Contacts of the helix formed by residues 133 - 141 (chain A) in PDB entry 1CG4
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 ILE 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLY* 5.1 0.4 - - - -
36A GLY* 4.0 7.2 - - - +
37A HIS 4.2 2.2 - - - +
38A ASN* 3.4 47.1 - - + +
73A VAL* 3.7 9.0 - - + -
106A ILE* 3.6 25.4 - - + -
114A ASP* 4.2 0.2 + - - -
131A ARG* 3.2 19.2 + - + -
132A GLY* 1.3 72.4 - - - +
134A GLY* 1.3 65.6 + - - +
136A ALA* 3.3 2.1 + - - +
137A TYR* 3.1 48.1 + - + -
239A THR* 4.5 4.9 - - - +
240A SER* 5.0 2.0 - - - -
440A IMO 3.9 18.6 - - - +
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Residues in contact with GLY 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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114A ASP* 4.4 5.1 + - - -
133A ILE* 1.3 77.0 - - - +
135A PRO* 1.4 66.7 - - - +
137A TYR* 3.1 6.8 + - - +
138A GLU* 2.9 31.5 + - - +
240A SER* 3.8 20.8 + - - -
440A IMO 4.5 5.4 + - - -
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Residues in contact with PRO 135 (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 HIS* 3.5 38.8 - - + +
113A LEU* 3.6 28.5 - - + -
114A ASP* 3.8 14.6 - - + +
117A ARG* 4.4 3.1 - - + +
132A GLY* 3.3 14.4 - - - +
134A GLY* 1.4 85.8 - - - +
136A ALA* 1.3 58.9 + - - +
138A GLU* 3.1 22.6 + - + +
139A ASP* 2.8 34.5 + - - +
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Residues in contact with ALA 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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73A VAL* 3.9 12.3 - - + -
104A PRO* 4.4 7.2 - - + +
105A LEU 4.3 6.3 - - - +
106A ILE* 3.7 26.7 - - + -
110A HIS* 3.8 18.5 - - - +
132A GLY 3.2 17.7 + - - +
133A ILE 3.6 3.8 - - - +
135A PRO* 1.3 77.5 - - - +
137A TYR* 1.3 63.6 + - - +
139A ASP* 3.4 3.3 + - - +
140A LYS* 3.0 21.3 + - - +
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Residues in contact with TYR 137 (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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34A GLN* 4.0 0.7 - - - -
35A GLY* 2.8 31.0 + - - -
71A GLY 3.0 20.9 + - - -
73A VAL* 3.4 22.7 - - + -
104A PRO* 5.2 0.2 - - + -
133A ILE* 3.1 39.8 + - + -
134A GLY 3.5 6.1 - - - +
136A ALA* 1.3 78.3 - - - +
138A GLU* 1.3 61.9 + - - +
140A LYS* 3.1 30.3 - - + +
141A VAL* 3.0 25.4 + - - +
240A SER* 3.7 32.3 - - - +
241A SER* 3.5 24.8 - - - -
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Residues in contact with GLU 138 (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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117A ARG* 2.5 44.1 + - - -
134A GLY* 2.9 15.7 + - - +
135A PRO* 3.1 20.4 + - + +
137A TYR* 1.3 74.9 - - - +
139A ASP* 1.3 56.6 + - - +
141A VAL* 3.3 9.1 + - - +
142A ALA* 2.7 38.2 + - - +
144A ARG* 5.2 5.8 + - - +
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Residues in contact with ASP 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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109A TYR* 4.0 0.9 + - - -
110A HIS* 3.4 19.2 + - + +
113A LEU* 5.3 0.2 - - - +
135A PRO* 2.8 22.4 + - - +
136A ALA* 3.6 5.2 - - - +
138A GLU* 1.3 71.8 - - - +
140A LYS* 1.3 64.6 + - - +
142A ALA* 4.4 1.3 - - - -
143A ARG 3.2 1.9 + - - -
144A ARG* 3.0 29.8 + - - -
145A GLY* 2.8 36.4 + - - -
164A VAL* 3.7 12.1 - - - +
168A HIS* 3.0 40.5 + - - -
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Residues in contact with LYS 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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70A ASN* 4.8 8.7 + - - +
71A GLY* 4.7 15.8 + - - -
104A PRO* 4.4 24.9 - - + +
136A ALA 3.0 14.2 + - - +
137A TYR* 3.1 35.1 - - + +
139A ASP* 1.3 74.7 - - - +
141A VAL* 1.3 64.3 + - + +
143A ARG* 2.7 32.6 + - - +
145A GLY* 4.6 3.8 - - - +
147A ARG* 6.3 2.5 - - - -
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Residues in contact with VAL 141 (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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137A TYR 3.0 12.4 + - - +
138A GLU* 4.0 7.2 - - - +
140A LYS* 1.3 90.1 - - + +
142A ALA* 1.3 63.5 + - + +
143A ARG* 3.1 17.4 + - - +
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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