Contacts of the helix formed by residues 120 - 129 (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 THR 120 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113T VAL* 4.1 4.3 - - - -
119T MET* 1.3 76.8 - - - +
121T GLU* 1.3 76.2 + - - +
122T GLU* 2.9 21.8 + - - +
123T GLU* 2.7 46.2 + - + +
124T VAL* 3.1 15.8 + - - +
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Residues in contact with GLU 121 (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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204S LYS 6.0 1.6 - - - -
109T ARG* 5.4 0.3 - - - -
113T VAL* 4.3 9.2 - - - +
120T THR* 1.3 84.4 - - - +
122T GLU* 1.3 72.7 + - + +
124T VAL* 2.9 24.4 - - - +
125T GLU* 3.1 14.1 + - - +
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Residues in contact with GLU 122 (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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120T THR* 2.9 7.5 + - - +
121T GLU* 1.3 86.4 - - + +
123T GLU* 1.3 67.1 + - - +
125T GLU* 2.9 9.2 + - - +
126T GLN* 2.9 38.4 + - + +
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Residues in contact with GLU 123 (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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804S ARG* 3.3 27.6 + - - +
807S LEU* 3.6 32.1 - - + +
119T MET* 2.9 27.4 - - + +
120T THR* 2.7 53.9 + - + +
122T GLU* 1.3 79.5 - - - +
124T VAL* 1.3 62.6 + - - +
126T GLN* 3.2 10.6 + - - +
127T LEU* 3.1 15.5 + - - +
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Residues in contact with VAL 124 (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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108T ILE* 6.2 0.4 - - + -
109T ARG* 3.8 27.4 - - + +
112T LEU* 3.5 29.6 - - + -
113T VAL* 3.4 30.7 - - + -
119T MET* 4.4 9.0 - - + -
120T THR 3.1 8.7 + - - +
121T GLU* 2.9 25.6 - - - +
123T GLU* 1.3 72.4 - - - +
125T GLU* 1.3 70.5 + - - +
127T LEU* 3.0 16.7 + - + +
128T VAL* 3.1 21.5 + - + +
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Residues in contact with GLU 125 (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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109T ARG* 2.6 47.6 + - - +
121T GLU 3.4 11.5 - - - +
122T GLU* 2.9 15.5 + - - +
124T VAL* 1.3 87.6 - - - +
126T GLN* 1.3 53.6 + - + +
129T ALA* 2.7 42.9 + - + +
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Residues in contact with GLN 126 (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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807S LEU* 4.3 26.0 - - + +
811S ALA* 5.1 8.8 - - - +
122T GLU* 2.9 31.2 + - + +
123T GLU* 3.5 9.6 - - - +
125T GLU* 1.3 71.7 - - + +
127T LEU* 1.3 61.7 + - - +
129T ALA* 4.2 10.4 - - - +
146T MET* 5.7 1.0 - - - +
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Residues in contact with LEU 127 (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* 4.7 4.9 - - + -
803S CYS* 3.9 32.1 - - + +
806S TYR* 4.2 17.0 - - + -
807S LEU* 5.0 10.1 - - + +
112T LEU* 4.4 15.5 - - + -
119T MET* 4.9 2.2 - - + -
123T GLU 3.1 11.0 + - - +
124T VAL* 3.0 14.2 + - + +
126T GLN* 1.3 79.2 - - - +
128T VAL* 1.3 71.4 + - + +
129T ALA 3.4 3.8 + - - +
131T HIS* 4.2 1.2 - - - -
143T LEU* 4.3 17.5 - - + +
146T MET* 3.8 23.5 - - - +
147T VAL* 3.5 28.7 - - + -
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Residues in contact with VAL 128 (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 4.9 0.2 - - - +
108T ILE* 3.5 23.3 - - + -
109T ARG* 3.5 35.9 - - + +
112T LEU* 6.4 0.2 - - + -
124T VAL* 3.1 18.6 - - + +
125T GLU 3.8 0.2 - - - +
127T LEU* 1.3 81.9 - - + +
129T ALA* 1.3 76.5 + - - +
130T GLY 3.0 0.2 + - - -
131T HIS* 2.8 26.2 + - - +
132T GLU* 3.6 4.0 + - - +
138T ILE* 3.3 28.7 - - + -
143T LEU* 4.2 21.1 - - + -
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Residues in contact with ALA 129 (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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109T ARG* 4.6 0.4 - - - +
125T GLU* 2.7 34.5 + - + +
126T GLN* 4.2 10.9 - - - +
127T LEU 3.2 4.2 - - - +
128T VAL* 1.3 79.1 - - - +
130T GLY* 1.3 59.0 + - - +
131T HIS* 3.5 9.4 + - - -
132T GLU* 3.8 9.2 - - - -
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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