Contacts of the helix formed by residues 100 - 118 (chain E) in PDB entry 3N1Q
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 THR 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76E ASP 5.3 2.5 - - - -
77E LEU* 4.1 7.9 - - + -
99E MET* 1.3 77.6 - - - +
101E GLU* 1.3 65.7 + - - +
102E ARG* 3.7 3.5 + - - +
103E CYS* 3.0 31.4 + - - +
104E LYS* 3.0 17.4 + - - +
143E GLU 3.5 26.0 - - - +
144E GLY 3.2 7.2 + - - +
145E ARG* 3.6 13.8 - - + +
186E VAL* 3.8 9.2 - - - +
187E LYS 5.0 0.7 + - - -
189E ASP* 3.7 16.1 + - - +
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Residues in contact with GLU 101 (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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76E ASP 5.4 3.8 + - - +
78E VAL* 4.2 20.8 - - + +
99E MET 4.1 0.6 + - - -
100E THR* 1.3 74.1 - - - +
102E ARG* 1.3 62.2 + - - +
104E LYS* 3.6 18.7 + - - +
105E GLU* 3.3 36.3 + - - +
189E ASP* 3.7 13.3 + - - +
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Residues in contact with ARG 102 (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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100E THR* 4.0 4.0 - - - +
101E GLU* 1.3 79.1 - - - +
103E CYS* 1.3 68.9 - - - +
105E GLU* 3.4 24.8 + - - +
106E ARG* 2.9 48.7 + - - +
172E ASP* 3.4 22.2 + - - -
186E VAL* 4.2 5.8 - - + -
187E LYS* 3.3 40.4 - - - +
188E ALA 4.8 3.4 - - - -
189E ASP* 2.9 21.9 + - - +
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Residues in contact with CYS 103 (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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99E MET* 4.0 8.3 - - + -
100E THR* 3.0 27.4 + - - +
102E ARG* 1.3 78.8 - - - +
104E LYS* 1.3 64.6 + - - +
106E ARG* 3.0 7.6 + - - +
107E VAL* 2.9 36.8 + - - +
144E GLY 3.9 12.8 - - - +
145E ARG 4.7 5.8 - - - -
146E ALA* 5.4 0.2 - - - -
147E LEU* 4.0 21.3 - - - -
171E PHE* 4.4 9.1 - - - -
186E VAL* 3.9 20.6 - - + +
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Residues in contact with LYS 104 (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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873C ASN* 5.7 0.2 + - - -
876C ASP* 5.4 4.9 + - - -
78E VAL* 2.9 50.9 + - + +
79E PRO 2.9 31.0 + - - -
80E ASN* 3.6 10.1 - - + +
99E MET* 3.4 26.9 - - + -
100E THR 3.0 14.1 + - - +
101E GLU* 3.7 20.6 - - - +
102E ARG 3.3 0.2 - - - -
103E CYS* 1.3 76.0 - - - +
105E GLU* 1.3 66.8 + - + +
107E VAL* 2.8 14.1 + - - -
108E ASN* 2.8 29.1 + - - +
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Residues in contact with GLU 105 (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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101E GLU* 3.3 29.1 - - - +
102E ARG* 3.6 12.8 + - - +
103E CYS 3.3 0.6 + - - -
104E LYS* 1.3 76.8 - - + +
106E ARG* 1.3 74.4 + - + +
108E ASN* 3.6 7.9 + - - +
109E ALA* 3.0 27.1 + - - +
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Residues in contact with ARG 106 (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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102E ARG* 2.9 63.9 + - - +
103E CYS 3.0 6.5 + - - +
105E GLU* 1.3 85.9 + - + +
107E VAL* 1.3 61.0 + - - +
109E ALA* 3.4 8.0 - - - +
110E LEU* 2.8 31.5 + - - +
169E ALA* 3.8 9.8 - - - +
170E GLY* 2.7 35.8 + - - -
171E PHE* 3.5 22.6 - - + +
172E ASP* 3.5 10.5 + - - -
186E VAL* 3.7 22.6 - - - +
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Residues in contact with VAL 107 (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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80E ASN* 4.2 7.0 - - - +
85E ILE* 3.5 23.8 - - + -
87E PHE* 5.3 0.7 - - + -
99E MET* 3.7 13.2 - - + -
103E CYS* 2.9 26.0 + - - +
104E LYS* 2.8 6.5 + - - +
106E ARG* 1.3 75.4 - - - +
108E ASN* 1.3 54.8 + - - +
110E LEU* 3.2 4.6 + - - +
111E ALA* 2.7 35.0 + - - +
123E LEU* 4.2 11.0 - - + +
125E VAL* 5.1 3.1 - - + -
147E LEU* 3.4 35.7 - - + -
171E PHE* 3.8 9.2 - - + -
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Residues in contact with ASN 108 (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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80E ASN* 3.1 27.9 + - - +
82E ASN* 3.9 20.8 + - - +
85E ILE* 4.4 0.4 - - - +
104E LYS* 2.8 27.7 + - - +
105E GLU* 3.9 6.4 - - - +
107E VAL* 1.3 71.6 - - - +
109E ALA* 1.3 63.7 + - - +
111E ALA* 3.3 9.6 + - - +
112E ILE* 3.0 31.9 + - + +
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Residues in contact with ALA 109 (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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105E GLU 3.0 19.9 + - - +
106E ARG* 3.4 10.1 - - - +
108E ASN* 1.3 76.5 - - - +
110E LEU* 1.3 62.5 + - - +
112E ILE* 3.1 14.8 + - - +
113E ALA* 3.0 20.5 + - - +
169E ALA* 4.1 18.6 - - + +
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Residues in contact with LEU 110 (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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106E ARG 2.8 20.4 + - - +
107E VAL 3.6 3.6 - - - +
109E ALA* 1.3 73.2 - - - +
111E ALA* 1.3 54.7 + - - +
113E ALA* 2.9 5.4 + - + +
114E VAL* 2.7 49.9 + - + +
123E LEU* 4.1 15.3 - - + -
149E ILE* 3.8 30.1 - - + -
162E LEU* 4.3 3.8 - - + -
165E LEU* 3.3 45.3 - - + +
166E ALA* 3.6 13.9 - - + +
169E ALA* 3.8 9.3 - - + +
171E PHE* 4.0 12.1 - - + -
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Residues in contact with ALA 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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82E ASN* 4.4 6.3 - - - +
84E ASP* 4.5 8.3 - - + +
85E ILE* 3.5 32.5 - - + -
107E VAL 2.7 20.4 + - - +
108E ASN* 3.3 8.7 - - - +
110E LEU* 1.3 72.8 - - - +
112E ILE* 1.3 58.5 + - + +
114E VAL* 3.8 1.4 + - - +
115E MET* 3.1 32.1 + - - +
123E LEU* 4.2 15.0 + - + +
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Residues in contact with ILE 112 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82E ASN* 6.2 1.1 - - - +
108E ASN* 3.0 20.8 + - + +
109E ALA* 3.3 10.5 - - - +
110E LEU 3.0 0.6 - - - -
111E ALA* 1.3 77.0 - - + +
113E ALA* 1.3 67.0 + - - +
114E VAL 3.3 0.2 + - - -
115E MET* 3.4 8.2 + - - +
116E ASN* 3.0 26.3 + - + +
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Residues in contact with ALA 113 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109E ALA 3.0 11.3 + - - +
110E LEU* 2.9 19.4 + - + +
112E ILE* 1.3 77.5 - - - +
114E VAL* 1.3 57.8 + - - +
116E ASN* 3.3 7.2 + - - +
117E MET* 2.8 31.2 + - - +
165E LEU* 4.2 20.5 - - + +
168E GLU* 6.4 1.3 - - + -
169E ALA* 5.9 1.8 - - + -
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Residues in contact with VAL 114 (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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110E LEU* 2.7 36.9 + - + +
111E ALA 3.9 4.7 - - - +
112E ILE 3.2 0.2 - - - -
113E ALA* 1.3 68.8 - - - +
115E MET* 1.3 57.7 + - - +
117E MET* 2.9 7.4 + - - +
118E TRP* 2.7 49.6 + - + +
121E VAL* 3.4 19.7 - - + +
122E ARG 4.0 2.7 - - - +
123E LEU* 4.0 24.5 - - + +
151E THR* 5.0 3.1 - - + -
162E LEU* 3.7 28.5 - - + -
165E LEU* 4.4 4.9 - - + -
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Residues in contact with MET 115 (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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895C GLN* 4.9 4.7 - - - +
84E ASP* 3.6 42.6 - - - +
111E ALA 3.1 17.5 - - - +
112E ILE* 3.4 6.4 + - - +
114E VAL* 1.3 75.1 - - - +
116E ASN* 1.3 61.6 + - - +
118E TRP 2.9 18.4 - - - +
119E PRO* 3.5 8.7 - - - +
120E GLY* 5.8 4.5 - - - +
121E VAL 3.4 21.5 - - - +
122E ARG* 4.2 22.7 - - + -
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Residues in contact with ASN 116 (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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112E ILE* 3.0 22.1 + - + +
113E ALA* 3.5 8.7 - - - +
115E MET* 1.3 76.9 - - - +
117E MET* 1.3 65.0 + - - +
118E TRP* 4.6 0.2 - - - -
119E PRO* 4.7 5.7 - - - +
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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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40E LEU* 4.2 13.0 - - + -
113E ALA 2.8 17.4 + - - +
114E VAL 3.4 3.8 - - - +
116E ASN* 1.3 79.6 - - - +
118E TRP* 1.3 91.9 + - + +
119E PRO* 3.8 5.7 - - - +
161E LEU* 5.1 10.8 - - + -
165E LEU* 3.6 35.9 - - + -
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Residues in contact with TRP 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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114E VAL* 2.7 36.6 + - + +
115E MET* 2.9 12.1 - - - +
117E MET* 1.3 91.9 - - + +
119E PRO* 1.3 67.7 - - + +
121E VAL* 3.2 37.2 + - + +
151E THR* 4.6 11.2 - - + -
158E LYS* 3.3 55.6 - - + +
161E LEU* 3.5 47.1 - - + +
162E LEU* 3.8 8.1 - - + -
165E LEU* 3.6 24.9 - - + -
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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