Contacts of the helix formed by residues 136 - 142 (chain A) in PDB entry 1QUD
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 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A PHE* 4.4 15.9 - - - -
132A ASN 5.1 0.2 - - - -
133A LEU 2.7 23.2 + - - -
134A ALA 2.9 4.6 + - - -
135A LYS* 1.3 76.4 - - - +
137A ARG* 1.3 68.0 - - - +
138A TRP* 3.6 13.0 + - - +
139A TYR* 3.1 18.7 + - - +
140A ASN* 3.0 28.5 + - - +
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Residues in contact with ARG 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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22A GLU* 3.1 39.6 + - - -
136A SER* 1.3 74.1 - - - +
138A TRP* 1.4 55.9 + - - +
140A ASN* 3.0 7.2 + - + +
141A GLN* 2.7 68.0 + - + +
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Residues in contact with TRP 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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101A ASN* 6.0 0.2 - - - -
102A MET* 3.5 39.9 - - + +
105A GLN* 2.9 30.6 + - - +
106A MET* 2.8 32.8 - - + +
114A PHE* 4.5 6.7 - + + -
133A LEU* 3.9 12.8 - - + -
136A SER* 3.7 20.0 - - - +
137A ARG* 1.4 79.5 - - - +
139A TYR* 1.3 63.2 + - - +
141A GLN* 4.1 2.6 - - - +
142A THR* 2.9 40.8 + - - -
145A ARG* 5.1 1.0 - - - +
146A ALA* 3.8 28.3 - - + +
149A VAL* 3.9 28.7 - - + -
150A ILE* 4.0 25.6 - - + -
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Residues in contact with TYR 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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133A LEU 4.2 1.1 - - - +
134A ALA* 3.3 49.6 - - + +
136A SER* 3.1 10.5 + - - +
138A TRP* 1.3 81.4 - - + +
140A ASN* 1.3 78.2 + - - +
143A PRO* 3.1 35.1 - - + +
146A ALA* 3.8 24.0 - - + -
147A LYS* 3.7 39.6 - - + +
150A ILE* 4.0 8.3 - - + -
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Residues in contact with ASN 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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134A ALA 4.3 7.8 - - - +
135A LYS* 5.6 0.3 - - - -
136A SER 3.0 23.6 + - - +
137A ARG* 3.0 10.2 + - - +
139A TYR* 1.3 89.9 - - - +
141A GLN* 1.3 69.8 + - - +
143A PRO* 3.7 9.1 - - - +
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Residues in contact with GLN 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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21A THR* 5.9 0.2 - - - -
22A GLU* 4.6 6.8 + - - +
137A ARG* 2.7 70.2 + - + +
138A TRP* 4.1 3.1 - - - +
140A ASN* 1.3 79.7 - - - +
142A THR* 1.3 68.5 + - + +
143A PRO* 3.1 11.8 - - - +
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Residues in contact with THR 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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21A THR* 4.2 30.5 - - + +
22A GLU* 5.5 1.3 - - - +
105A GLN* 3.6 26.0 + - - +
138A TRP* 2.9 21.9 + - - -
139A TYR 3.6 1.8 - - - -
141A GLN* 1.3 87.2 - - + +
143A PRO* 1.3 63.8 - - - +
144A ASN 3.4 2.6 + - - -
145A ARG* 3.5 6.7 + - - +
146A ALA* 2.9 24.8 + - - +
500A CL 3.4 15.7 - - + -
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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