Contacts of the helix formed by residues 98 - 106 (chain A) in PDB entry 1QWN
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLY* 4.1 1.3 - - - -
97A GLN* 1.3 75.0 - - - +
99A PHE* 1.3 66.0 + - - +
100A GLU* 3.5 6.1 + - - +
101A GLU* 2.9 42.6 + - - +
102A TYR* 2.9 23.0 + - - -
481A HIS* 3.7 20.9 - - + +
482A VAL* 3.7 12.5 - - + +
485A ASP* 3.9 34.3 - - + +
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Residues in contact with PHE 99 (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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93A PRO* 3.8 23.8 - - + +
94A GLY* 3.9 9.3 - - - +
98A THR* 1.3 73.9 - - - +
100A GLU* 1.3 68.3 + - - +
103A TYR* 2.9 28.6 + - + +
132A SER* 3.6 41.3 - - - -
133A TYR* 3.5 44.9 + + - -
136A ARG* 4.1 26.9 - - + -
467A LEU* 4.0 16.4 - - + -
485A ASP* 4.5 3.3 + - - +
486A TYR* 5.9 1.7 - - + -
489A ARG* 3.9 26.0 - - - +
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Residues in contact with GLU 100 (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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98A THR* 3.2 6.4 + - - +
99A PHE* 1.3 84.5 - - + +
101A GLU* 1.3 64.1 + - - +
103A TYR* 3.3 4.5 + - - +
104A GLN* 3.0 44.8 + - + +
136A ARG* 2.8 46.3 + - - -
489A ARG* 4.6 9.0 + - - +
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Residues in contact with GLU 101 (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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97A GLN* 3.4 22.5 - - + +
98A THR* 2.9 37.8 + - - +
100A GLU* 1.3 75.9 - - + +
102A TYR* 1.3 58.8 + - - +
104A GLN* 3.3 2.9 + - - -
105A HIS* 2.9 49.0 + - + -
481A HIS* 2.9 35.2 + - - -
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Residues in contact with TYR 102 (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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92A ASP 3.3 24.5 - - - -
94A GLY 3.9 1.8 - - - -
95A TRP* 3.5 26.0 - - + +
96A ILE* 3.1 25.3 + - + +
97A GLN* 3.3 50.4 + - + -
98A THR 2.9 21.7 + - - +
101A GLU* 1.3 76.5 - - - +
103A TYR* 1.3 58.4 + - - +
106A ASP* 2.8 36.4 + - - -
107A THR* 2.9 9.1 + - - -
133A TYR* 3.2 16.2 - - - +
342A PHE* 3.4 35.8 - + + -
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Residues in contact with TYR 103 (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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99A PHE* 2.9 21.3 + - + +
100A GLU* 3.6 9.6 - - - +
101A GLU 3.3 0.4 - - - -
102A TYR* 1.3 77.1 - - - +
104A GLN* 1.3 81.4 + - - +
107A THR* 3.6 9.1 + - + -
108A LYS* 2.9 61.5 + - + +
133A TYR* 4.0 21.1 - + + -
136A ARG* 3.5 55.4 + - + -
137A PHE* 3.3 40.3 + - + -
140A ASP* 4.2 10.6 + - - +
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Residues in contact with GLN 104 (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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100A GLU* 3.0 45.7 + - + +
101A GLU* 3.9 4.3 - - - +
103A TYR* 1.3 88.9 - - - +
105A HIS* 1.3 69.8 + - + +
108A LYS* 2.8 38.0 + - - +
109A HIS* 3.2 22.7 + - - -
136A ARG* 3.5 13.5 - - - +
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Residues in contact with HIS 105 (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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97A GLN* 2.6 28.5 + - - +
101A GLU* 2.9 32.3 + - + +
104A GLN* 1.3 89.8 - - + +
106A ASP* 1.3 70.5 - - - +
109A HIS* 3.4 7.9 - - - -
345A LYS* 3.0 25.5 + - - +
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Residues in contact with ASP 106 (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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97A GLN* 4.0 6.4 + - - -
102A TYR* 2.8 30.4 + - - +
104A GLN 3.5 0.6 - - - -
105A HIS* 1.3 88.3 - - - +
107A THR* 1.3 65.9 + - - +
108A LYS 3.4 1.6 - - - -
109A HIS* 3.1 8.8 + - - +
110A ILE* 3.0 28.3 + - + +
342A PHE* 3.8 31.8 - - + +
345A LYS* 3.0 30.6 + - + +
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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