Contacts of the helix formed by residues 106 - 113 (chain B) in PDB entry 2I65
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 TYR 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B PHE* 4.1 14.6 - + - -
92B ALA* 3.4 23.3 - - + -
93B PHE* 4.4 1.9 - - - +
101B ILE* 3.7 19.3 - - + -
102B THR 4.0 11.4 - - - -
103B GLU 2.9 9.8 + - - +
105B ASP* 1.3 77.8 - - - +
107B GLN* 1.3 58.2 + - - +
108B PRO* 3.4 2.7 - - - -
109B LEU* 3.1 25.0 + - + +
110B MET* 2.8 41.3 + - + +
159B TRP* 2.9 17.8 + - - -
184B PRO* 2.5 35.2 + - - +
187B VAL* 4.0 5.4 - - + -
188B PHE* 3.6 36.6 - + + -
191B THR* 4.9 4.7 - - + -
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Residues in contact with GLN 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 GLU* 3.5 19.8 + - - +
104B GLU* 3.2 22.6 + - + +
106B TYR* 1.3 76.0 - - - +
108B PRO* 1.3 71.4 - - + +
110B MET* 3.0 14.1 + - - +
111B LYS* 2.7 67.2 + - + +
191B THR* 4.6 8.5 - - - +
194B ARG* 5.6 4.2 - - - +
195B ARG* 4.5 6.9 + - - +
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Residues in contact with PRO 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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88B ALA* 4.0 20.0 - - + +
104B GLU 3.9 4.0 - - - +
105B ASP 3.7 12.8 - - - +
106B TYR 3.6 3.1 - - - -
107B GLN* 1.3 92.9 - - + +
109B LEU* 1.3 62.5 + - - +
111B LYS* 3.3 6.6 + - + +
112B LEU* 3.0 27.6 + - + +
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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
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85B VAL* 3.8 37.9 - - + +
88B ALA* 3.7 20.5 + - + +
89B PHE* 3.9 26.2 - - + +
106B TYR* 3.1 28.3 + - + +
108B PRO* 1.3 79.5 - - - +
110B MET* 1.3 53.7 + - + +
112B LEU* 3.2 3.6 + - + +
113B GLY* 2.8 32.4 + - - -
150B LEU* 3.7 20.2 - - + +
153B LEU* 4.8 0.2 - - + -
188B PHE* 3.7 29.2 - - + -
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Residues in contact with MET 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 TYR* 2.8 38.7 + - + +
107B GLN* 3.0 12.5 + - - +
109B LEU* 1.3 77.4 - - + +
111B LYS* 1.3 77.0 + - - +
113B GLY 3.3 2.8 + - - -
114B THR* 3.1 22.2 + - - -
150B LEU* 3.8 14.8 - - + +
188B PHE* 3.9 17.9 - - + -
191B THR* 4.2 21.5 - - + -
192B VAL* 3.4 36.6 - - + -
195B ARG* 4.1 26.9 + - - +
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Residues in contact with LYS 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 GLN* 2.7 49.1 + - + +
108B PRO* 3.6 6.7 - - + +
110B MET* 1.3 83.0 - - - +
112B LEU* 1.3 64.9 + - + +
114B THR* 2.6 27.8 + - - +
195B ARG* 3.2 26.1 - - - +
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Residues in contact with LEU 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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79B HIS* 5.1 3.1 + - - -
80B VAL* 3.8 22.4 - - + +
81B ASP 6.3 0.4 - - - +
84B SER* 3.6 41.3 - - - +
85B VAL* 4.1 16.6 - - + +
88B ALA* 3.7 17.9 - - + -
108B PRO* 3.0 11.7 + - + +
109B LEU* 3.7 8.1 - - + +
111B LYS* 1.3 80.9 - - + +
113B GLY* 1.3 56.7 + - - +
114B THR* 3.2 4.4 + - - +
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Residues in contact with GLY 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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77B MET* 4.0 4.3 - - - +
85B VAL* 5.4 0.6 - - - +
109B LEU 2.8 15.5 + - - -
110B MET 3.3 5.1 + - - -
111B LYS 3.2 0.2 - - - -
112B LEU* 1.3 76.0 - - - +
114B THR* 1.3 66.7 + - - +
115B GLN* 3.2 12.8 + - - +
149B LEU* 4.2 13.8 - - - +
150B LEU* 3.9 31.5 - - - +
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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