Contacts of the helix formed by residues 101 - 115 (chain B) in PDB entry 6T2C
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 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B ASP* 5.2 3.2 + - - -
99B HIS 3.5 0.8 + - - -
100B PRO* 1.3 72.4 - - - +
102B LEU* 1.3 59.6 + - - +
103B PHE 3.6 1.6 - - - -
104B GLU* 4.2 15.6 + - - -
105B THR* 2.3 34.2 + - - -
265B ARG* 5.3 0.2 + - - -
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Residues in contact with LEU 102 (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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95B LEU* 5.2 3.4 - - + +
96B ASP* 5.3 0.2 + - - -
99B HIS* 3.6 38.2 + - + +
100B PRO 3.2 3.2 + - - +
101B GLY* 1.3 76.1 - - - +
103B PHE* 1.3 84.5 + - + +
105B THR* 3.3 2.8 + - - -
106B ALA* 3.0 29.6 + - + +
261B ASN 5.1 0.4 - - - +
262B ILE* 4.2 18.8 - - + +
265B ARG* 3.7 42.2 - - + +
266B LEU* 4.1 23.3 - - + -
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Residues in contact with PHE 103 (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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92B ILE* 3.8 27.4 - - + -
95B LEU* 4.4 15.0 - - + -
96B ASP* 3.6 48.4 + - + +
102B LEU* 1.3 98.1 - - + +
104B GLU* 1.3 69.6 + - - +
106B ALA* 3.5 3.8 + - - +
107B CYS* 2.9 36.4 + - - -
262B ILE* 3.9 31.2 - - + -
324B ARG* 4.9 4.7 - - - -
325B ILE* 3.8 39.7 - - + +
418B VAL* 5.9 0.9 - - + -
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Residues in contact with GLU 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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96B ASP* 4.8 7.4 - - - +
101B GLY* 4.0 14.7 + - - +
102B LEU 3.3 0.4 - - - -
103B PHE* 1.3 87.5 + - - +
105B THR* 1.3 55.8 + - - +
107B CYS* 3.8 4.1 - - - +
108B GLN* 2.6 50.8 + - - +
325B ILE 5.0 2.3 - - - +
327B ALA 3.6 14.4 - - - +
328B GLY* 5.3 0.3 - - - -
329B GLN* 3.4 24.7 + - - +
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Residues in contact with THR 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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101B GLY* 2.3 28.2 + - - -
102B LEU 3.9 0.9 - - - -
104B GLU* 1.3 75.1 - - - +
106B ALA* 1.3 61.5 + - - +
108B GLN* 3.4 7.1 + - + +
109B GLU* 3.0 44.6 + - + +
265B ARG* 3.4 34.8 + - - +
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Residues in contact with ALA 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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102B LEU* 3.0 18.3 + - + +
103B PHE 3.9 3.1 - - - +
105B THR* 1.3 78.2 - - - +
107B CYS* 1.3 52.8 + - - +
109B GLU* 3.4 2.4 + - - +
110B THR* 2.4 38.0 + - - -
258B LEU* 3.9 7.6 - - + -
261B ASN* 4.1 22.9 + - + +
262B ILE* 3.7 31.6 - - + +
265B ARG* 5.2 4.2 - - - +
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Residues in contact with CYS 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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103B PHE 2.9 25.0 + - - +
104B GLU 4.0 1.3 - - - +
106B ALA* 1.3 73.9 - - - +
108B GLN* 1.3 60.1 + - - +
110B THR* 3.3 5.5 + - - -
111B ILE* 2.9 34.8 + - - +
258B LEU* 4.0 11.7 - - - -
325B ILE* 4.1 15.7 - - - -
326B THR* 3.7 30.5 - - - -
329B GLN* 3.4 28.7 - - - +
333B PHE* 3.6 10.0 - - + -
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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 GLU* 2.6 50.0 + - - +
105B THR* 3.7 7.9 - - + +
107B CYS* 1.3 77.0 - - - +
109B GLU* 1.3 59.0 + - + +
111B ILE* 3.4 8.3 + - + +
112B ASP* 2.9 38.5 + - - +
329B GLN* 3.4 22.2 + - - +
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Residues in contact with GLU 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 THR* 3.0 23.2 + - + +
108B GLN* 1.3 74.4 - - + +
110B THR* 1.3 61.5 + - - +
112B ASP* 3.4 12.8 + - - +
113B ALA* 2.9 27.9 + - - +
261B ASN* 3.3 28.6 + - - +
265B ARG* 3.6 27.0 + - - -
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Residues in contact with THR 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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106B ALA 2.4 24.6 + - - -
107B CYS 3.7 4.5 - - - -
109B GLU* 1.3 75.4 - - - +
111B ILE* 1.3 60.4 + - - +
113B ALA* 3.1 5.6 + - - +
114B ILE* 2.9 39.8 + - + +
254B PHE* 4.4 8.1 - - + +
257B LEU* 4.4 12.9 + - + +
258B LEU* 3.4 38.1 - - + +
261B ASN* 4.5 5.3 + - - +
333B PHE* 3.8 22.0 - - + -
337B LEU* 5.0 2.0 - - + -
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Residues in contact with ILE 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 CYS 2.9 21.6 + - - +
108B GLN* 3.8 7.9 - - - +
110B THR* 1.3 74.2 - - - +
112B ASP* 1.3 66.2 + - - +
114B ILE* 3.3 14.9 + - - +
115B GLN* 3.8 20.5 + - - +
329B GLN* 4.0 13.0 - - - +
330B PRO* 4.4 14.1 - - + -
332B TRP* 3.8 25.8 - - + -
333B PHE* 3.6 41.7 - - + -
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Residues in contact with ASP 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* 2.9 23.2 + - - +
109B GLU* 3.6 12.7 - - - +
110B THR 3.2 0.2 - - - -
111B ILE* 1.3 82.6 - - - +
113B ALA* 1.3 56.8 + - - +
114B ILE 3.6 0.3 + - - -
115B GLN* 4.2 3.3 + - - +
116B GLN* 3.1 34.6 + - - +
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Residues in contact with ALA 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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109B GLU 2.9 17.7 + - - +
110B THR 3.1 4.9 + - - +
112B ASP* 1.3 75.4 - - - +
114B ILE* 1.3 56.5 + - - +
115B GLN 3.5 0.2 - - - -
116B GLN* 4.0 10.0 + - - +
117B THR* 2.4 30.7 + - - -
254B PHE* 4.5 2.6 - - - -
257B LEU* 3.8 23.7 - - + +
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Residues in contact with ILE 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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110B THR* 2.9 19.5 + - + +
111B ILE* 3.3 7.7 + - - +
113B ALA* 1.3 79.0 - - - +
115B GLN* 1.3 62.9 + - + +
116B GLN 3.2 6.0 + - - -
117B THR* 3.6 13.7 + - - +
162B ARG* 5.9 0.2 - - - -
164B ILE* 4.3 24.8 + - + +
254B PHE* 3.7 35.5 - - + -
332B TRP* 3.9 24.7 - - + -
333B PHE* 3.6 34.1 - - + -
336B LEU* 3.7 23.8 - - + -
337B LEU* 4.9 2.2 - - + -
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Residues in contact with GLN 115 (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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202A GLU 5.1 1.2 - - - -
203A GLU* 3.2 44.1 + - + +
111B ILE* 3.8 18.1 + - - +
112B ASP* 4.2 2.8 + - - +
113B ALA 3.5 0.2 - - - -
114B ILE* 1.3 83.6 - - + +
116B GLN* 1.3 59.7 + - + +
117B THR 3.8 0.9 - - - -
162B ARG* 3.9 37.3 + - - +
164B ILE* 5.4 1.6 - - + -
332B TRP* 4.2 11.1 - - - -
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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