Contacts of the helix formed by residues 105 - 111 (chain B) in PDB entry 2I10
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 CYS 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B TYR* 3.2 18.4 - - - +
65B MSE 4.4 0.4 - - - -
66B CYS* 2.1 54.3 - - - +
96B PHE* 4.6 7.6 - - + -
101B GLN* 4.5 1.6 - - - +
104B GLY* 1.3 77.1 - - - +
106B MSE 1.3 69.0 + - - +
107B THR 4.1 7.2 - - - -
108B VAL* 3.0 17.2 + - - +
109B GLN* 3.1 11.0 + - - +
167B TYR* 4.0 13.0 - - - -
170B SER* 3.0 14.4 + - - +
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Residues in contact with MSE 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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112A LEU* 6.1 1.6 - - + -
19B MSE 3.7 30.7 - - + +
23B TRP* 3.5 19.7 - - + -
61B LEU* 3.7 31.9 - - + -
64B TYR* 2.9 32.4 + - + +
65B MSE 3.8 14.1 - - + +
105B CYS* 1.3 73.2 - - - +
107B THR* 1.3 58.4 + - - +
109B GLN* 3.2 6.9 + - + +
110B ALA* 2.8 27.2 + - - +
121B ILE* 3.7 30.5 - - + -
124B LEU* 4.6 6.1 - - + -
125B LEU* 3.9 22.0 - - + -
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Residues in contact with THR 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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171A VAL* 4.0 8.9 - - + +
175A SER* 3.8 21.3 + - - +
67B GLU* 2.7 28.0 + - - -
105B CYS* 3.3 2.6 - - - -
106B MSE 1.3 79.3 - - - +
108B VAL* 1.3 63.0 + - - +
110B ALA* 3.4 4.1 + - + +
111B GLY* 3.1 19.6 + - - -
125B LEU* 3.7 19.2 - - - +
129B ARG* 3.9 13.6 - - - +
167B TYR* 3.5 29.8 - - + +
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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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107A THR* 3.6 22.5 + - - +
108A VAL* 3.8 25.8 - - + -
171A VAL* 4.0 16.9 - - + +
103B PHE 4.0 6.3 - - - +
104B GLY* 4.5 1.3 - - - -
105B CYS* 3.0 19.2 + - - +
107B THR* 1.3 75.8 - - - +
109B GLN* 1.3 63.7 + - - +
111B GLY* 3.0 15.4 + - - -
112B LEU* 3.7 8.5 + - - +
167B TYR* 3.8 17.7 - - + +
170B SER* 3.9 12.6 - - - +
171B VAL* 3.7 20.0 - - + -
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Residues in contact with GLN 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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108A VAL* 3.5 8.7 - - - +
110A ALA 2.9 25.1 + - - -
111A GLY* 3.7 3.6 - - - -
112A LEU* 3.0 45.5 + - + +
113A ALA 4.7 0.7 + - - -
23B TRP* 3.6 20.7 - - + -
103B PHE* 2.6 37.2 + - + +
104B GLY 4.4 1.3 - - - +
105B CYS 3.1 12.0 + - - +
106B MSE 3.4 9.9 - - - +
108B VAL* 1.3 75.8 - - - +
110B ALA* 1.3 62.1 + - - +
112B LEU* 3.2 31.4 + - - +
114B SER 4.6 4.0 - - - +
117B PRO* 5.6 0.5 - - - +
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Residues in contact with ALA 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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23B TRP* 3.5 10.9 - - + -
106B MSE 2.8 20.1 + - - +
107B THR* 3.8 6.3 - - + +
108B VAL 3.4 0.4 - - - -
109B GLN* 1.3 72.3 - - - +
111B GLY* 1.3 59.6 + - - +
112B LEU 3.2 7.5 + - - +
117B PRO* 4.4 16.1 - - + +
122B VAL* 6.2 1.3 - - + -
125B LEU* 3.8 20.6 - - + -
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Residues in contact with GLY 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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104A GLY* 3.2 27.4 - - - -
105A CYS 4.5 0.4 + - - -
171A VAL* 5.7 2.9 - - - -
174A ALA* 3.9 21.1 - - - +
175A SER* 5.4 4.5 - - - -
107B THR 3.1 9.2 + - - -
108B VAL* 3.0 12.7 + - - -
110B ALA* 1.3 74.6 - - - +
112B LEU* 1.3 62.1 + - - +
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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