Contacts of the helix formed by residues 78 - 86 (chain A) in PDB entry 2KK0
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 GLY 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A VAL* 3.0 20.4 + - - -
74A THR* 3.9 2.0 + - - -
77A GLY* 1.3 79.7 - - - +
79A LEU* 1.3 65.8 + - - -
80A VAL 3.5 2.2 - - - -
81A GLU 3.3 2.2 + - - -
82A VAL* 3.0 23.2 + - - +
120A GLU* 3.5 17.9 - - - -
126A LEU* 4.0 6.5 - - - -
127A SER* 3.9 1.8 - - - -
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Residues in contact with LEU 79 (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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73A VAL* 3.5 9.0 - - - +
78A GLY* 1.3 68.7 - - - -
80A VAL* 1.3 65.7 + - - +
82A VAL* 3.1 5.7 + - - +
83A ILE* 2.9 37.3 + - + +
88A TRP* 3.7 26.2 - - + -
109A ARG 4.3 7.6 - - - +
112A TYR* 3.5 26.2 - - + -
113A MET* 3.8 27.8 - - + -
117A TYR* 3.4 28.3 - - + -
120A GLU* 3.1 15.2 + - - +
132A LEU* 3.6 18.8 - - + -
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Residues in contact with VAL 80 (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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79A LEU* 1.3 74.6 - - - +
81A GLU* 1.3 57.9 + - - +
83A ILE* 3.2 10.3 + - - +
84A ASN* 2.8 49.6 + - - +
117A TYR* 4.5 1.1 - - + +
127A SER* 3.3 23.6 + - - +
128A ASN 4.1 0.2 - - - +
131A GLU* 3.3 35.4 - - + +
132A LEU* 3.4 39.3 - - + +
135A ALA* 3.7 16.2 - - + -
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Residues in contact with GLU 81 (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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76A LYS 3.1 25.9 - - - +
77A GLY* 3.7 18.6 - - - +
78A GLY 3.3 9.7 + - - +
80A VAL* 1.3 77.4 - - - +
82A VAL* 1.3 58.2 + - - +
84A ASN* 3.0 12.0 + - - +
85A LYS* 2.8 63.3 + - + +
127A SER* 4.3 1.4 + - - -
131A GLU* 5.1 0.6 + - - -
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Residues in contact with VAL 82 (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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73A VAL* 3.6 31.0 - - + +
76A LYS* 3.9 17.7 - - + -
78A GLY 3.0 18.6 + - - +
79A LEU 3.4 7.4 - - - +
81A GLU* 1.3 75.2 - - - +
83A ILE* 1.3 56.4 + - - +
85A LYS* 3.3 1.3 + - - -
86A LYS* 2.9 23.7 + - - -
87A LEU* 3.5 25.6 + - + -
88A TRP* 3.4 37.4 + - + -
91A ILE* 4.0 11.7 - - + -
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Residues in contact with ILE 83 (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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79A LEU* 2.9 28.0 + - + +
80A VAL* 3.4 8.3 - - - +
82A VAL* 1.3 75.6 - - - +
84A ASN* 1.3 61.2 + - - +
86A LYS* 3.2 25.3 + - - +
88A TRP* 3.9 9.0 - - + +
109A ARG* 3.8 35.7 - - + +
132A LEU* 3.7 30.5 - - + -
135A ALA* 3.6 20.6 - - + +
136A ILE* 4.1 7.6 - - + +
139A ASN* 3.2 30.8 + - - +
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Residues in contact with ASN 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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80A VAL* 2.8 41.2 + - - +
81A GLU* 3.0 15.0 + - - +
83A ILE* 1.3 72.9 - - - +
85A LYS* 1.3 69.4 + - - +
86A LYS* 4.4 4.8 - - - +
131A GLU* 5.4 0.2 + - - -
135A ALA* 3.3 24.4 - - - +
138A SER* 5.7 1.4 - - - -
139A ASN* 5.2 1.6 + - - +
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Residues in contact with LYS 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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76A LYS* 5.5 1.8 - - + +
81A GLU* 2.8 46.6 + - + +
83A ILE 3.2 0.2 - - - -
84A ASN* 1.3 86.2 - - - +
86A LYS* 1.3 65.4 + - - +
87A LEU* 2.9 40.8 + - + +
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Residues in contact with LYS 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 VAL 2.9 9.8 + - - -
83A ILE 3.2 18.5 + - - +
84A ASN 4.4 4.9 - - - +
85A LYS* 1.3 78.4 - - - +
87A LEU* 1.3 55.1 + - - +
88A TRP* 3.0 20.0 + - - +
89A ARG* 4.5 4.7 + - - +
105A ALA* 5.9 0.5 - - - +
109A ARG* 4.7 6.3 - - - +
139A ASN* 3.3 31.5 + - - +
142A GLU* 3.4 38.1 + - - +
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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