Contacts of the strand formed by residues 100 - 110 (chain E) in PDB entry 6NQN
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 ILE 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B SER* 3.8 32.3 - - - +
94B ASN* 6.2 0.4 - - - +
100B ILE* 4.4 4.3 - - + -
102B ASN* 3.1 16.3 + - - +
92E SER* 3.7 22.2 - - - +
93E MET 3.4 7.4 - - - +
94E ASN* 3.1 40.4 - - + +
98E GLY* 3.1 18.4 - - - +
99E GLY* 1.3 79.7 - - - +
101E CYS* 1.3 66.2 + - - +
102E ASN* 4.2 2.5 - - - +
122E GLY* 3.1 0.3 - - - -
123E VAL* 2.9 32.9 + - + +
125E PHE* 4.3 1.2 - - - -
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Residues in contact with CYS 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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56E ILE* 4.2 4.0 - - - -
92E SER* 3.5 1.9 - - - -
93E MET* 2.8 56.4 + - + +
95E TYR* 4.2 7.6 - - + +
100E ILE* 1.3 73.4 - - - +
102E ASN* 1.3 62.1 + - - +
120E PHE* 3.5 36.8 - - + -
121E ASP 3.3 3.8 - - - -
122E GLY* 3.7 7.6 - - - -
125E PHE* 3.4 36.8 - - - -
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Residues in contact with ASN 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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100B ILE* 3.2 23.2 + - - +
102B ASN* 3.6 24.9 + - - +
121B ASP* 3.0 34.6 + - + +
123B VAL* 3.7 21.1 - - + +
91E ARG 3.3 2.7 - - - -
92E SER* 3.1 26.3 + - - -
93E MET* 4.6 0.2 - - - -
100E ILE* 4.2 0.3 - - - +
101E CYS* 1.3 73.6 - - - +
103E ALA* 1.3 62.7 + - - +
119E ARG 4.6 0.5 - - - -
120E PHE* 3.5 1.9 - - - -
121E ASP* 2.8 34.7 + - - +
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Residues in contact with ALA 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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123B VAL* 4.2 1.3 - - - +
60E VAL* 3.8 34.5 - - + -
89E TRP* 3.8 8.5 - - + -
90E GLU* 3.4 0.3 - - - -
91E ARG 2.8 34.5 + - - +
93E MET* 3.8 10.1 - - + -
102E ASN* 1.3 75.8 - - - +
104E THR* 1.3 66.8 + - - +
119E ARG 3.2 12.3 - - - +
120E PHE* 4.0 5.4 - - + -
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Residues in contact with THR 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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17B ALA* 6.3 1.1 - - + -
20B GLY* 4.1 29.9 - - - +
123B VAL* 3.7 22.0 - - + -
89E TRP* 3.3 14.6 - - - +
90E GLU* 4.2 7.0 - - + -
103E ALA* 1.3 80.9 - - - +
105E ASN* 1.3 62.9 + - - +
117E GLU 4.3 1.7 + - - -
118E ILE* 3.2 8.1 - - - +
119E ARG* 3.0 47.5 + - + +
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Residues in contact with ASN 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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60E VAL 4.2 0.2 + - - -
63E KZ4 3.1 24.7 + - - -
88E SER* 3.2 5.9 - - - -
89E TRP* 2.9 58.0 + - + +
104E THR* 1.3 76.6 - - - +
106E ASP* 1.3 73.2 + - - +
107E ILE* 3.5 11.3 + - - +
116E TYR* 3.2 40.4 - - - +
117E GLU 3.4 4.7 - - - +
118E ILE* 3.4 16.0 - - + +
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Residues in contact with ASP 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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88E SER* 3.8 10.5 - - - -
104E THR 4.3 0.2 - - - -
105E ASN* 1.3 71.9 + - - +
107E ILE* 1.3 57.9 + - - +
108E THR* 3.9 14.9 + - - +
115E ILE 3.4 4.2 - - - +
117E GLU* 2.9 54.4 + - + +
180E LYS* 2.8 31.6 + - - -
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Residues in contact with ILE 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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63E KZ4 3.8 19.1 - - - +
65E ASN* 3.7 11.2 - - - +
83E PHE* 3.9 21.3 - - + -
86E GLY* 3.6 5.0 - - - -
87E TYR* 3.0 69.6 + - + +
89E TRP* 4.1 3.6 - - + +
105E ASN* 3.5 24.2 - - - +
106E ASP* 1.3 71.2 - - - +
108E THR* 1.3 76.0 + - - +
114E TYR* 4.3 4.0 - - + -
115E ILE 3.3 2.7 - - - -
116E TYR* 3.8 21.1 - - + -
180E LYS* 3.8 3.3 - - - -
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Residues in contact with THR 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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83E PHE* 4.4 4.3 - - - -
85E GLU 4.6 9.0 - - - +
106E ASP* 3.9 16.2 + - - +
107E ILE* 1.3 82.8 - - - +
109E LEU* 1.3 63.8 + - - +
114E TYR* 3.4 5.7 - - - +
115E ILE* 2.9 50.8 + - - +
180E LYS* 4.5 9.9 - - - -
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Residues in contact with LEU 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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3E VAL 3.9 22.0 - - - +
4E ILE* 5.7 0.2 - - + -
8E MET* 3.7 19.3 - - + -
83E PHE* 3.8 27.6 - - + -
84E PRO* 3.8 31.0 + - + +
108E THR* 1.3 78.7 - - - +
110E ASP* 1.3 61.1 + - - +
111E GLY 3.6 26.0 + - - +
113E CYS 3.3 24.5 - - - +
114E TYR* 3.9 9.0 - - + -
115E ILE* 4.9 0.4 - - - -
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Residues in contact with ASP 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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108E THR 4.3 0.2 - - - -
109E LEU* 1.3 73.4 - - - +
111E GLY* 1.3 62.8 + - - +
112E ASP* 3.1 1.4 + - - +
113E CYS* 2.9 33.7 + - + +
115E ILE* 3.5 26.3 - - + +
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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