Contacts of the helix formed by residues 106 - 113 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A PHE* 4.1 14.4 - + - -
92A ALA* 3.4 24.2 - - + -
93A PHE* 4.5 1.6 - - - -
101A ILE* 3.7 19.5 - - + -
102A THR 4.0 3.8 - - - -
103A GLU* 2.9 10.2 + - - +
105A ASP* 1.3 75.9 - - - +
107A GLN* 1.3 59.9 + - - +
108A PRO* 3.4 2.5 - - - -
109A LEU* 3.1 17.4 + - + +
110A MET* 2.8 41.2 + - + +
159A TRP* 2.9 19.1 + - - -
184A PRO* 2.6 35.7 + - + +
187A VAL* 4.0 17.5 - - + -
188A PHE* 3.6 40.2 - + + -
191A THR* 5.0 4.7 - - + -
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 2.9 25.9 + - - +
104A GLU* 3.0 29.1 + - + +
106A TYR* 1.3 77.6 - - - +
108A PRO* 1.3 61.5 - - + +
110A MET* 3.3 22.5 + - - +
111A LYS* 2.8 52.4 + - - +
191A THR* 4.3 10.7 - - - +
194A ARG* 5.6 2.4 - - - +
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Residues in contact with PRO 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ALA* 3.8 20.2 - - + +
91A GLY 6.6 0.2 - - - -
104A GLU 3.8 4.3 - - - +
105A ASP 3.6 13.0 - - - +
106A TYR 3.6 3.4 - - - -
107A GLN* 1.3 92.4 - - + +
109A LEU* 1.3 56.4 + - - +
111A LYS* 3.3 13.5 + - + +
112A LEU* 3.0 32.6 + - - +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.8 36.3 - - + +
88A ALA* 3.7 19.3 + - + +
89A PHE* 3.8 28.7 - - + +
106A TYR* 3.1 24.5 + - + +
108A PRO* 1.3 75.6 - - - +
110A MET* 1.3 58.0 + - + +
112A LEU* 3.3 2.0 + - + +
113A GLY* 2.8 34.2 + - - +
150A LEU* 3.6 22.1 - - + +
188A PHE* 3.8 29.2 - - + -
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Residues in contact with MET 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 2.8 37.1 + - + +
107A GLN* 3.6 27.6 - - - +
109A LEU* 1.3 89.2 - - + +
111A LYS* 1.3 63.5 + - + +
113A GLY 3.6 0.2 - - - -
114A THR* 3.1 22.3 + - - -
150A LEU* 3.8 13.9 - - + -
188A PHE* 4.1 5.2 - - + -
191A THR* 4.3 13.5 - - + -
192A VAL* 3.5 34.3 - - + -
195A ARG* 3.2 33.9 + - - +
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLN* 2.8 42.6 + - - +
108A PRO* 3.5 10.8 - - + +
110A MET* 1.3 75.4 - - + +
112A LEU* 1.3 64.9 + - + +
114A THR* 2.5 26.9 + - - -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A HIS* 4.7 3.8 + - - -
80A VAL* 4.0 20.8 - - - +
84A SER* 3.2 47.1 - - - +
85A VAL* 3.7 15.8 - - + +
88A ALA* 3.7 14.1 - - + -
108A PRO 3.0 13.6 + - - +
109A LEU* 3.9 4.5 - - + +
111A LYS* 1.3 83.8 - - + +
113A GLY* 1.3 56.9 + - - +
114A THR* 3.2 4.7 + - - +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A MET* 3.9 4.0 - - - +
85A VAL* 5.6 0.9 - - - -
109A LEU* 2.8 17.2 + - - +
110A MET 3.6 3.6 - - - -
112A LEU* 1.3 75.0 - - - +
114A THR* 1.3 66.1 + - - +
115A GLN* 3.1 9.7 + - - +
149A LEU* 4.5 12.5 - - - +
150A LEU* 3.9 22.2 - - - +
195A ARG* 3.1 17.2 + - - -
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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