ALA 2.8 21.3 - - - +
113E VAL* 2.9 17.5 - - + +
115E LEU* 1.3 72.2 - - - +
117E MET* 1.3 55.0 + - + +
118E ARG 3.1 1.6 - - - -
119E ARG* 2.8 9.0 + - - +
120E ILE* 2.6 50.2 + - + +
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Residues in contact with MET 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E LEU* 4.3 7.4 - - + -
85E VAL* 5.0 12.1 - - + -
88E ILE* 4.1 28.0 - - + +
89E GLN* 4.6 20.4 - - + +
92E LEU* 3.3 38.4 - - + -
113E VAL 3.2 10.9 + - - +
114E SER* 4.5 6.5 - - - +
116E VAL* 1.3 79.1 - - - +
118E ARG* 1.3 58.2 + - - +
120E ILE* 4.1 21.1 - - + -
121E ARG* 2.8 46.2 + - - +
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Residues in contact with ARG 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ALA* 3.7 32.8 + - + +
37B PHE* 3.9 18.8 - - - -
101B ARG* 4.1 12.7 - - - +
122D T 3.5 28.5 + - - -
123D T 3.2 24.5 + - - -
114E SER 3.8 17.6 + - - +
115E LEU* 4.0 5.2 - - - +
116E VAL 3.1 0.6 - - - -
117E MET* 1.3 79.1 - - - +
119E ARG* 1.3 62.2 + - - +
121E ARG* 4.3 20.7 + - - +
122E LYS* 3.5 21.8 + - - +
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Residues in contact with ARG 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ARG 4.7 4.0 + - - -
33B ASP* 3.1 38.4 + - - +
35B GLN* 3.7 20.9 - - + +
36B ALA* 3.6 15.2 - - - +
72E ARG* 5.8 0.9 - - - -
76E LEU* 3.3 34.3 - - - +
79E GLN* 4.2 1.2 + - - -
115E LEU 3.4 11.9 + - - +
116E VAL* 2.8 11.3 + - - +
118E ARG* 1.3 77.8 - - - +
120E ILE* 1.3 60.3 + - - +
122E LYS* 3.9 1.2 - - - +
123E GLU* 2.8 69.4 + - - +
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Residues in contact with ILE 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E LEU* 4.2 30.5 - - + +
76E LEU* 4.5 3.4 - - + +
79E GLN* 3.6 24.2 - - + +
85E VAL* 5.3 3.1 - - + -
88E ILE* 4.0 21.8 - - + -
116E VAL* 2.6 40.1 + - + +
117E MET* 3.8 22.7 - - + +
119E ARG* 1.3 71.5 - - + +
121E ARG* 1.3 57.7 + - - +
123E GLU* 2.9 7.7 + - - +
124E ASN* 2.6 55.7 + - - +
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Residues in contact with ARG 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 4.1 30.7 + - + +
205B SER* 5.4 5.2 - - - +
206B THR* 5.9 3.4 - - + -
85E VAL* 4.0 33.0 - - + +
89E GLN* 4.9 11.1 - - - +
117E MET* 2.8 43.8 + - - +
118E ARG* 4.3 21.1 + - - +
120E ILE* 1.3 73.1 - - - +
122E LYS* 1.3 52.0 + - - +
124E ASN* 3.6 1.2 - - - +
125E VAL* 2.7 39.1 + - + +
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Residues in contact with LYS 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLN* 3.4 25.3 + - + +
36B ALA 3.9 9.4 - - - +
37B PHE 2.9 27.0 + - - -
38B SER* 3.2 20.0 - - - +
39B GLU* 3.9 3.4 - - - +
199B ARG* 3.3 30.5 - - - +
204B VAL* 4.0 16.1 - - + +
118E ARG 3.5 15.9 + - - +
119E ARG 3.9 1.1 - - - +
120E ILE 3.3 0.4 - - - -
121E ARG* 1.3 78.3 - - - +
123E GLU* 1.3 64.7 + - - +
125E VAL* 2.8 27.8 - - - +
126E ASP* 3.0 12.0 + - - +
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Residues in contact with GLU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLN* 3.2 25.9 - - + +
79E GLN* 3.5 21.7 + - - +
119E ARG* 2.8 67.1 + - - +
120E ILE* 2.9 6.3 + - - +
122E LYS* 1.3 80.2 - - - +
124E ASN* 1.3 59.6 + - - +
126E ASP* 3.8 5.0 + - - +
127E ALA* 3.4 18.9 + - - +
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Residues in contact with ASN 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E GLN* 2.7 38.7 + - - +
82E GLY* 5.9 1.2 - - - -
83E LEU 4.3 8.9 + - - -
85E VAL* 3.5 17.6 - - + +
88E ILE* 5.5 0.8 - - - +
120E ILE* 2.6 31.1 + - - +
123E GLU* 1.3 70.6 - - - +
125E VAL* 1.3 63.8 + - - +
126E ASP 3.1 1.8 - - - -
127E ALA* 3.2 13.5 + - - +
128E GLY 3.3 0.2 + - - -
129E GLU* 2.7 54.2 + - - +
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Residues in contact with VAL 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B GLY* 4.0 16.7 - - - +
199B ARG* 3.9 4.3 - - + +
204B VAL* 3.3 28.5 - - + -
205B SER* 3.0 45.5 - - - +
206B THR* 4.2 6.5 - - + +
85E VAL* 5.2 0.2 - - - +
121E ARG* 2.7 17.5 + - + +
122E LYS* 2.8 24.2 - - - +
124E ASN* 1.3 72.9 - - - +
126E ASP* 1.3 70.1 + - - +
128E GLY* 3.3 12.3 + - - -
129E GLU* 4.2 8.7 + - - +
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Residues in contact with ASP 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B ARG* 4.4 13.2 + - - +
181B ARG* 4.4 13.5 + - - -
199B ARG* 3.0 57.4 + - - +
122E LYS* 3.0 14.2 + - - +
123E GLU* 4.0 5.6 - - - +
125E VAL* 1.3 78.3 - - - +
127E ALA* 1.3 61.4 + - - +
128E GLY* 3.0 7.3 + - - -
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Residues in contact with ALA 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ARG* 5.2 5.5 + - - -
183B LYS* 4.9 8.1 + - - -
123E GLU 3.4 12.2 + - - +
124E ASN* 3.2 14.2 + - - +
126E ASP* 1.3 78.2 - - - +
128E GLY* 1.3 58.0 + - - +
129E GLU* 4.7 1.6 - - + +
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Residues in contact with GLY 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ARG* 6.3 0.4 - - - -
183B LYS* 5.4 10.7 + - - -
124E ASN 3.3 1.0 + - - -
125E VAL 3.3 7.4 + - - -
126E ASP 3.0 6.0 - - - -
127E ALA* 1.3 81.4 - - - +
129E GLU* 1.3 62.3 + - - +
130E ARG* 2.8 20.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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