Contacts of the helix formed by residues 129 - 137 (chain A) in PDB entry 4QG0
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 HIS 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A MET* 3.5 24.0 - - + -
127A GLU 4.1 1.6 + - - -
128A LEU* 1.3 72.4 - - - +
130A PRO* 1.3 81.1 - - + +
131A LEU* 3.0 34.5 + - + +
132A LEU* 2.9 27.6 + - + +
133A VAL 3.0 9.0 + - - -
197A LEU* 3.7 35.6 - - + +
200A GLN* 5.1 2.9 - - - +
257A TYR* 3.5 40.2 - + + +
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Residues in contact with PRO 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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113A ASP* 3.9 27.1 - - + +
114A THR* 3.9 24.7 - - - +
115A MET* 4.2 8.5 - - + +
128A LEU 3.7 0.2 - - - -
129A HIS* 1.3 102.6 - - + +
131A LEU* 1.3 54.0 + - - +
133A VAL* 3.2 13.8 + - + +
134A ARG* 2.9 32.7 + - - +
257A TYR* 3.5 29.2 - - + +
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Residues in contact with LEU 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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129A HIS* 3.0 20.2 + - + +
130A PRO* 1.3 73.2 - - - +
132A LEU* 1.3 67.6 + - + +
134A ARG* 3.0 9.7 + - + +
135A ILE* 2.9 27.2 + - + +
197A LEU* 4.3 17.5 - - + -
201A ILE* 3.9 28.0 - - + -
250A ILE* 4.2 17.3 - - + -
253A VAL* 3.7 22.7 - - + -
254A MET* 3.9 20.4 - - + +
257A TYR* 4.0 13.1 - - + -
259A LEU* 4.0 20.6 - - + -
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Residues in contact with LEU 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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127A GLU 5.2 0.4 - - - +
128A LEU* 4.0 21.8 - - + -
129A HIS* 2.9 32.3 + - + +
131A LEU* 1.3 76.4 - - + +
133A VAL* 1.3 62.6 + - - +
135A ILE* 3.2 8.1 + - - +
136A ILE* 2.9 29.6 + - + +
197A LEU* 4.3 9.6 - - + -
200A GLN* 3.9 40.4 - - + +
201A ILE* 3.6 31.4 - - + -
204A LEU* 4.0 21.5 - - + +
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Residues in contact with VAL 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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113A ASP* 6.2 0.2 - - - +
114A THR 4.8 1.8 - - - +
116A LYS* 4.0 38.1 - - + +
128A LEU* 3.8 29.4 - - + +
129A HIS 3.0 17.0 + - - +
130A PRO* 3.3 14.4 - - + +
131A LEU 3.2 0.2 - - - -
132A LEU* 1.3 76.3 - - - +
134A ARG* 1.3 59.3 + - + +
136A ILE* 3.2 8.4 + - + +
137A ASP* 2.9 46.6 + - - +
702D DGT 4.3 2.5 - - + +
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Residues in contact with ARG 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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113A ASP* 4.6 16.2 + - - +
130A PRO 2.9 17.8 + - - +
131A LEU* 3.0 10.5 + - + +
133A VAL* 1.3 79.7 - - + +
135A ILE* 1.3 62.6 + - - +
136A ILE 3.4 0.2 + - - -
137A ASP* 3.5 10.5 + - - +
138A THR* 3.5 16.8 - - - +
248A ASN* 3.6 22.0 + - - +
249A GLY 4.6 1.4 + - - -
250A ILE* 4.2 16.6 - - + +
253A VAL* 3.8 39.8 - - + +
257A TYR* 6.1 0.2 - - + -
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Residues in contact with ILE 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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131A LEU* 2.9 22.3 + - + +
132A LEU* 3.2 11.4 + - + +
134A ARG* 1.3 75.9 - - - +
136A ILE* 1.3 59.6 + - + +
138A THR* 3.0 24.8 + - - +
141A PHE* 3.6 10.4 - - + +
201A ILE* 3.7 44.4 - - + -
204A LEU* 5.4 4.7 - - + -
205A CYS* 3.9 24.5 - - - -
241A PHE* 4.9 4.9 - - + -
244A LEU* 3.7 24.4 - - + +
245A ILE* 5.2 1.1 - - + -
250A ILE* 4.2 24.7 - - + -
254A MET* 5.2 0.2 - - + -
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Residues in contact with ILE 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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118A ILE* 6.0 1.1 - - + -
128A LEU* 3.6 24.7 - - + -
132A LEU 2.9 21.6 + - - +
133A VAL* 3.6 5.4 - - - +
135A ILE* 1.3 72.5 - - + +
137A ASP* 1.3 63.9 + - - +
138A THR 2.8 12.7 + - - -
141A PHE* 3.4 39.2 - - + +
142A GLN* 3.1 32.0 + - - +
165A PHE* 4.4 5.6 - - + -
169A LEU* 3.6 22.9 - - + -
204A LEU* 4.1 18.8 - - + -
702D DGT 3.9 15.0 - - + +
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Residues in contact with ASP 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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116A LYS* 5.1 0.3 - - - -
133A VAL* 2.9 28.3 + - - +
134A ARG* 3.5 6.6 + - - +
135A ILE 3.4 0.2 - - - -
136A ILE* 1.3 75.4 - - - +
138A THR* 1.3 63.8 + - - +
142A GLN* 4.0 3.3 + - - +
449D GLU 3.6 13.6 - - - +
450D TYR* 3.8 18.7 - - - +
451D ARG* 3.6 30.2 - - + +
702D DGT 2.8 48.3 + - - -
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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