Contacts of the helix formed by residues 110 - 122 (chain B) in PDB entry 2I2R
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 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A HIS* 3.7 4.5 - - + +
105A TYR 5.2 4.2 + - - +
106A PRO* 6.3 0.6 - - - +
107A ARG 5.9 0.4 - - - +
131A CYS* 3.8 6.5 - - - -
132A CYS* 3.8 8.5 - - - -
601A ZN 2.6 34.5 - - - -
105B TYR* 4.9 0.4 - - - -
108B TYR 3.8 0.8 + - - -
109B GLU* 1.3 81.0 + - - +
111B ILE* 1.3 71.2 - - - +
112B SER* 3.4 11.9 - - - -
113B ALA* 3.0 39.9 + - + +
114B TYR* 3.3 7.8 + - - +
139B ARG* 3.7 10.8 - - - +
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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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105B TYR* 3.5 33.0 + - + +
109B GLU 3.6 2.8 + - - -
110B CYS* 1.3 69.6 - - - +
112B SER* 1.3 66.1 + - - +
114B TYR* 2.9 15.3 + - - +
115B ASP* 3.0 35.9 + - - +
136B TYR* 3.7 34.8 - - + +
139B ARG* 2.9 35.6 - - + +
140B LYS* 4.0 16.2 - - + -
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Residues in contact with SER 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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102A LYS* 3.7 27.4 + - - +
104A HIS* 4.6 0.4 - - - -
131A CYS* 4.2 17.4 - - - +
110B CYS* 3.4 12.2 - - - -
111B ILE* 1.3 81.3 - - - +
113B ALA* 1.3 64.7 + - - +
114B TYR 3.0 1.2 + - - -
115B ASP* 4.1 6.2 - - - +
116B ASP* 3.2 29.0 + - - +
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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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104A HIS* 3.9 27.1 - - + +
90B VAL* 4.7 2.4 - - + +
109B GLU* 4.2 18.6 - - - +
110B CYS* 3.0 31.4 + - + +
112B SER* 1.3 80.4 - - - +
114B TYR* 1.3 55.9 + - - +
116B ASP* 3.8 8.4 - - - +
117B GLU* 3.4 21.5 - - - +
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Residues in contact with TYR 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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90B VAL* 3.9 31.4 - - + -
93B CYS* 4.6 10.1 - - + -
94B VAL* 6.3 0.2 - - + -
103B LEU* 3.9 11.7 - - + +
104B HIS 3.3 18.7 + - - -
105B TYR* 3.6 32.3 - + - -
106B PRO* 3.8 24.7 - - + -
109B GLU* 4.8 6.1 - - + -
110B CYS 3.8 8.7 - - - +
111B ILE 2.9 5.3 + - - -
113B ALA* 1.3 78.0 - - + +
115B ASP* 1.3 69.3 + - - +
116B ASP 3.4 0.7 - - - -
117B GLU* 3.8 4.0 - - - +
118B LEU* 3.1 51.8 + - + +
128B ILE* 3.7 14.8 - - + +
136B TYR* 4.1 15.7 - + - -
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 3.0 33.6 + - - +
112B SER* 4.1 5.6 + - - +
114B TYR* 1.3 81.0 - - - +
116B ASP* 1.3 68.6 + - - +
118B LEU* 2.9 11.3 + - - +
119B ALA* 2.8 25.3 + - - +
136B TYR* 3.2 35.9 + - - -
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Residues in contact with ASP 116 (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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100A THR* 3.9 21.2 - - + +
102A LYS* 3.6 32.1 + - - +
104A HIS* 5.4 0.9 + - - -
86B ARG* 4.7 5.2 + - - +
112B SER* 3.2 23.8 + - - +
113B ALA* 3.8 8.7 - - - +
115B ASP* 1.3 81.2 - - - +
117B GLU* 1.3 64.2 + - + +
119B ALA* 3.3 8.5 + - - +
120B PHE* 3.2 19.1 + - - +
65E PRO* 4.8 4.4 - - - +
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Residues in contact with GLU 117 (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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96A ASN* 4.9 2.3 - - - +
100A THR* 5.5 4.0 - - - +
86B ARG* 3.0 52.1 + - - +
87B ASP* 4.1 21.2 + - + +
90B VAL* 3.4 33.3 - - + +
113B ALA 3.4 17.3 - - - +
114B TYR 3.6 4.4 + - - +
115B ASP 3.1 0.4 - - - -
116B ASP* 1.3 79.4 - - + +
118B LEU* 1.3 65.6 + - - +
120B PHE* 3.0 11.3 + - - +
121B TYR* 3.1 40.4 + - + -
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Residues in contact with LEU 118 (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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90B VAL* 5.9 0.4 - - + -
94B VAL* 4.3 16.2 - - + -
103B LEU* 3.9 26.2 - - + -
114B TYR* 3.1 51.3 + - + +
115B ASP* 2.9 13.3 + - - +
117B GLU* 1.3 75.3 - - - +
119B ALA* 1.3 62.4 + - - +
121B TYR* 3.5 3.4 + - - +
122B GLY 3.2 4.3 + - - -
123B ILE* 3.1 62.0 + - + +
125B PRO* 4.4 21.5 - - + +
128B ILE* 5.4 0.2 - - + -
136B TYR* 5.5 0.9 - - - +
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Residues in contact with ALA 119 (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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115B ASP 2.8 12.1 + - - +
116B ASP* 3.5 11.9 - - - +
117B GLU 3.2 0.2 - - - -
118B LEU* 1.3 77.3 - - - +
120B PHE* 1.3 62.7 + - - +
122B GLY* 3.6 8.5 + - - -
123B ILE 4.8 2.0 - - - -
125B PRO* 6.3 1.3 - - - +
61E LYS* 3.6 4.0 + - - -
65E PRO* 3.5 26.5 - - + +
66E SER* 4.6 1.8 + - - +
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Residues in contact with PHE 120 (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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65B LEU* 3.2 26.9 - - + +
74B PHE* 3.7 28.5 - + - -
84B PHE* 4.2 7.2 - + - -
86B ARG* 3.2 60.6 - - + +
116B ASP 3.2 10.6 + - - +
117B GLU 3.0 10.2 + - - +
119B ALA* 1.3 76.3 - - - +
121B TYR* 1.3 76.7 + + - +
122B GLY 3.2 0.4 - - - -
61E LYS* 2.3 65.3 + - + +
62E ASN* 4.2 12.1 - - - -
65E PRO* 3.6 7.6 - - + +
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Residues in contact with TYR 121 (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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46B VAL* 4.8 0.5 - - - +
64B THR* 3.7 1.2 - - - -
65B LEU* 3.0 32.2 + - + +
66B LEU* 3.8 20.6 - - + -
84B PHE* 4.8 8.0 - + - +
86B ARG* 3.3 28.3 - - + +
87B ASP 4.3 0.2 + - - -
90B VAL* 5.1 0.2 - - + -
91B PHE* 3.3 42.3 - + - +
94B VAL* 3.8 37.9 - - + -
98B TYR* 4.4 1.2 + - - -
117B GLU* 3.1 45.9 + - + +
118B LEU* 4.5 1.6 - - - +
120B PHE* 1.3 95.9 - + - +
122B GLY* 1.3 60.7 + - - +
123B ILE* 3.5 13.2 - - + +
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Residues in contact with GLY 122 (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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63B ASP 4.6 2.5 - - - +
64B THR* 3.4 20.4 - - - +
65B LEU 4.5 5.6 - - - -
118B LEU 3.2 4.3 + - - -
119B ALA* 3.6 6.9 + - - -
120B PHE 3.2 6.2 + - - -
121B TYR* 1.3 79.0 - - - +
123B ILE* 1.3 61.6 + - - +
124B LEU* 4.1 11.5 + - - +
61E LYS* 5.3 1.6 - - - -
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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