Contacts of the helix formed by residues 106 - 112 (chain T) in PDB entry 1I84
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 ALA 106 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201S HIS* 6.4 0.2 - - - +
261S TYR* 5.1 9.2 + - + +
104T MET* 2.5 16.3 + - + -
105T GLY* 1.3 76.3 - - - +
107T GLU* 1.3 59.4 + - - +
108T ILE 3.3 0.2 - - - -
109T ARG* 3.4 9.3 + - - +
110T HIS* 3.0 25.5 + - - +
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Residues in contact with GLU 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259S THR* 4.1 11.9 - - + +
261S TYR* 4.6 11.0 + - - +
95T PHE* 3.1 52.2 - - + +
103T VAL* 4.2 5.8 - - + -
104T MET* 2.7 41.0 + - + +
106T ALA* 1.3 78.2 - - - +
108T ILE* 1.3 65.1 + - - +
110T HIS* 3.0 18.1 + - + +
111T VAL* 3.1 21.6 + - - +
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Residues in contact with ILE 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799S PHE* 5.2 0.2 - - + -
92T LEU* 3.8 33.0 - - + -
95T PHE* 6.2 5.2 - - + -
103T VAL* 4.5 22.1 - - + +
104T MET 3.0 13.1 + - - +
105T GLY* 4.5 3.8 - - - +
107T GLU* 1.3 77.3 - - - +
109T ARG* 1.3 67.4 + - - +
110T HIS 3.1 1.0 + - - -
111T VAL* 4.1 4.4 - - + +
112T LEU* 3.3 45.9 + - + +
124T VAL* 6.2 0.4 - - + -
128T VAL* 3.5 31.9 - - + -
138T ILE* 4.4 10.3 - - + -
140T TYR* 6.0 1.3 - - + -
143T LEU* 4.5 12.6 - - + -
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Residues in contact with ARG 109 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105T GLY 2.5 42.6 + - - +
106T ALA* 3.4 10.5 + - - +
107T GLU 3.1 0.6 - - - -
108T ILE* 1.3 84.9 - - - +
110T HIS* 1.3 62.0 + - - +
112T LEU* 4.7 0.2 - - - -
113T VAL* 3.2 22.5 - - - +
121T GLU 5.4 0.2 - - - -
124T VAL* 3.8 28.8 - - + +
125T GLU* 2.6 46.5 + - - +
128T VAL* 3.5 17.7 - - + +
129T ALA* 4.5 2.2 - - - +
132T GLU* 2.6 35.8 + - - -
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Residues in contact with HIS 110 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142S LYS* 5.6 10.1 + - - -
201S HIS* 5.2 15.2 - + - -
261S TYR* 5.1 9.7 + - - +
106T ALA 3.0 13.6 + - - +
107T GLU* 3.0 16.2 + - + +
109T ARG* 1.3 74.2 - - - +
111T VAL* 1.3 59.3 + - + +
112T LEU 3.0 0.9 - - - -
113T VAL* 2.4 34.0 + - - -
114T THR* 2.6 35.0 + - + +
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Residues in contact with VAL 111 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800S GLN* 4.4 0.6 + - - -
92T LEU* 5.5 4.7 - - + -
95T PHE* 3.3 49.6 - - + -
107T GLU* 3.1 15.1 + - - +
108T ILE* 4.1 5.8 - - + +
110T HIS* 1.3 79.5 - - + +
112T LEU* 1.3 79.1 + - + +
113T VAL 2.9 1.6 + - - -
114T THR* 3.0 15.7 + - - -
115T LEU* 3.2 40.6 + - + +
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Residues in contact with LEU 112 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799S PHE* 3.6 35.2 - - + -
800S GLN* 2.9 29.2 + - + +
92T LEU* 5.3 3.4 - - + -
108T ILE* 3.3 31.9 + - + +
110T HIS 2.8 2.6 + - - -
111T VAL* 1.3 92.5 - - + +
113T VAL* 1.3 58.1 + - - +
114T THR 3.6 0.4 - - - -
119T MET* 3.3 45.8 + - + +
124T VAL* 3.5 21.3 - - + -
127T LEU* 4.4 10.5 - - + -
128T VAL* 6.4 0.2 - - + -
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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