Contacts of the helix formed by residues 101 - 112 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B TRP* 3.5 20.4 + - + +
100B ALA* 1.3 75.6 - - - +
102B ALA* 1.3 61.0 + - - +
103B TYR* 3.0 12.9 + - - +
104B TYR* 2.7 37.9 + - - +
105B ALA* 3.4 18.8 + - - +
128B ALA 4.9 1.6 - - - +
132B SER* 3.8 28.7 + - - +
133B PHE 4.6 1.2 + - - -
134B MET* 4.0 37.9 - - + +
148B THR* 4.3 8.5 - - + +
396B PRO* 6.2 0.4 - - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B TRP* 4.5 4.9 - - + +
100B ALA 4.0 0.2 + - - -
101B ASN* 1.3 72.9 - - - +
103B TYR* 1.3 59.3 + - - +
105B ALA* 3.6 8.0 - - - +
106B SER* 2.8 31.4 + - - -
147B GLN* 5.3 9.4 - - - +
151B ASP* 4.4 16.8 - - - +
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASN* 3.0 10.3 - - - +
102B ALA* 1.3 77.5 - - - +
104B TYR* 1.3 65.9 + - + +
106B SER* 3.0 16.7 + - - -
107B GLU* 3.1 33.5 + - - +
134B MET* 3.8 17.7 - - + +
141B LYS* 4.5 20.8 + - - -
144B LEU* 3.4 33.9 - - + +
399B GLU* 3.5 22.7 - - - -
428B GLY 5.0 5.0 + - - -
505B MAN 3.1 30.4 + - - -
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Residues in contact with TYR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASN* 2.7 26.4 + - - +
103B TYR* 1.3 74.9 - - + +
105B ALA* 1.3 63.6 + - - +
107B GLU* 2.9 32.3 + - - +
108B VAL* 3.0 30.3 + - + +
127B VAL* 3.7 34.4 - - + +
128B ALA* 4.3 11.4 - - - -
130B VAL 5.0 5.2 - - - -
132B SER* 4.2 18.2 - - - +
375B PHE* 3.9 4.7 - - - -
393B TRP* 5.9 4.5 - + - -
396B PRO* 3.7 28.3 - - + -
397B GLY 2.7 32.3 + - - -
399B GLU* 4.1 1.1 - - + +
430B TRP* 3.9 13.9 - + - -
435B PHE* 3.8 5.9 - - - -
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ASN 3.4 13.4 + - - +
102B ALA* 3.6 11.9 - - - +
103B TYR 3.3 0.4 - - - -
104B TYR* 1.3 80.0 - - - +
106B SER* 1.3 58.5 + - - +
108B VAL* 3.5 0.7 + - - +
109B SER* 2.9 34.7 + - - -
128B ALA* 3.9 22.6 + - + +
506B MAN 3.7 22.2 - - - +
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA 2.8 14.0 + - - -
103B TYR* 3.0 6.5 + - - -
105B ALA* 1.3 74.1 - - - +
107B GLU* 1.3 56.8 + - - +
110B SER* 2.8 36.1 + - - -
505B MAN 1.4 57.2 - - - -
506B MAN 5.3 0.4 - - - -
507B MAN 3.3 18.8 - - - -
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 3.5 28.6 + - - +
104B TYR* 2.9 20.2 + - - +
106B SER* 1.3 77.0 + - - +
108B VAL* 1.3 57.6 + - - +
111B LEU* 2.8 47.2 + - + +
112B ALA 3.3 1.4 + - - -
399B GLU* 2.4 35.9 - - - +
428B GLY 4.2 7.8 - - - +
430B TRP* 3.5 33.1 + - + -
505B MAN 3.8 19.9 + - - +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B TYR* 3.0 49.1 + - + +
105B ALA 3.8 5.2 - - - +
107B GLU* 1.3 75.3 - - - +
109B SER* 1.3 58.2 + - - +
112B ALA* 3.0 14.0 + - + +
113B ILE* 2.9 37.3 + - + +
124B ALA* 3.6 29.6 - - + +
128B ALA* 4.1 15.3 - - + +
430B TRP* 3.9 9.9 - - + -
435B PHE* 4.0 16.4 - - + -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ALA 2.9 7.4 + - - -
106B SER 4.1 0.9 - - - -
108B VAL* 1.3 76.3 - - - +
110B SER* 1.3 61.3 + - - +
113B ILE* 3.8 14.8 - - - +
114B PRO* 3.2 19.1 - - - +
506B MAN 1.4 65.4 + - - -
507B MAN 4.6 7.9 - - - -
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Residues in contact with SER 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B SER* 2.8 14.9 + - - -
109B SER* 1.3 73.1 - - - +
111B LEU* 1.3 65.5 + - - +
114B PRO* 3.5 18.3 - - - +
505B MAN 4.6 7.9 - - - -
507B MAN 1.4 66.1 + - - -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU* 2.8 35.2 + - + +
110B SER* 1.3 83.0 - - - +
112B ALA* 1.3 59.5 + - - +
114B PRO* 4.2 2.5 - - - -
430B TRP* 3.6 40.5 + - + -
432B GLN* 3.4 8.1 - - - +
505B MAN 3.5 35.2 - - - +
508B MAN 3.8 19.4 + - - +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU 3.3 1.4 + - - -
108B VAL* 3.0 16.7 + - + +
111B LEU* 1.3 78.1 - - - +
113B ILE* 1.3 60.8 + - - +
114B PRO 3.3 1.3 - - - -
115B SER* 2.9 28.9 + - - -
116B LEU* 3.5 11.5 + - + +
430B TRP* 3.9 10.5 - - + -
432B GLN* 3.1 17.0 + - - +
435B PHE* 3.7 30.1 - - + -
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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