Contacts of the helix formed by residues 118 - 128 (chain A) in PDB entry 4IBR
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 VAL 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A VAL* 3.6 31.4 - - + -
88A GLU* 3.9 23.1 - - + +
89A GLN 3.5 23.3 - - - +
90A LEU* 3.3 7.4 + - + +
92A ARG* 2.9 23.9 + - + +
94A ILE* 4.0 19.5 - - + -
117A THR* 1.3 72.6 - - - +
119A GLY* 1.3 56.5 + - - +
121A LEU* 3.3 10.6 + - + +
122A CYS* 3.1 26.4 + - - +
137A LEU* 3.8 9.8 - - + +
140A THR* 5.0 2.7 - - + +
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Residues in contact with GLY 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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90A LEU* 2.9 29.0 + - - -
117A THR* 4.1 0.7 - - - -
118A VAL* 1.3 74.9 - - - +
120A GLU* 1.3 59.7 + - - +
122A CYS* 3.2 4.3 + - - +
123A SER* 2.9 25.8 + - - -
209A TRP* 3.6 22.8 - - - -
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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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93A ARG* 4.3 9.5 + - - -
111A HIS* 5.8 3.8 + - - -
115A GLY 4.5 0.5 - - - +
116A MET* 3.3 28.5 - - + +
117A THR* 3.0 42.0 + - - +
119A GLY* 1.3 75.0 - - - +
121A LEU* 1.3 57.7 + - - +
123A SER* 3.2 8.5 + - - -
124A ALA* 2.8 29.8 + - - +
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Residues in contact with LEU 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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94A ILE* 4.0 37.2 - - + +
96A TYR* 4.8 1.1 - - + -
108A THR* 4.1 2.2 - - + -
116A MET* 3.9 31.9 - - + +
117A THR 2.9 19.2 + - - +
118A VAL* 3.5 9.9 - - - +
120A GLU* 1.3 77.9 - - - +
122A CYS* 1.3 56.8 + - - +
124A ALA 3.4 0.2 + - - -
125A ALA* 2.9 27.0 + - - +
133A ALA* 3.4 22.0 - - - +
136A LEU* 3.6 36.8 - - + -
137A LEU* 3.6 19.2 - - + +
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Residues in contact with CYS 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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76A CYS* 2.0 51.4 - - - -
79A VAL* 4.4 9.6 - - - -
118A VAL 3.1 10.3 + - - +
119A GLY 3.2 3.3 + - - +
121A LEU* 1.3 73.1 - - - +
123A SER* 1.3 66.1 + - - +
125A ALA 3.9 0.4 - - - +
126A ILE* 3.0 30.3 + - - +
137A LEU* 3.8 18.4 - - - -
209A TRP* 3.4 33.2 - - + -
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Residues in contact with SER 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 GLY 2.9 13.4 + - - -
120A GLU* 3.2 13.0 + - - -
122A CYS* 1.3 75.8 - - - +
124A ALA* 1.3 52.5 + - - +
127A THR* 2.6 56.7 + - - +
209A TRP* 3.9 23.4 - - - +
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Residues in contact with ALA 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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107A VAL* 3.8 31.6 - - + -
116A MET* 4.0 4.5 - - + -
120A GLU 2.8 16.8 + - - +
121A LEU 3.7 4.3 - - - +
123A SER* 1.3 77.7 - - - +
125A ALA* 1.3 60.2 + - - +
127A THR* 4.3 3.4 - - - -
128A MET* 3.2 7.2 + - - +
129A SER 3.1 8.1 + - - -
130A ASP* 3.0 34.6 + - + +
133A ALA* 4.0 5.8 - - + -
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Residues in contact with ALA 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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72A LYS* 3.3 24.3 - - + +
75A LEU* 5.7 0.9 - - + -
76A CYS* 5.0 1.6 - - - -
121A LEU 2.9 17.5 + - - +
122A CYS* 4.0 3.8 - - - +
123A SER 3.4 0.2 - - - -
124A ALA* 1.3 77.0 - - - +
126A ILE* 1.3 61.5 + - + +
129A SER* 3.0 21.1 - - - -
130A ASP 3.8 20.4 - - - +
133A ALA* 3.9 5.8 - - + +
134A ALA* 4.1 12.3 - - + +
137A LEU* 4.1 10.5 - - + -
233A LYS* 3.4 2.6 - - - -
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Residues in contact with ILE 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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72A LYS* 4.1 14.6 - - + +
73A VAL* 4.0 20.4 - - + -
76A CYS* 4.0 15.9 - - + -
122A CYS 3.0 18.0 + - - +
123A SER 4.2 0.7 - - - +
125A ALA* 1.3 79.6 - - - +
127A THR* 1.3 62.5 + - - +
128A MET 3.4 0.8 + - - -
129A SER 4.2 0.2 + - - -
206A LEU* 4.0 19.5 - - + -
209A TRP* 3.6 44.6 - - + +
210A MET* 3.8 15.0 - - + +
213A ASP* 3.9 10.3 - - + +
215A VAL* 5.4 0.2 - - - +
232A ASP 4.8 1.6 - - - +
233A LYS* 3.3 27.2 + - + +
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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 SER* 2.6 46.5 + - - +
124A ALA* 4.3 0.3 - - - -
126A ILE* 1.3 72.6 - - - +
128A MET* 1.3 65.8 + - - +
209A TRP* 3.2 29.6 - - + +
212A ALA* 3.5 26.9 - - + +
213A ASP* 4.0 8.1 - - - +
214A LYS* 3.0 37.7 + - - +
215A VAL* 3.8 3.5 + - - -
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Residues in contact with MET 128 (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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104A TYR* 2.7 42.4 + - - +
106A PRO* 3.8 30.3 - - + -
107A VAL* 3.8 25.1 - - + -
124A ALA 3.2 11.1 + - - +
127A THR* 1.3 93.2 + - - +
129A SER* 1.3 65.5 + - - +
130A ASP 4.3 0.7 - - - +
214A LYS* 4.1 17.5 - - + -
215A VAL* 4.1 14.5 - - + +
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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