Contacts of the helix formed by residues 97 - 110 (chain E) in PDB entry 1VCB
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 PRO 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95E ILE 3.7 3.6 - - - +
96E ALA* 1.3 85.1 - - + +
98E GLU* 1.3 78.2 + - - +
99E ILE 3.3 0.7 + - - -
100E ALA* 3.3 18.4 + - + +
101E LEU* 4.6 2.1 + - - +
165F VAL* 5.2 2.0 - - + -
169F LEU* 4.0 37.3 - - + +
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Residues in contact with GLU 98 (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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96D PRO* 3.8 30.0 - - + +
97D PRO* 4.5 7.1 - - - +
98D GLU* 4.8 26.1 - - + +
96E ALA* 3.6 17.3 - - - +
97E PRO* 1.3 92.9 - - - +
99E ILE* 1.3 60.9 + - + +
100E ALA 3.9 0.2 + - - -
101E LEU* 4.9 3.9 + - - +
102E GLU* 3.7 14.2 + - - +
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Residues in contact with ILE 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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96D PRO* 4.6 6.7 - - + -
68E HIS* 3.8 40.2 - - + +
69E VAL* 5.2 4.0 - - + -
72E LYS* 4.4 22.9 - - + -
95E ILE* 4.4 4.7 - - + -
96E ALA* 3.2 24.5 + - + +
98E GLU* 1.3 79.2 - - + +
100E ALA* 1.3 56.3 + - - +
101E LEU 3.5 1.1 - - - -
102E GLU* 3.3 9.5 + - - +
103E LEU* 2.7 59.3 + - + +
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Residues in contact with ALA 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 ILE* 4.0 15.9 - - + -
96E ALA 3.3 8.1 + - - +
97E PRO* 3.3 17.6 + - + +
99E ILE* 1.3 77.3 - - - +
101E LEU* 1.3 60.1 + - + +
103E LEU* 3.9 1.8 - - - +
104E LEU* 2.9 31.8 + - - +
162F CYS* 4.2 6.1 - - + +
165F VAL* 4.4 12.6 - - + -
166F VAL* 4.0 20.9 - - + -
169F LEU* 4.9 4.3 - - + -
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Residues in contact with LEU 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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98D GLU* 5.6 6.1 - - - +
97E PRO 4.6 2.1 + - - +
98E GLU 4.9 3.2 + - - +
99E ILE 3.5 0.6 - - - -
100E ALA* 1.3 76.4 - - + +
102E GLU* 1.3 65.1 + - + +
104E LEU* 3.4 8.6 - - + +
105E MET* 3.2 30.6 + - + +
166F VAL* 4.1 21.3 - - + -
178F LEU* 4.0 36.3 - - + -
179F ASP* 5.4 4.5 - - + +
180F ILE* 4.2 24.2 - - + -
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Residues in contact with GLU 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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97D PRO* 3.0 38.3 - - + +
66E PRO* 4.2 11.2 - - + +
68E HIS* 3.1 26.8 + - - -
69E VAL* 3.5 17.5 - - + +
98E GLU 3.7 11.1 + - - +
99E ILE* 3.3 4.6 + - - +
101E LEU* 1.3 76.8 - - + +
103E LEU* 1.3 67.7 + - - +
105E MET* 3.2 23.1 + - + +
106E ALA* 2.9 23.2 + - - +
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Residues in contact with LEU 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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69E VAL* 4.0 12.0 - - + +
72E LYS* 4.1 20.2 - - + -
73E VAL* 4.0 19.3 - - + -
93E PHE* 4.8 0.7 - - + -
95E ILE* 3.8 17.5 - - + -
99E ILE* 2.7 41.8 + - + +
100E ALA* 3.9 1.3 - - - +
102E GLU* 1.3 73.3 - - - +
104E LEU* 1.3 52.6 + - - +
106E ALA* 3.0 1.4 + - + -
107E ALA* 2.6 34.8 + - - +
158F LEU* 3.4 44.9 - - + -
162F CYS* 3.7 13.5 - - - -
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Residues in contact with LEU 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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100E ALA 2.9 17.1 + - - +
101E LEU* 3.4 17.0 - - + +
103E LEU* 1.3 74.9 - - - +
105E MET* 1.3 53.3 + - + +
107E ALA* 3.3 3.5 + - - +
108E ASN* 2.8 30.7 + - - +
159F LYS* 4.5 13.2 - - + -
162F CYS* 3.6 24.0 - - + -
163F LEU* 4.2 26.2 - - + -
166F VAL* 4.3 19.5 - - + -
180F ILE* 5.0 9.6 - - + -
184F LEU* 3.7 35.9 - - + -
188F LEU* 5.4 2.5 - - + -
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Residues in contact with MET 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 LEU* 3.2 21.5 - - + +
102E GLU* 3.2 26.6 + - + +
104E LEU* 1.3 72.3 - - + +
106E ALA* 1.3 65.0 + - - +
108E ASN* 3.4 7.1 + - - +
109E PHE* 3.1 23.6 + - - +
179F ASP 4.6 7.6 - - - +
180F ILE* 4.2 20.4 - - + -
181F VAL* 5.7 4.7 - - + -
184F LEU* 4.0 20.2 - - + -
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Residues in contact with ALA 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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65E ILE* 4.1 25.6 - - + -
69E VAL* 3.4 30.5 - - + -
73E VAL* 4.5 6.1 - - + -
102E GLU 2.9 8.0 + - - +
103E LEU* 3.4 10.1 - - + +
105E MET* 1.3 76.2 - - - +
107E ALA* 1.3 63.8 + - - +
109E PHE* 3.2 4.3 + - - +
110E LEU* 3.0 30.6 + - + +
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Residues in contact with ALA 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 LEU 2.6 21.0 + - - +
104E LEU* 3.5 5.2 - - - +
106E ALA* 1.3 75.1 - - - +
108E ASN* 1.3 61.7 + - - +
110E LEU* 3.4 0.9 + - - -
111E ASP* 3.1 19.4 + - - -
112E CYS* 3.5 16.8 + - - +
158F LEU* 3.6 26.2 - - + +
159F LYS* 3.6 31.8 - - - +
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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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104E LEU* 2.8 21.1 + - + +
105E MET* 3.7 7.4 - - - +
107E ALA* 1.3 74.7 - - - +
109E PHE* 1.3 61.0 + - - +
111E ASP* 3.7 8.1 + - - +
159F LYS* 3.0 31.4 + - + +
181F VAL* 5.9 2.8 - - - +
183F SER* 4.6 7.5 + - - -
184F LEU* 3.2 34.8 - - + +
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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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41E THR* 2.6 49.5 + - + -
45E MET* 4.7 9.4 - - + -
62E PHE* 4.1 24.2 - + - -
65E ILE* 4.4 10.8 - - + -
105E MET 3.1 16.9 + - - +
106E ALA* 3.7 3.1 - - - +
108E ASN* 1.3 79.0 - - - +
110E LEU* 1.3 63.1 + - + +
111E ASP* 3.5 1.2 + - - +
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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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39E SER* 2.5 32.6 + - - +
40E GLY 3.5 2.4 + - - -
41E THR* 3.4 9.5 + - - -
42E ILE* 4.0 13.0 - - + -
62E PHE* 4.0 23.3 - - + -
65E ILE* 4.5 11.4 - - + -
70E LEU* 5.5 2.2 - - + -
73E VAL* 3.6 40.4 - - + -
77E PHE* 4.9 2.9 - - + -
106E ALA 3.0 22.0 + - - +
107E ALA 3.4 0.6 + - - +
109E PHE* 1.3 93.1 - - + +
111E ASP* 1.3 72.7 + - - +
112E CYS* 4.0 15.3 - - - -
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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