Contacts of the helix formed by residues 95 - 112 (chain A) in PDB entry 1VGX
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 ASP 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A TYR* 2.8 12.6 + - - +
71A LEU* 6.1 0.5 - - - +
93A GLU* 3.3 10.1 + - + +
94A PRO* 1.3 76.9 - - - +
96A GLU* 1.3 63.1 + - - +
97A GLN* 3.8 7.3 + - - +
98A GLY* 3.1 26.3 + - - -
99A VAL* 3.0 25.3 + - + +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 4.1 6.5 - - + +
23A ARG* 3.7 4.6 - - - +
24A LEU* 2.7 50.9 + - + +
39A TYR* 4.1 13.0 - - + -
94A PRO* 4.0 1.9 - - + +
95A ASP* 1.3 73.8 - - - +
97A GLN* 1.3 57.6 + - - +
99A VAL* 3.9 1.2 - - - +
100A MET* 2.8 31.9 + - - +
150A VAL* 3.6 36.7 - - + +
151A GLN 4.1 4.7 - - - +
152A GLU* 5.8 0.3 - - - -
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Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ASP* 3.3 6.4 + - - +
96A GLU* 1.3 77.8 - - - +
98A GLY* 1.3 58.9 + - - +
100A MET* 3.3 30.0 + - - +
101A LYS* 2.9 44.7 + - + +
150A VAL* 4.2 9.6 - - + +
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 4.6 7.4 - - - +
95A ASP* 3.1 24.7 + - - -
97A GLN* 1.3 80.1 - - - +
99A VAL* 1.3 57.5 + - - +
101A LYS* 3.2 7.5 + - - +
102A ALA* 2.9 28.6 + - - +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.7 18.2 - - + -
39A TYR* 3.5 37.5 - - + +
41A LEU* 4.2 7.2 - - + -
67A MET* 4.6 1.5 - - + +
71A LEU* 4.2 22.2 - - + -
88A MET* 3.8 23.1 - - + -
90A VAL* 4.8 1.6 - - + -
95A ASP* 3.0 20.3 + - + +
96A GLU 3.9 2.9 - - - +
98A GLY* 1.3 73.2 - - - +
100A MET* 1.3 61.5 + - - +
102A ALA* 3.2 6.2 + - - +
103A PHE* 2.8 28.6 + - - +
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Residues in contact with MET 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.9 21.3 - - + +
96A GLU 2.8 18.4 + - - +
97A GLN* 3.4 34.3 - - - +
99A VAL* 1.3 77.5 - - - +
101A LYS* 1.3 67.4 + - + +
103A PHE* 3.4 1.8 + - - +
104A GLU* 2.9 28.5 + - + +
148A LEU* 4.0 20.9 - - + +
149A LYS* 3.5 40.6 - - - -
150A VAL* 3.8 8.3 - - + +
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLN* 2.9 41.2 + - + +
98A GLY* 3.2 8.9 + - - +
100A MET* 1.3 86.1 - - + +
102A ALA* 1.3 63.7 + - - +
104A GLU* 2.6 35.1 + - - +
105A ALA* 3.0 22.7 + - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A MET* 4.1 8.0 - - + +
70A HIS* 3.5 38.6 - - + +
71A LEU* 3.9 19.3 - - + -
98A GLY 2.9 16.9 + - - +
99A VAL 3.6 4.3 - - - +
101A LYS* 1.3 76.9 - - - +
103A PHE* 1.3 57.7 + - - +
105A ALA* 3.2 3.8 + - - +
106A ALA* 2.8 29.8 + - - +
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Residues in contact with PHE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR 4.6 1.6 - - - -
22A VAL* 3.6 23.8 - - + -
41A LEU* 3.9 34.3 - - + -
42A ARG 4.9 1.8 - - - -
43A PHE* 3.6 32.1 - + - -
63A LEU* 4.4 10.3 - - + -
67A MET* 3.7 25.3 - - + +
99A VAL 2.8 20.6 + - - +
100A MET 3.7 3.6 - - - +
102A ALA* 1.3 68.9 - - - +
104A GLU* 1.3 59.6 + - - +
106A ALA 3.2 0.7 + - - -
107A LEU* 2.8 61.5 + - + +
143A VAL* 4.9 1.6 - - + -
148A LEU* 3.7 29.6 - - + -
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Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A MET* 2.9 18.9 + - + +
101A LYS* 2.6 40.0 + - - +
103A PHE* 1.3 78.9 - - - +
105A ALA* 1.3 62.9 + - - +
107A LEU* 3.3 2.1 + - - +
108A LYS* 3.0 49.3 + - - +
144A LEU* 3.9 15.5 - - + +
148A LEU* 4.1 19.2 + - + +
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Residues in contact with ALA 105 (chain A).
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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70A HIS* 3.6 35.4 - - + +
101A LYS 3.0 14.1 + - - +
102A ALA* 3.2 3.3 + - - +
104A GLU* 1.3 78.5 - - - +
106A ALA* 1.3 61.8 + - - +
108A LYS* 3.2 14.3 + - - +
109A ASP* 3.1 25.1 + - - +
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.9 7.0 - - + -
66A TYR* 3.6 27.5 - - + +
67A MET* 3.5 24.7 - - - -
70A HIS* 3.6 7.3 - - - -
102A ALA 2.8 20.7 + - - +
103A PHE 3.8 1.8 - - - +
105A ALA* 1.3 73.3 - - - +
107A LEU* 1.3 56.5 + - - +
109A ASP* 3.3 6.6 + - - +
110A THR* 2.8 32.8 + - - -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 4.0 16.6 - - + -
59A LEU* 5.4 0.4 - - + -
63A LEU* 4.5 9.2 - - + -
103A PHE* 2.8 59.8 + - + +
104A GLU 3.7 4.0 - - - +
106A ALA* 1.3 70.7 - - - +
108A LYS* 1.4 62.6 + - - +
110A THR* 3.6 4.3 - - + -
111A ALA* 2.8 31.4 + - - +
140A ALA* 3.6 25.3 - - + +
143A VAL* 3.5 33.9 - - + -
144A LEU* 3.8 16.3 - - + +
148A LEU* 4.2 6.1 - - + -
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLU* 3.0 44.0 + - - +
105A ALA* 3.2 13.1 + - - +
107A LEU* 1.4 78.6 - - - +
109A ASP* 1.3 64.0 + - - +
111A ALA* 3.4 3.4 + - - +
112A GLY* 3.1 19.9 + - - -
144A LEU* 3.9 20.9 - - + -
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A TYR* 3.6 39.1 + - + -
69A ASP* 4.8 1.7 - - - +
70A HIS* 2.7 34.6 + - - -
105A ALA 3.1 14.3 + - - +
106A ALA* 3.4 7.2 - - - +
107A LEU 3.2 0.2 - - - -
108A LYS* 1.3 77.6 - - - +
110A THR* 1.3 61.4 + - - +
112A GLY* 3.3 3.8 + - - -
113A HIS* 3.1 23.0 + - - +
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Residues in contact with THR 110 (chain A).
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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59A LEU* 3.9 20.2 - - + -
62A LEU* 3.9 23.7 - - + +
63A LEU* 3.7 14.9 - - - +
66A TYR* 3.6 18.8 - - - -
106A ALA 2.8 26.6 + - - -
107A LEU* 3.6 7.0 - - + -
109A ASP* 1.3 72.0 - - - +
111A ALA* 1.3 63.4 + - - +
113A HIS* 3.0 19.4 + - - +
136A ALA 4.2 6.1 - - - +
137A ARG* 3.4 11.4 - - - +
140A ALA* 3.7 18.2 - - + -
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU 2.8 20.5 + - - +
108A LYS* 3.8 4.5 - - - +
110A THR* 1.3 73.5 - - - +
112A GLY* 1.3 57.3 + - - +
137A ARG* 2.9 37.7 + - - +
140A ALA* 3.9 0.4 - - - +
141A ARG* 3.5 43.8 + - + +
144A LEU* 4.5 6.3 - - + -
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LYS 3.1 13.9 + - - -
109A ASP* 3.5 5.6 - - - -
110A THR 3.1 0.2 - - - -
111A ALA* 1.3 76.2 - - - +
113A HIS* 1.3 58.2 + - - +
114A ASP* 3.0 17.5 + - - +
137A ARG* 3.9 7.9 + - - -
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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