Contacts of the helix formed by residues 96 - 110 (chain E) in PDB entry 3CQ6
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 ASN 96 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ALA* 1.3 67.0 - - - +
97E GLY* 1.3 63.9 + - - +
99E ASN* 4.6 2.3 + - - +
100E GLU* 2.9 41.6 + - + +
236E ARG* 3.4 29.7 + - + +
258E HIS 2.6 32.6 + - - +
259E LEU* 3.7 12.4 - - - +
260E SER 5.3 0.7 + - - -
263E SER* 4.4 10.0 + - - -
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Residues in contact with GLY 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E ALA 2.9 9.2 + - - -
96E ASN* 1.3 75.5 - - - +
98E SER* 1.3 66.1 + - - -
99E ASN 3.0 2.5 - - - -
100E GLU* 3.2 0.5 + - - +
101E ILE* 3.1 19.6 + - - +
228E LLP 3.6 14.4 - - - -
236E ARG* 3.3 14.1 + - - -
237E LEU 4.0 4.9 - - - -
238E GLY* 3.2 17.6 - - - +
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Residues in contact with SER 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E GLY* 1.3 69.2 - - - -
99E ASN* 1.3 57.5 + - - +
101E ILE* 3.6 9.9 - - - -
102E LEU* 2.8 44.3 + - - +
197E ASP* 5.2 0.2 + - - -
199E ALA* 5.6 0.2 - - - +
223E SER* 4.0 13.3 + - - -
224E ARG 3.4 19.8 + - - -
225E THR* 3.6 6.8 - - - -
228E LLP 2.9 45.2 + - - -
238E GLY* 3.5 3.5 - - - -
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Residues in contact with ASN 99 (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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96E ASN 4.7 5.2 - - - +
97E GLY 3.0 0.6 - - - -
98E SER* 1.3 76.9 - - - +
100E GLU* 1.3 57.9 + - - +
102E LEU* 5.5 0.4 - - - +
103E GLN* 3.0 27.1 + - - +
123E TYR* 4.1 10.1 + - - -
125E MET* 3.6 45.9 - - - +
129E LEU* 3.7 20.3 - - + +
228E LLP 3.2 16.6 + - - +
236E ARG* 4.0 9.4 + - - +
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Residues in contact with GLU 100 (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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95E ALA* 3.8 3.8 - - + -
96E ASN* 2.9 58.7 + - + +
97E GLY 3.2 3.7 + - - +
99E ASN* 1.3 77.3 - - - +
101E ILE* 1.3 61.3 + - - +
103E GLN* 3.6 18.4 - - - +
104E GLN* 2.9 43.1 + - + +
255E LEU* 4.7 13.5 - - - +
258E HIS* 3.5 24.8 - - - +
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Residues in contact with ILE 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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93E TRP* 3.5 46.7 - - + +
95E ALA* 3.7 16.8 - - + +
97E GLY 3.1 10.5 + - - +
98E SER* 3.1 10.6 + - - +
100E GLU* 1.3 75.7 - - - +
102E LEU* 1.3 63.5 + - + +
104E GLN* 3.2 8.6 + - - +
105E LEU* 3.1 31.9 + - + +
223E SER* 4.7 10.1 - - - +
238E GLY* 3.6 24.9 - - - +
239E TYR* 3.7 6.5 - - - +
240E PHE* 3.8 27.4 - - + -
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E SER* 2.8 31.2 + - - +
99E ASN* 5.1 0.4 - - - +
101E ILE* 1.3 69.8 - - + +
103E GLN* 1.3 60.8 + - - +
105E LEU* 3.9 10.5 - - + +
106E LEU* 3.0 41.1 + - + +
123E TYR* 5.1 5.2 - - + -
126E HIS* 3.6 33.0 - - + +
129E LEU* 3.7 20.6 - - + -
166E PHE* 4.3 11.2 - - + -
195E ILE* 3.8 29.8 - - + -
197E ASP* 4.3 8.5 - - - +
223E SER* 3.9 17.3 - - - +
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Residues in contact with GLN 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ASN 3.0 19.1 + - - +
100E GLU* 3.6 21.5 - - - +
101E ILE 3.2 0.2 - - - -
102E LEU* 1.3 77.4 - - - +
104E GLN* 1.3 58.3 + - - +
106E LEU* 3.4 9.5 + - - +
107E GLN* 3.0 49.3 + - - +
129E LEU* 4.5 14.2 - - + +
132E GLY* 6.1 2.2 - - - -
133E THR* 4.1 15.9 - - + +
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Residues in contact with GLN 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E TRP* 2.9 30.2 + - - -
95E ALA* 3.9 6.5 - - - +
100E GLU* 2.9 40.9 + - + +
101E ILE* 3.2 5.9 + - - +
103E GLN* 1.3 77.5 - - + +
105E LEU* 1.3 60.9 + - - +
107E GLN* 3.4 12.6 + - - +
108E ALA* 3.2 18.4 + - - +
240E PHE* 6.4 0.2 - - + -
250E VAL* 4.4 11.3 - - + +
253E VAL* 3.3 20.2 - - + +
254E ARG* 3.4 36.5 - - + +
255E LEU 4.5 1.0 - - - +
258E HIS* 3.9 17.2 + - - -
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Residues in contact with LEU 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 ILE* 3.1 36.0 + - + +
102E LEU* 3.9 11.0 - - + +
103E GLN 3.3 0.2 - - - -
104E GLN* 1.3 75.1 - - - +
106E LEU* 1.3 59.3 + - - +
108E ALA 3.4 0.2 + - - -
109E PHE* 2.9 54.4 + - + +
164E ILE* 4.5 1.7 - - - +
193E ILE* 5.0 2.9 - - + -
195E ILE* 3.9 29.4 - - + -
221E VAL* 3.9 33.0 - - + -
223E SER* 5.6 0.4 - - - -
240E PHE* 4.2 15.7 - - + -
246E PHE* 4.6 1.8 - - + -
250E VAL* 4.1 18.6 - - + -
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Residues in contact with LEU 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 LEU* 3.0 25.1 + - + +
103E GLN* 3.7 5.2 - - - +
105E LEU* 1.3 75.0 - - + +
107E GLN* 1.3 59.9 + - - +
110E GLY* 2.8 33.7 + - - +
111E GLY* 3.4 2.9 + - - -
116E ALA* 4.5 3.8 - - + -
129E LEU* 3.6 40.6 - - + +
130E ALA* 3.8 4.7 - - - +
133E THR* 3.6 13.7 - - + +
135E THR* 3.9 21.8 - - + +
164E ILE* 3.5 25.8 - - + -
166E PHE* 4.3 24.7 - - + -
195E ILE* 5.7 1.1 - - + -
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Residues in contact with GLN 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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103E GLN* 3.0 44.3 + - - +
104E GLN* 3.6 14.8 - - - +
105E LEU 3.3 0.2 - - - -
106E LEU* 1.3 79.7 - - - +
108E ALA* 1.3 58.9 + - - +
110E GLY 4.5 5.7 - - - +
111E GLY* 5.3 3.1 - - - +
133E THR* 4.4 15.0 - - + -
253E VAL* 3.7 39.6 + - + +
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Residues in contact with ALA 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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104E GLN 3.2 14.4 + - - +
105E LEU* 4.9 0.2 - - - -
107E GLN* 1.3 79.6 - - - +
109E PHE* 1.3 86.2 + - + +
110E GLY 5.1 0.7 - - - -
114E ARG* 4.6 5.0 + - - -
249E ALA* 4.1 23.3 - - + +
250E VAL* 5.0 0.9 - - - +
252E LEU* 6.1 0.4 - - + -
253E VAL* 4.2 11.0 - - + -
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Residues in contact with PHE 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 LEU* 2.9 29.4 + - + +
108E ALA* 1.3 87.8 - - + +
110E GLY* 1.3 60.6 + - - +
114E ARG* 3.2 28.7 + - - +
163E ASP* 3.9 7.0 - - - +
164E ILE* 3.7 13.6 - - + +
193E ILE* 3.4 40.2 - - + -
246E PHE* 3.3 38.6 - + - -
249E ALA* 3.6 29.2 - - + -
250E VAL* 5.2 1.3 - - + -
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Residues in contact with GLY 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 LEU 2.8 16.0 + - - +
107E GLN 4.5 5.1 - - - +
108E ALA 5.1 0.7 - - - -
109E PHE* 1.3 79.6 - - - +
111E GLY* 1.3 62.7 + - - -
114E ARG* 3.4 27.1 + - - +
135E THR* 3.8 8.3 - - - -
163E ASP* 5.2 0.4 - - - -
164E ILE* 3.9 12.9 - - - +
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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