Contacts of the helix formed by residues 106 - 114 (chain B) in PDB entry 6B3I
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 GLU 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B ALA* 4.7 3.5 - - - +
99B MET* 4.5 4.3 - - - +
101B GLY 4.8 0.3 - - - +
103B GLY 5.2 1.7 + - - -
104B THR* 3.4 9.6 + - - +
105B ASP* 1.3 84.8 + - - +
107B SER* 1.3 64.3 + - - +
108B VAL 3.3 2.7 - - - -
109B LEU* 3.3 23.2 + - + +
110B ILE* 3.0 28.7 + - + +
143B ASP* 2.8 39.9 - - - +
144B THR* 3.4 22.4 - - + +
148B LEU* 4.1 12.3 - - + +
152B LEU* 4.9 0.4 - - + -
231B ASP* 3.6 27.3 + - - +
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Residues in contact with SER 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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105B ASP* 3.0 24.4 + - - -
106B GLU* 1.3 78.3 - - - +
108B VAL* 1.3 67.2 + - - +
110B ILE* 3.3 6.4 + - - +
111B GLU* 2.8 30.6 + - - +
231B ASP* 5.4 0.4 + - - -
234B LYS* 3.8 30.1 - - - +
253B ARG* 4.5 14.7 + - - -
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Residues in contact with VAL 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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94B GLN* 4.1 21.8 - - + +
95B LEU* 4.2 10.1 - - + -
98B ALA* 3.8 21.3 - - + +
105B ASP* 5.8 0.4 - - - +
106B GLU 3.3 0.6 - - - -
107B SER* 1.3 82.9 + - - +
109B LEU* 1.3 63.4 + - - +
111B GLU* 3.2 5.6 + - - +
112B VAL* 3.1 25.8 + - + +
267B THR* 5.7 0.7 - - - +
270B ARG* 4.0 45.8 - - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.7 27.6 - - + +
98B ALA* 5.2 4.0 - - + +
99B MET* 4.5 17.0 - - + -
106B GLU* 3.3 25.3 + - + +
108B VAL* 1.3 79.0 - - - +
110B ILE* 1.3 60.8 + - - +
112B VAL* 4.4 0.2 - - - -
113B LEU* 3.3 45.4 + - + +
136B LEU* 5.0 0.2 - - + -
140B VAL* 4.0 24.7 - - + -
143B ASP* 5.0 0.2 - - - +
144B THR* 3.9 17.9 - - + -
152B LEU* 3.8 26.8 - - + +
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Residues in contact with ILE 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 GLU* 3.0 20.2 + - + +
107B SER* 3.7 4.7 - - - +
109B LEU* 1.3 75.6 - - - +
111B GLU* 1.3 64.4 + - - +
114B CYS* 3.2 31.4 + - - +
148B LEU* 4.3 15.7 - - + -
152B LEU* 4.7 7.6 - - + -
231B ASP* 3.4 41.7 - - + +
234B LYS* 3.9 23.1 - - + -
235B ALA* 3.8 19.1 - - + +
238B THR* 3.7 22.1 - - + +
249B TYR* 5.7 0.7 - - - +
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Residues in contact with GLU 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 SER 2.8 17.7 + - - +
108B VAL 3.2 3.8 + - - +
110B ILE* 1.3 79.0 - - - +
112B VAL* 1.3 56.4 + - + +
115B THR* 2.5 36.7 + - - +
116B ARG* 5.1 3.1 + - - +
238B THR* 4.9 1.3 - - - -
249B TYR* 3.8 22.9 - - + +
250B PHE* 4.3 15.3 - - + -
253B ARG* 2.4 37.3 + - - +
267B THR* 4.3 1.7 - - - +
270B ARG* 2.7 40.8 + - - +
271B ILE* 3.9 18.7 - - - +
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Residues in contact with VAL 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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91B ALA* 4.3 9.6 - - + +
94B GLN* 5.5 0.2 - - + -
95B LEU* 3.8 31.4 - - + -
108B VAL* 3.1 24.3 + - + +
111B GLU* 1.3 82.6 - - + +
113B LEU* 1.3 64.2 + - + +
114B CYS 3.4 0.3 + - - -
115B THR* 3.5 4.0 + - - -
116B ARG* 3.2 47.4 + - - +
124B ILE* 3.7 28.7 - - + -
270B ARG* 4.5 14.8 - - - -
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Residues in contact with LEU 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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95B LEU* 4.6 15.5 - - + -
109B LEU* 3.3 38.4 + - + +
112B VAL* 1.3 84.3 - - + +
114B CYS* 1.3 58.9 + - - +
115B THR 3.5 0.7 + - - -
116B ARG 4.1 3.6 + - - +
121B ILE* 4.0 32.2 - - + +
124B ILE* 5.6 4.0 - - + -
136B LEU* 4.7 2.9 - - + -
140B VAL* 4.8 1.3 - - + -
152B LEU* 4.0 30.5 - - + +
155B LEU* 3.6 25.8 - - + +
156B LEU* 3.7 36.6 - - + -
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Residues in contact with CYS 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 ILE* 3.2 34.4 + - - +
113B LEU* 1.3 76.5 - - - +
115B THR* 1.3 63.9 + - - +
116B ARG 3.8 0.7 - - - -
152B LEU* 4.6 4.3 - - - -
155B LEU* 3.6 19.5 - - - -
160B ARG* 6.0 0.4 - - - -
202B TYR* 4.5 4.1 + - - -
235B ALA* 4.0 17.7 - - - -
238B THR* 3.6 16.1 - - + +
239B LEU* 3.7 35.6 - - + +
242B CYS* 3.6 17.3 - - - +
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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