Contacts of the helix formed by residues 82 - 90 (chain A) in PDB entry 1KNY
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 GLU 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LYS* 3.3 33.7 + - - +
56A VAL* 3.9 12.6 - - + -
57A MET 3.4 7.7 + - - -
58A SER 5.2 1.2 + - - -
81A SER* 1.3 75.5 + - - +
83A GLU* 1.3 58.4 + - - +
85A LEU* 4.0 2.6 - - - +
86A LEU* 2.9 37.8 + - + +
115A TYR* 3.6 16.9 - - + +
118A LYS* 2.3 45.6 + - - +
119A VAL* 5.8 2.9 - - + +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 4.7 18.2 - - + +
81A SER* 3.2 9.4 + - - +
82A GLU* 1.3 73.9 - - - +
84A ILE* 1.3 64.1 + - + +
85A LEU 3.0 1.3 - - - -
86A LEU* 2.7 32.9 + - - +
87A ASP* 3.0 20.3 + - - +
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Residues in contact with ILE 84 (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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60A GLU* 5.9 0.4 - - + -
61A GLU* 3.8 26.2 - - + +
62A ALA 4.0 4.9 - - - +
63A GLU* 3.9 35.7 - - + +
80A TYR* 4.1 14.1 - - + -
81A SER* 3.2 39.7 + - - +
83A GLU* 1.3 86.0 - - + +
85A LEU* 1.3 55.7 + - - +
87A ASP* 3.9 7.1 - - - +
88A TYR* 3.1 27.7 + - + +
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Residues in contact with LEU 85 (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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54A MET* 4.4 13.0 - - - -
56A VAL* 3.5 30.7 - - + -
80A TYR* 3.4 44.9 - - + -
81A SER 3.3 14.8 + - - +
82A GLU* 4.0 4.9 - - - +
83A GLU 2.8 4.9 + - - -
84A ILE* 1.3 74.6 - - - +
86A LEU* 1.3 54.2 + - - +
88A TYR* 3.3 10.6 + - + +
89A ALA* 2.7 36.0 + - - +
103A PHE* 4.0 18.6 - - + -
116A LEU* 6.2 0.2 - - + -
119A VAL* 4.1 24.2 - - + -
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Residues in contact with LEU 86 (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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82A GLU* 2.9 42.2 - - + +
83A GLU* 2.7 14.4 + - - +
85A LEU* 1.3 66.5 - - - +
87A ASP* 1.3 58.0 + - - +
89A ALA* 2.8 14.9 + - - +
90A SER* 2.2 27.5 + - - -
118A LYS* 4.3 12.8 - - + +
119A VAL* 4.0 31.9 - - + +
122A THR* 3.8 28.8 - - + +
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Residues in contact with ASP 87 (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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83A GLU* 3.0 17.6 + - - +
84A ILE* 3.9 10.5 - - - +
86A LEU* 1.3 74.8 - - - +
88A TYR* 1.3 64.8 + - - +
90A SER* 2.8 25.0 + - - -
91A GLN* 3.5 19.3 + - - +
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Residues in contact with TYR 88 (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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80A TYR* 4.2 20.6 - + + -
84A ILE* 3.1 20.1 + - + +
85A LEU* 3.4 14.4 - - + +
87A ASP* 1.3 80.4 - - - +
89A ALA* 1.3 58.0 + - - +
90A SER 2.9 5.7 + - - -
91A GLN* 2.9 36.3 + - - +
99A THR* 4.3 10.6 - - - -
100A HIS* 3.0 36.9 + + - -
102A GLN* 4.2 13.5 + - - -
103A PHE* 3.6 26.0 - + - -
556A APC 4.7 4.0 + - - -
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Residues in contact with ALA 89 (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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85A LEU 2.7 20.7 + - - +
86A LEU* 2.8 9.2 + - - +
88A TYR* 1.3 73.3 - - - +
90A SER* 1.3 55.8 + - - +
91A GLN 3.3 1.3 - - - -
96A TRP* 5.2 0.7 + - - -
100A HIS* 3.6 12.0 - - - -
103A PHE* 3.8 28.5 - - + -
119A VAL* 4.4 13.5 - - + +
122A THR* 4.3 2.9 - - + +
123A ALA* 3.5 32.9 - - + +
126A VAL* 4.6 4.3 - - - +
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Residues in contact with SER 90 (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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86A LEU 2.2 34.5 + - - -
87A ASP* 2.8 14.7 + - - -
88A TYR 2.9 0.4 + - - -
89A ALA* 1.3 73.8 - - - +
91A GLN* 1.3 58.0 + - - +
92A VAL* 3.7 3.7 + - - +
122A THR* 4.1 13.3 - - - +
126A VAL* 4.6 18.0 - - - +
130A THR* 5.4 2.6 + - - +
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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