Contacts of the helix formed by residues 80 - 93 (chain E) in PDB entry 3VZC
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 GLY 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77E VAL* 4.5 3.3 - - - +
79E SER* 1.3 90.4 + - - +
81E ASP* 1.3 65.8 + - - -
82E GLY 3.1 4.1 + - - -
83E LEU* 3.6 8.7 + - - +
84E MET* 3.7 9.5 + - - +
107E SER* 5.1 6.3 + - - -
111E GLY* 4.1 6.0 - - - +
112E SER 4.6 7.6 - - - -
113E GLY 3.3 13.2 - - - -
114E ASN* 3.9 4.3 - - - -
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Residues in contact with ASP 81 (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 GLY* 1.3 72.0 - - - -
82E GLY* 1.3 58.0 + - - +
84E MET* 3.5 9.0 + - - +
85E HIS* 3.0 26.5 + - - +
112E SER 5.0 0.8 + - - -
113E GLY* 2.9 26.2 + - - +
114E ASN* 3.8 2.8 - - - -
115E ALA* 2.9 28.0 + - - +
116E LEU* 3.0 32.3 + - + +
117E ALA 4.6 0.2 + - - -
166E VAL* 4.9 3.6 - - + +
167E LEU* 3.7 19.3 - - + +
341E ASP* 3.9 19.8 - - + +
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Residues in contact with GLY 82 (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 GLY* 3.1 2.0 - - - -
81E ASP* 1.3 75.9 - - - +
83E LEU* 1.3 65.5 + - - +
85E HIS* 2.9 7.1 + - - +
86E GLU* 2.9 27.4 + - - +
341E ASP 4.3 3.6 + - - -
343E GLU* 3.7 28.8 - - - +
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Residues in contact with LEU 83 (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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20E LEU* 3.3 34.8 - - + +
22E ASN* 4.2 7.2 - - + +
54E THR* 4.0 14.8 - - + +
60E ALA* 3.3 32.8 - - + -
77E VAL* 3.4 19.7 - - + -
79E SER* 3.6 33.6 + - - +
80E GLY 3.6 3.4 + - - +
81E ASP 3.5 0.6 - - - -
82E GLY* 1.3 73.5 - - - +
84E MET* 1.3 57.4 + - - +
86E GLU* 3.3 5.0 + - + -
87E VAL* 2.9 37.9 + - + +
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Residues in contact with MET 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E VAL* 3.5 26.9 - - + +
80E GLY 3.7 6.1 + - - +
81E ASP* 3.5 13.0 + - - +
82E GLY 3.1 0.4 - - - -
83E LEU* 1.3 76.2 - - - +
85E HIS* 1.3 59.7 + - - +
87E VAL* 3.8 2.4 - - - +
88E VAL* 3.0 45.8 + - + +
105E LEU* 4.4 11.9 - - + -
106E CYS 3.5 33.2 - - - +
107E SER* 3.8 18.8 - - - +
116E LEU* 3.7 25.8 - - + -
166E VAL* 4.1 13.9 - - + -
359E PHE* 5.5 1.6 - - - -
361E MET* 4.6 5.4 - - + +
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Residues in contact with HIS 85 (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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61E ARG* 4.4 11.2 - - - -
81E ASP 3.0 14.1 + - - +
82E GLY* 2.9 12.4 + - - +
84E MET* 1.3 76.3 - - - +
86E GLU* 1.3 69.3 + - - +
88E VAL* 3.7 2.5 + - - +
89E ASN* 2.9 52.4 + - - +
163E LEU* 4.2 14.3 - - + +
164E PHE 3.2 19.5 + - - -
166E VAL* 4.8 3.8 - - - +
340E VAL* 4.0 16.3 - - + +
341E ASP* 2.9 40.4 - - + +
343E GLU* 4.2 20.0 - - + +
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Residues in contact with GLU 86 (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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58E ASN* 3.3 37.7 + - - +
59E HIS 4.4 0.2 + - - -
60E ALA* 4.1 18.6 - - + +
61E ARG* 2.8 52.8 + - - +
82E GLY 2.9 17.0 + - - +
83E LEU* 3.6 10.1 - - + +
85E HIS* 1.3 82.2 + - - +
87E VAL* 1.3 58.7 + - - +
89E ASN 3.9 0.2 - - - -
90E GLY* 2.9 25.6 + - - -
343E GLU* 5.2 5.8 - - - +
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Residues in contact with VAL 87 (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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20E LEU* 3.7 27.1 - - + -
60E ALA* 4.8 1.8 - - + -
61E ARG* 5.3 0.4 - - - +
64E VAL* 3.5 15.3 - - + +
75E LEU* 4.0 26.5 - - + -
77E VAL* 3.8 24.5 - - + -
83E LEU* 2.9 29.0 + - + +
84E MET* 3.3 4.9 + - - +
86E GLU* 1.3 74.9 - - - +
88E VAL* 1.3 57.7 + - + +
90E GLY 3.3 1.6 + - - -
91E LEU* 3.1 34.9 + - + +
105E LEU* 4.6 9.0 - - + -
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Residues in contact with VAL 88 (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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84E MET* 3.0 25.5 + - - +
85E HIS* 4.4 2.0 - - - +
87E VAL* 1.3 73.4 - - + +
89E ASN* 1.3 67.2 + - - +
91E LEU* 3.3 8.5 + - - +
92E MET* 3.1 26.1 + - + +
101E ILE* 3.8 18.4 - - + -
105E LEU* 3.8 27.8 - - + -
152E LEU* 3.8 29.2 - - + -
164E PHE* 4.9 3.8 - - + +
166E VAL* 3.7 20.0 - - + -
359E PHE* 4.9 3.4 - - + -
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Residues in contact with ASN 89 (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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61E ARG* 3.6 28.1 - - - +
85E HIS* 2.9 36.0 + - - +
86E GLU 4.0 0.4 - - - +
88E VAL* 1.3 75.4 - - - +
90E GLY* 1.3 58.1 + - - +
92E MET* 3.1 6.8 + - - +
93E GLU* 2.9 37.8 + - - +
162E ARG 5.1 0.4 + - - -
163E LEU* 3.5 13.7 - - - +
164E PHE* 2.7 56.9 - - - +
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Residues in contact with GLY 90 (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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61E ARG* 3.7 27.0 - - - +
64E VAL* 4.0 8.1 - - - -
65E ARG* 3.6 21.8 - - - +
86E GLU 2.9 15.2 + - - -
87E VAL 3.6 5.4 - - - -
88E VAL 3.3 0.2 - - - -
89E ASN* 1.3 76.1 - - - +
91E LEU* 1.3 59.4 + - - +
93E GLU* 3.6 9.8 + - - +
94E ARG* 3.8 4.5 + - - +
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Residues in contact with LEU 91 (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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64E VAL* 3.5 18.6 - - + +
69E LEU* 3.7 27.4 - - + -
75E LEU* 4.5 4.3 - - + -
87E VAL* 3.1 32.6 + - + +
88E VAL* 3.7 9.9 - - - +
89E ASN 3.3 0.2 - - - -
90E GLY* 1.3 75.5 - - - +
92E MET* 1.3 62.7 + - - +
94E ARG* 3.4 21.3 + - - +
97E TRP* 3.5 12.6 - - - +
100E ALA* 3.5 27.4 - - + +
101E ILE* 4.4 19.3 - - + -
103E LYS* 5.0 1.1 - - + -
105E LEU* 4.2 27.6 - - + -
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Residues in contact with MET 92 (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 VAL* 3.1 19.7 + - + +
89E ASN 3.1 3.9 + - - +
91E LEU* 1.3 77.0 - - - +
93E GLU* 1.3 59.0 + - + +
94E ARG 3.2 4.9 + - - +
97E TRP* 3.4 39.2 - - + +
101E ILE* 3.6 39.3 - - + -
152E LEU* 4.4 4.0 - - + -
164E PHE* 3.5 59.5 - - + -
231E GLN 5.9 0.2 + - - -
232E GLY* 5.6 2.5 + - - -
233E PRO* 4.1 6.5 - - + -
358E TYR* 3.9 22.0 - - + -
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Residues in contact with GLU 93 (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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61E ARG* 2.9 42.2 + - - +
65E ARG* 2.7 47.6 + - - -
89E ASN* 2.9 18.6 + - + +
90E GLY* 3.9 2.7 - - - +
91E LEU 3.3 0.8 - - - -
92E MET* 1.3 75.9 - - + +
94E ARG* 1.3 61.8 + - - +
95E PRO* 3.9 3.5 - - - +
162E ARG 6.2 0.2 - - - +
164E PHE* 6.4 0.4 - - + -
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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