Contacts of the helix formed by residues 103 - 114 (chain B) in PDB entry 2V1T
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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ILE* 4.0 28.7 - - + +
100B CYS* 3.5 32.1 - - + +
101B GLY 3.6 5.2 - - - +
102B GLN* 1.3 91.1 - - - +
104B GLN* 1.3 57.8 + - - +
105B GLN 3.4 2.0 - - - -
106B LEU* 3.3 9.1 + - + +
107B LEU* 2.9 42.1 + - + +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLN* 3.2 26.7 + - + +
103B PRO* 1.3 77.3 - - - +
105B GLN* 1.3 68.6 + - + +
107B LEU* 3.4 8.9 + - - +
108B GLN* 3.0 46.5 + - + +
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLN 4.7 2.6 + - - +
104B GLN* 1.3 87.3 - - + +
106B LEU* 1.3 61.3 + - - +
108B GLN* 3.3 17.3 + - - +
109B VAL* 2.9 35.2 + - + +
21D ALA 5.0 0.5 - - - +
22D ALA* 3.1 35.6 - - + +
23D GLY 5.3 0.4 - - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PHE* 3.8 31.0 - - + -
74B ILE* 5.2 2.0 - - + -
96B ALA* 5.2 1.8 - - + -
97B ILE* 3.9 24.0 - - + +
100B CYS* 4.2 13.2 - - - -
103B PRO* 3.3 12.8 + - + +
105B GLN* 1.3 78.5 - - - +
107B LEU* 1.3 56.5 + - - +
109B VAL* 3.3 1.7 + - - +
110B LEU* 2.9 43.9 + - + +
19D LEU* 3.6 48.0 - - + +
22D ALA* 3.6 11.2 - - + +
23D GLY 4.4 7.0 + - - +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ILE* 3.8 27.6 - - + -
103B PRO* 2.9 38.5 + - + +
104B GLN* 3.6 7.2 - - - +
106B LEU* 1.3 76.3 - - - +
108B GLN* 1.3 57.0 + - + +
110B LEU* 3.3 5.0 + - + +
111B GLN* 2.9 31.3 + - - +
119B PHE* 3.7 12.5 - - + -
122B LEU* 4.3 15.0 - - + -
123B LEU* 5.3 3.4 - - + -
126B LEU* 4.3 18.8 - - + -
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Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLN* 3.0 39.1 + - + +
105B GLN* 3.3 20.6 + - - +
107B LEU* 1.3 73.9 - - + +
109B VAL* 1.3 63.7 + - + +
111B GLN* 3.0 29.6 + - - +
112B GLN* 3.0 25.2 - - + +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLN* 2.9 21.3 + - + +
106B LEU* 3.9 4.3 - - - +
108B GLN* 1.3 75.5 - - + +
110B LEU* 1.3 61.0 + - - +
112B GLN* 3.1 7.4 + - + +
113B THR* 2.9 44.1 + - + +
18D LEU* 3.8 32.3 - - + +
19D LEU* 3.7 23.3 - - + -
22D ALA* 4.3 12.1 - - + -
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU* 4.9 2.5 - - - +
93B LEU* 4.4 14.8 - - + +
97B ILE* 3.6 31.4 - - + -
106B LEU* 2.9 35.0 + - + +
107B LEU* 3.5 7.0 - - + +
109B VAL* 1.3 77.9 - - - +
111B GLN* 1.3 57.2 + - - +
113B THR* 3.7 5.6 - - - +
114B LEU* 2.9 47.6 + - + +
119B PHE* 3.9 11.7 - - + -
122B LEU* 4.0 15.9 - - + -
19D LEU* 3.8 33.2 - - + -
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU 2.9 17.4 + - - +
108B GLN* 3.0 40.5 + - - +
110B LEU* 1.3 73.2 - - - +
112B GLN* 1.3 66.8 + - - +
113B THR 3.7 0.2 + - - -
114B LEU 4.0 9.9 - - - +
119B PHE* 3.4 41.5 - - + +
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Residues in contact with GLN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLN* 3.0 22.7 + - + +
109B VAL* 3.1 12.1 + - + +
111B GLN* 1.3 88.7 - - - +
113B THR* 1.3 64.2 + - + +
114B LEU 4.8 1.8 - - - +
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU* 5.4 2.6 + - - -
109B VAL* 2.9 30.2 + - + +
110B LEU* 3.6 14.6 + - - +
112B GLN* 1.3 86.4 - - + +
114B LEU* 1.3 66.2 + - - +
115B PRO* 4.1 3.3 - - - +
15D LEU* 5.0 17.1 - - + +
18D LEU* 4.0 26.2 - - + -
19D LEU* 4.6 3.5 - - + +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU* 4.6 6.7 - - - +
81B LEU* 3.6 30.5 - - + -
93B LEU* 4.5 6.5 - - + -
110B LEU* 2.9 33.5 + - + +
111B GLN 4.0 11.3 - - - +
112B GLN 4.8 1.0 - - - +
113B THR* 1.3 82.1 + - - +
115B PRO* 1.3 79.7 - - + +
116B PRO* 3.5 4.9 - - - +
118B VAL* 4.1 17.5 - - + -
119B PHE* 4.1 19.7 - - + +
122B LEU* 3.8 29.4 - - + -
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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