Contacts of the helix formed by residues 116 - 127 (chain A) in PDB entry 2IAG
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 SER 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A ARG* 5.0 5.2 + - - +
115A TYR* 1.3 83.2 - - - +
117A PRO* 1.3 66.9 - - - +
118A SER* 3.3 20.3 + - - -
119A ASP* 3.3 30.5 + - - +
120A GLU* 3.1 16.3 + - - +
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Residues in contact with PRO 117 (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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91A ARG* 3.7 37.7 - - - +
96A PHE* 3.9 19.1 - - + -
97A HIS* 3.7 35.0 - - + +
115A TYR* 3.3 20.8 - - + +
116A SER* 1.3 85.1 - - - +
118A SER* 1.3 59.6 + - - +
120A GLU* 3.5 0.9 + - - +
121A LYS* 2.9 41.1 + - - +
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Residues in contact with SER 118 (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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91A ARG* 6.0 0.4 + - - -
96A PHE* 5.2 5.4 - - - -
116A SER* 3.3 10.9 + - - -
117A PRO* 1.3 80.2 - - - +
119A ASP* 1.3 68.0 + - - +
121A LYS* 4.1 6.4 - - - +
122A ALA* 3.4 21.7 + - - +
438A HIS* 5.9 8.3 - - - -
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Residues in contact with ASP 119 (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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116A SER* 3.3 29.7 + - - +
117A PRO 3.4 0.6 - - - -
118A SER* 1.3 82.8 + - - +
120A GLU* 1.3 58.9 + - - +
122A ALA* 3.5 5.8 + - - +
123A ARG* 3.0 25.8 + - - +
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Residues in contact with GLU 120 (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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115A TYR* 4.0 22.2 - - + -
116A SER 3.1 15.1 + - - +
117A PRO 4.1 1.3 - - - +
119A ASP* 1.3 77.0 - - - +
121A LYS* 1.3 59.4 + - + +
123A ARG* 2.5 49.3 + - - -
124A MET* 2.8 50.5 + - + +
259A TYR* 3.5 10.2 - - + -
262A HIS* 3.7 26.8 + - + +
600A HEM 6.0 1.8 - - - +
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Residues in contact with LYS 121 (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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96A PHE* 3.7 20.0 - - + -
117A PRO* 2.9 30.4 + - - +
118A SER* 4.4 5.6 - - - +
120A GLU* 1.3 74.6 - - + +
122A ALA* 1.3 57.9 + - - +
124A MET* 4.5 0.2 - - - -
125A LYS* 2.8 37.9 + - - +
438A HIS* 3.4 21.6 + - + +
439A ASN* 3.1 30.9 + - - +
440A HIS 5.0 4.9 + - - -
442A LEU* 3.7 27.4 - - + +
600A HEM 3.9 33.4 + - + +
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Residues in contact with ALA 122 (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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118A SER 3.4 17.9 + - - +
119A ASP* 3.5 7.2 - - - +
120A GLU 3.3 0.2 - - - -
121A LYS* 1.3 76.3 - - - +
123A ARG* 1.3 66.5 + - - +
125A LYS* 3.5 4.4 + - - +
126A LEU* 3.4 25.5 + - - +
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Residues in contact with ARG 123 (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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119A ASP 3.0 15.4 + - - +
120A GLU* 2.5 48.1 + - - +
122A ALA* 1.3 79.1 - - - +
124A MET* 1.3 77.9 + - - +
126A LEU* 3.3 18.5 + - - +
127A THR* 3.6 14.1 + - + +
255A TRP 5.0 1.0 + - - -
258A SER* 3.0 44.2 + - - -
259A TYR* 3.7 22.4 - - - +
262A HIS* 4.0 14.2 - - - +
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Residues in contact with MET 124 (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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120A GLU* 2.8 42.4 + - + +
123A ARG* 1.3 83.2 - - - +
125A LYS* 1.3 63.2 + - - +
127A THR* 2.6 25.4 + - - -
128A LEU* 3.5 9.9 + - + +
255A TRP* 3.4 33.2 - - + +
259A TYR* 3.5 25.8 - - + -
280A GLN* 4.0 6.1 - - - +
442A LEU* 3.6 16.8 - - + -
600A HEM 3.5 41.1 - - - +
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Residues in contact with LYS 125 (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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121A LYS 2.8 23.3 + - - +
122A ALA* 4.2 4.7 - - - +
123A ARG 3.3 0.4 + - - -
124A MET* 1.3 72.7 - - - +
126A LEU* 1.3 62.0 + - - +
128A LEU* 3.1 14.5 + - - +
129A LEU* 3.3 43.4 - - + +
440A HIS* 3.5 31.8 + - + +
441A CYS 4.7 4.0 + - - -
442A LEU* 3.6 37.9 - - + +
444A ARG* 6.6 0.2 - - - -
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Residues in contact with LEU 126 (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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122A ALA 3.4 14.4 + - - +
123A ARG* 3.3 11.8 + - - +
124A MET 3.2 0.6 - - - -
125A LYS* 1.3 73.9 - - - +
127A THR* 1.3 59.2 + - + +
128A LEU 3.0 9.4 + - - -
129A LEU* 3.2 24.2 + - + +
130A HIS* 4.4 24.7 + - + +
132A GLU* 4.4 4.5 - - - +
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Residues in contact with THR 127 (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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123A ARG* 4.0 12.5 + - + +
124A MET* 2.6 23.7 + - - -
126A LEU* 1.3 78.6 - - + +
128A LEU* 1.3 62.3 + - - +
129A LEU 3.5 0.7 - - - -
132A GLU* 3.5 23.6 - - - +
136A LEU* 4.0 7.8 - - - +
254A LYS* 3.9 18.8 - - + -
255A TRP* 3.6 34.4 + - - +
258A SER* 3.3 26.3 + - - +
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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