Contacts of the helix formed by residues 128 - 140 (chain A) in PDB entry 1IZC
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 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A VAL* 3.9 1.6 - - - +
127A GLU* 1.3 92.4 - - + +
129A VAL* 1.3 64.2 + - - +
130A GLU* 3.3 18.7 + - - +
131A GLU* 3.0 42.6 + - - +
132A VAL* 3.5 14.9 + - - +
192A ASN* 3.8 7.9 - - - +
196A ILE* 4.5 5.6 - - - -
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Residues in contact with VAL 129 (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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128A THR* 1.3 74.6 - - - +
130A GLU* 1.3 70.7 + - - +
132A VAL* 3.2 4.0 + - - +
133A ARG* 2.7 58.5 + - - +
192A ASN* 4.5 3.6 - - - +
195A ALA* 3.8 39.3 - - + +
196A ILE* 4.3 2.7 - - + +
199A MET* 3.2 29.6 - - + -
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Residues in contact with GLU 130 (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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128A THR* 3.1 22.3 - - - +
129A VAL* 1.3 87.3 + - - +
131A GLU* 1.3 62.9 + - + +
133A ARG* 3.2 10.3 + - - +
134A GLU* 3.1 28.6 + - + +
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Residues in contact with GLU 131 (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 LYS* 2.6 38.6 + - - -
105A HIS* 5.6 4.2 - - + -
123A ILE* 5.8 1.8 - - + -
126A VAL* 3.5 6.7 - - + -
127A GLU* 2.6 39.0 + - - +
128A THR* 3.0 25.3 + - + +
130A GLU* 1.3 76.9 - - + +
132A VAL* 1.3 63.1 + - - +
134A GLU* 3.4 16.3 + - - +
135A PHE* 3.5 20.4 + - + -
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Residues in contact with VAL 132 (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 ILE* 4.6 7.0 - - + -
126A VAL* 3.6 33.9 - - + -
128A THR 3.7 5.6 - - - +
129A VAL 3.2 7.9 + - - +
131A GLU* 1.3 78.8 - - - +
133A ARG* 1.3 57.0 + - - +
135A PHE* 3.0 19.1 + - - +
136A VAL* 3.0 16.0 + - + +
180A ILE* 4.4 16.2 - - + -
182A PRO* 4.0 12.1 - - + -
196A ILE* 4.6 1.6 - - + -
199A MET* 3.6 31.0 - - + -
201A GLU* 5.4 0.2 - - + -
202A ILE* 3.9 17.3 - - + -
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Residues in contact with ARG 133 (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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129A VAL* 2.7 50.2 + - - +
130A GLU* 3.2 10.5 + - - +
132A VAL* 1.3 73.2 - - - +
134A GLU* 1.3 67.3 + - - +
135A PHE 3.2 0.2 - - - -
136A VAL* 3.6 10.2 - - + +
137A LYS* 3.1 33.4 + - - +
199A MET* 3.6 11.0 - - + +
200A PRO* 4.1 11.5 - - - +
201A GLU* 2.7 38.0 + - - +
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Residues in contact with GLU 134 (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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130A GLU* 3.1 19.8 + - + +
131A GLU* 3.6 11.9 - - - +
132A VAL 3.1 0.4 - - - -
133A ARG* 1.3 77.2 - - - +
135A PHE* 1.3 65.6 + - + +
137A LYS* 2.7 43.4 + - - +
138A GLU* 3.3 24.9 + - - +
146A ARG* 4.3 9.9 + - - -
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Residues in contact with PHE 135 (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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102A VAL* 3.6 32.1 - - + -
103A PRO 4.3 0.4 - - - -
104A LYS* 3.3 31.0 - - + -
105A HIS* 5.5 0.2 - - - -
106A ASP 5.8 1.3 - - - -
110A LEU* 3.9 28.9 - - + -
121A ILE* 4.4 0.9 - - + -
123A ILE* 3.4 49.1 - - + -
131A GLU* 3.5 15.0 + - + -
132A VAL 3.0 9.0 + - - +
134A GLU* 1.3 81.2 - - + +
136A VAL* 1.3 66.1 + - - +
138A GLU* 3.1 4.0 + - - +
139A MET* 2.8 44.2 + - - +
180A ILE* 4.7 0.9 - - + -
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Residues in contact with VAL 136 (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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132A VAL* 3.0 17.7 + - + +
133A ARG* 3.3 14.6 + - + +
135A PHE* 1.3 78.5 - - - +
137A LYS* 1.3 64.3 + - + +
140A TYR* 3.2 33.6 + - + +
144A ILE* 4.1 24.2 - - + +
145A GLY* 4.0 1.9 - - - -
180A ILE* 3.4 24.9 - - + -
201A GLU* 3.9 34.1 - - + +
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Residues in contact with LYS 137 (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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133A ARG* 3.1 23.0 + - - +
134A GLU* 2.7 37.3 + - - +
135A PHE 3.2 0.2 - - - -
136A VAL* 1.3 78.7 - - + +
138A GLU* 1.3 58.6 + - - +
140A TYR 3.6 0.3 - - - +
145A GLY* 4.0 11.9 - - - -
146A ARG* 2.7 67.0 + - + +
147A ARG 3.1 6.9 + - - -
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Residues in contact with GLU 138 (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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107A GLU* 4.4 29.9 - - + +
110A LEU* 3.6 24.3 - - + +
114A LEU* 3.9 6.2 - - - +
134A GLU* 3.3 15.0 + - - +
135A PHE* 3.1 3.1 + - - +
137A LYS* 1.3 77.0 - - + +
139A MET* 1.3 59.2 + - - +
140A TYR 3.6 0.2 - - - -
146A ARG* 2.7 44.4 + - - +
147A ARG* 3.3 27.9 - - - +
148A SER 5.6 1.2 + - - -
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Residues in contact with MET 139 (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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110A LEU* 3.9 22.7 - - + -
114A LEU* 3.8 12.0 - - + +
121A ILE* 3.5 30.7 - - + -
135A PHE* 2.8 26.7 + - - +
136A VAL 3.3 0.2 + - - -
138A GLU* 1.3 79.0 - - - +
140A TYR* 1.3 74.5 + - + +
147A ARG* 3.4 22.6 + - - -
174A SER* 5.5 0.9 - - - +
175A ASN* 4.7 0.5 - - - +
178A VAL* 3.6 19.6 - - + +
179A CYS 3.4 18.4 - - - +
180A ILE* 3.2 41.1 - - + -
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Residues in contact with TYR 140 (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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29A ARG* 3.8 11.7 - - - -
136A VAL* 3.2 26.0 + - + +
139A MET* 1.3 90.4 - - + +
141A TYR* 1.3 59.8 + - - +
144A ILE* 3.6 27.8 - - + -
145A GLY* 3.1 4.3 - - - -
146A ARG 3.1 10.9 + - - -
147A ARG* 3.0 22.9 + - - -
174A SER 4.3 1.6 - - - -
175A ASN* 3.5 28.0 - - + +
178A VAL* 2.7 44.4 + - + +
179A CYS* 3.7 0.3 - - - -
180A ILE* 3.3 41.4 - - + +
201A GLU* 5.6 0.9 - - + -
203A HIS* 3.4 12.2 - + - -
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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