Contacts of the helix formed by residues 130 - 142 (chain A) in PDB entry 1QCO
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A TYR 3.5 2.7 + - - +
129A SER* 1.3 74.6 - - - +
131A ARG* 1.3 64.7 + - - +
132A GLN 3.9 0.2 + - - -
133A HIS* 3.1 8.2 + - - +
134A ALA* 3.0 22.5 + - - +
152A TRP* 3.9 1.6 - - - -
321A HIS 3.5 10.0 + - - -
322A MET* 3.8 16.3 - - - +
348A SER 4.8 0.2 + - - -
350A THR 2.9 27.4 + - - -
352A SER 3.0 34.1 + - - -
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Residues in contact with ARG 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 SER 3.5 5.1 + - - -
130A SER* 1.3 71.9 + - - +
132A GLN* 1.3 58.1 + - - +
134A ALA* 3.4 1.6 + - - +
135A THR* 2.7 41.8 + - - +
148A LEU* 4.2 14.0 - - + +
152A TRP* 3.4 25.5 - - + -
153A LEU* 3.8 33.8 - - - +
280A ASP 4.9 4.0 + - - -
321A HIS 4.5 3.6 + - - -
323A TYR* 3.8 32.8 + - + +
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Residues in contact with GLN 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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130A SER* 3.3 1.6 + - - -
131A ARG* 1.3 78.3 - - - +
133A HIS* 1.3 59.7 + - - +
135A THR* 4.3 14.1 - - - +
136A ASN* 2.8 68.3 + - - +
139A ILE* 5.7 0.8 - - - +
321A HIS 5.6 0.2 + - - -
352A SER* 3.6 13.9 + - - +
353A GLY 3.1 30.7 - - - +
354A SER* 4.1 17.1 - - - +
359A PHE* 4.1 5.5 - - + -
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Residues in contact with HIS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A TYR* 3.6 18.1 - + - -
130A SER* 3.1 13.4 + - - +
132A GLN* 1.3 78.5 - - - +
134A ALA* 1.3 55.9 + - - +
136A ASN* 3.3 1.9 + - - +
137A VAL* 3.0 52.3 + - + +
199A GLU* 4.4 8.2 + - - -
237A ARG* 5.2 1.8 - - - -
350A THR* 3.3 42.6 + - + +
352A SER* 3.6 7.5 - - - +
361A SER* 4.5 4.7 - - - -
364A GLU* 2.7 35.5 + - - -
1008A FUM 4.3 4.6 + - - -
1010A AAE 3.1 29.8 + - - -
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A TYR* 3.7 29.0 + - + -
130A SER 3.0 14.4 + - - +
131A ARG 3.8 1.6 - - - +
133A HIS* 1.3 78.0 - - - +
135A THR* 1.3 57.2 + - - +
138A GLY* 2.9 26.9 + - - -
142A ARG* 4.7 0.3 + - - -
147A ALA 4.2 1.2 - - - +
148A LEU* 3.6 18.0 - - + +
152A TRP* 3.4 31.4 - - + +
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Residues in contact with THR 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 ARG* 2.7 31.7 + - - +
132A GLN* 3.8 17.2 - - - +
134A ALA* 1.3 74.0 - - - +
136A ASN* 1.3 59.7 + - - +
138A GLY* 3.2 1.0 + - - -
139A ILE* 2.8 51.8 + - + +
147A ALA* 3.8 14.2 - - + +
148A LEU* 3.8 17.9 - - + +
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Residues in contact with ASN 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 GLN* 2.8 45.2 + - - +
133A HIS 3.7 0.4 - - - +
135A THR* 1.3 74.2 - - - +
137A VAL* 1.3 61.7 + - - +
139A ILE* 3.3 6.9 + - - +
140A MET* 3.2 28.9 + - - +
359A PHE* 3.5 36.2 - - - -
364A GLU* 2.9 35.5 + - + +
367A TRP* 3.8 26.0 - - + -
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Residues in contact with VAL 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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128A TYR* 3.7 9.2 - - - +
133A HIS* 3.0 48.3 + - + +
136A ASN* 1.3 73.8 - - - +
138A GLY* 1.3 63.4 + - - +
140A MET* 3.1 13.5 + - + +
141A PHE* 3.0 44.7 + - + -
363A LEU* 4.3 16.6 - - + -
364A GLU* 4.9 2.7 - - + -
1008A FUM 3.4 34.1 - - + +
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Residues in contact with GLY 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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134A ALA 2.9 13.6 + - - -
135A THR 3.6 1.1 - - - -
137A VAL* 1.3 78.1 - - - +
139A ILE* 1.3 54.8 + - - +
142A ARG* 2.7 48.0 + - - +
143A GLY 3.1 4.2 + - - -
147A ALA* 3.3 30.1 - - - -
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Residues in contact with ILE 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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132A GLN* 5.7 0.9 - - - +
135A THR* 2.8 40.7 + - + +
136A ASN* 3.6 11.9 - - - +
138A GLY* 1.3 72.2 - - - +
140A MET* 1.3 60.3 + - - +
143A GLY* 3.1 26.2 + - - -
144A LYS* 4.2 27.1 - - + +
147A ALA* 3.8 12.9 - - + +
367A TRP* 4.0 23.6 - - + +
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Residues in contact with MET 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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136A ASN* 3.2 29.7 + - + +
137A VAL* 3.1 12.7 + - - +
139A ILE* 1.3 79.6 - - - +
141A PHE* 1.3 69.3 + - + +
363A LEU* 3.8 29.6 - - + +
364A GLU* 4.1 18.6 - - + -
367A TRP* 3.9 31.0 - - + +
368A LYS* 3.6 59.5 + - + +
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Residues in contact with PHE 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 VAL* 3.0 39.3 + - + +
138A GLY 4.4 0.2 - - - +
140A MET* 1.3 91.6 - - + +
142A ARG* 1.3 71.6 + - + +
143A GLY 3.8 0.2 - - - -
237A ARG* 5.7 5.6 - - + -
240A GLN* 5.5 0.7 - - - -
241A GLN* 4.6 20.4 - - + +
244A TYR* 4.0 21.8 - + - +
363A LEU* 4.4 22.2 - - + -
368A LYS* 4.2 23.6 - - + +
1008A FUM 3.9 20.9 - - + -
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Residues in contact with ARG 142 (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 TYR* 4.3 4.9 + - - -
134A ALA 4.7 0.8 + - - -
138A GLY* 2.7 28.5 + - - +
141A PHE* 1.3 81.9 - - + +
143A GLY* 1.3 58.6 + - - +
146A ASN* 3.1 45.3 + - + +
147A ALA 2.9 19.6 + - - -
149A LEU* 4.0 37.2 - - - +
244A TYR* 4.5 2.2 + - - -
1008A FUM 2.8 41.0 + - - -
746B PRO* 4.4 3.2 - - - +
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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