Contacts of the helix formed by residues 101 - 112 (chain A) in PDB entry 1QK0
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 ASN 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TRP* 3.4 23.1 + - + +
100A ALA* 1.3 76.2 - - - +
102A ALA* 1.3 61.4 + - - +
103A TYR* 3.0 14.2 + - - +
104A TYR* 2.7 38.6 + - - +
105A ALA* 3.3 18.2 + - - +
128A ALA 4.9 1.0 - - - +
132A SER* 3.8 28.3 + - - -
133A PHE 4.5 1.0 + - - -
134A MET* 4.0 28.5 - - + +
148A THR* 4.3 14.6 - - + +
165A GLN 5.4 0.2 + - - -
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Residues in contact with ALA 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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99A TRP* 4.4 6.7 - - + +
100A ALA 3.9 0.4 + - - -
101A ASN* 1.3 72.1 - - - +
103A TYR* 1.3 59.4 + - - +
105A ALA* 3.8 7.9 - - - +
106A SER* 2.9 31.5 + - - -
147A GLN* 5.2 9.6 - - - +
151A ASP* 4.2 18.5 + - - +
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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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101A ASN* 3.0 10.4 + - - +
102A ALA* 1.3 77.4 - - - +
104A TYR* 1.3 64.0 + - + +
106A SER* 3.2 7.6 + - - -
107A GLU* 3.2 36.0 + - - +
134A MET* 3.7 22.1 - - + +
141A LYS* 4.3 20.0 + - + +
144A LEU* 3.4 35.1 - - + +
147A GLN* 6.0 0.4 - - - +
399A GLU* 3.7 25.4 - - - -
428A GLY 5.2 4.5 + - - -
505A MAN 3.4 31.4 + - - -
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Residues in contact with TYR 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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101A ASN* 2.7 25.1 + - - +
103A TYR* 1.3 73.1 - - + +
105A ALA* 1.3 66.5 + - - +
107A GLU* 3.1 22.0 + - - +
108A VAL* 3.0 38.6 + - + +
127A VAL* 3.6 36.8 - - + +
128A ALA* 4.2 11.9 - - - -
130A VAL 4.9 4.3 - - - -
132A SER* 4.1 17.7 - - - +
375A PHE* 4.1 4.3 - - - -
393A TRP* 5.3 5.0 - + - -
396A PRO* 3.7 26.9 - - + -
397A GLY 2.7 32.1 + - - -
399A GLU* 4.0 2.5 - - - +
430A TRP* 3.9 12.8 - + - -
435A PHE* 3.8 5.5 - - - -
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Residues in contact with ALA 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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100A ALA 5.7 0.7 - - - +
101A ASN 3.3 16.4 + - - +
102A ALA* 3.8 8.7 - - - +
103A TYR 3.3 0.4 - - - -
104A TYR* 1.3 78.2 - - - +
106A SER* 1.3 58.5 + - - +
108A VAL* 4.0 0.2 - - - +
109A SER* 2.9 36.3 + - - -
128A ALA* 3.9 22.9 + - + +
506A MAN 4.0 21.3 - - - +
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Residues in contact with SER 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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102A ALA 2.9 19.0 + - - -
103A TYR* 3.4 1.6 - - - -
104A TYR 3.1 0.2 - - - -
105A ALA* 1.3 75.5 - - - +
107A GLU* 1.3 57.0 + - - +
109A SER* 4.8 0.2 - - - -
110A SER* 2.8 34.7 + - - -
505A MAN 1.4 81.2 - - - -
506A MAN 5.4 0.2 - - - -
507A MAN 3.4 16.0 - - - -
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Residues in contact with GLU 107 (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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103A TYR* 3.2 25.7 + - - +
104A TYR* 3.1 21.5 + - - +
106A SER* 1.3 76.6 + - - +
108A VAL* 1.3 56.7 + - - +
111A LEU* 2.7 49.4 + - + +
112A ALA* 3.3 1.4 + - - +
399A GLU* 2.6 40.2 - - - +
428A GLY 4.2 7.3 - - - +
430A TRP* 3.6 31.1 + - + +
505A MAN 3.9 19.3 + - - +
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Residues in contact with VAL 108 (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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104A TYR* 3.0 43.3 + - + +
105A ALA 4.0 2.9 - - - +
107A GLU* 1.3 76.2 - - - +
109A SER* 1.3 56.8 + - - +
112A ALA* 3.1 11.2 + - + +
113A ILE* 2.8 35.6 + - + +
124A ALA* 3.4 29.8 - - + +
128A ALA* 4.1 13.0 - - + +
430A TRP* 3.7 17.7 - - + -
435A PHE* 3.9 16.8 - - + -
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Residues in contact with SER 109 (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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105A ALA 2.9 8.3 + - - -
106A SER* 4.3 2.0 - - - -
108A VAL* 1.3 75.9 - - - +
110A SER* 1.3 62.2 + - - +
113A ILE* 3.7 15.1 - - - +
114A PRO* 3.3 18.1 - - - +
128A ALA* 4.6 0.3 - - - +
506A MAN 1.4 87.8 - - - -
507A MAN 4.9 5.4 - - - -
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Residues in contact with SER 110 (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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106A SER* 2.8 16.0 + - - -
109A SER* 1.3 74.0 + - - +
111A LEU* 1.3 66.8 + - - +
114A PRO* 3.5 16.9 - - - +
505A MAN 4.4 7.0 - - - -
507A MAN 1.4 67.2 + - - -
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Residues in contact with LEU 111 (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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106A SER 4.5 1.1 - - - +
107A GLU* 2.7 36.2 + - + +
110A SER* 1.3 83.4 - - - +
112A ALA* 1.3 58.5 + - - +
114A PRO* 4.0 3.9 - - - +
115A SER* 4.2 0.7 + - - -
430A TRP* 3.8 38.7 + - + -
432A GLN* 3.8 5.7 - - - +
505A MAN 3.2 37.2 - - - +
508A MAN 4.0 19.8 + - - +
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Residues in contact with ALA 112 (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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107A GLU 3.3 0.2 + - - -
108A VAL* 3.1 13.6 + - + +
111A LEU* 1.3 77.5 - - - +
113A ILE* 1.3 65.7 + - - +
114A PRO* 3.3 2.5 - - - -
115A SER* 3.0 20.8 + - - -
116A LEU* 3.4 11.3 - - + +
430A TRP* 3.8 12.8 - - + -
432A GLN* 3.2 20.0 + - - +
435A PHE* 3.8 30.7 - - + -
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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