Contacts of the helix formed by residues 67 - 81 (chain A) in PDB entry 1CK7
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 LEU 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LYS* 5.1 8.3 - - - +
66A ASN* 1.3 78.3 - - - +
68A PHE* 1.3 60.9 + - - +
70A LEU* 3.7 15.1 - - + +
71A LYS* 3.0 49.1 + - - +
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Residues in contact with PHE 68 (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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66A ASN* 3.2 15.9 + - - +
67A LEU* 1.3 80.3 - - - +
69A VAL* 1.3 67.8 + - + +
71A LYS* 3.9 5.0 - - + +
72A ASP* 3.3 37.0 + - + +
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Residues in contact with VAL 69 (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 CYS* 4.3 7.4 - - - -
64A SER* 2.8 33.2 - - - +
65A CYS* 3.0 16.6 - - - -
66A ASN* 2.7 55.1 + - - +
68A PHE* 1.3 79.7 - - + +
70A LEU* 1.3 57.8 + - - +
72A ASP* 4.8 2.7 - - - -
73A THR* 2.5 43.3 + - + +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 3.1 40.2 - - + +
50A ALA* 4.3 13.5 - - + -
51A VAL* 4.5 11.0 - - + +
54A LEU* 3.5 25.8 - - + -
65A CYS* 4.5 11.4 - - - -
66A ASN 2.8 18.8 + - - +
67A LEU* 3.7 13.2 - - + +
69A VAL* 1.3 79.8 - - + +
71A LYS* 1.3 54.8 + - + +
73A THR* 3.4 2.4 + - - -
74A LEU* 2.6 60.0 + - + +
87A GLY 5.0 1.6 - - - +
89A LEU* 4.1 1.6 - - + -
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Residues in contact with LYS 71 (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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47A LYS* 5.4 7.3 - - - +
67A LEU* 3.0 38.8 + - - +
68A PHE* 3.4 5.8 + - + +
70A LEU* 1.3 77.2 - - + +
72A ASP* 1.3 68.2 + - - +
74A LEU* 3.0 3.6 - - - +
75A LYS* 2.8 34.0 + - - +
87A GLY* 3.2 37.7 + - - +
88A ASP* 3.2 23.3 + - - +
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Residues in contact with ASP 72 (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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68A PHE* 3.3 31.6 + - + +
69A VAL* 4.2 2.9 - - - +
71A LYS* 1.3 82.1 - - - +
73A THR* 1.3 66.9 + - + +
75A LYS* 3.0 32.2 + - - +
76A LYS* 3.2 29.4 + - - +
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Residues in contact with THR 73 (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 LEU* 3.4 25.2 - - - +
58A TYR* 5.2 7.6 - - + +
60A CYS* 3.5 32.4 - - + +
69A VAL* 2.5 29.1 + - + +
72A ASP* 1.3 78.5 - - + +
74A LEU* 1.3 72.7 + - - +
76A LYS* 2.7 42.5 + - + +
77A MET* 3.1 8.5 + - - +
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Residues in contact with LEU 74 (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 LEU* 4.1 15.7 - - + -
70A LEU* 2.6 44.4 + - + +
71A LYS 3.0 6.3 - - - +
73A THR* 1.3 76.9 + - - +
75A LYS* 1.3 51.0 + - - +
77A MET* 2.9 11.7 + - - +
78A GLN* 2.8 64.5 + - - +
87A GLY* 2.8 23.3 - - - +
88A ASP 3.6 4.3 - - - +
89A LEU* 3.3 36.3 - - + -
93A THR* 3.7 9.6 - - + -
97A MET* 5.9 1.3 - - + -
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Residues in contact with LYS 75 (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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71A LYS* 2.8 28.7 + - - +
72A ASP* 3.2 18.8 + - - +
74A LEU* 1.3 72.9 - - - +
76A LYS* 1.3 54.2 + - + +
78A GLN* 3.0 10.2 - - - +
79A LYS* 2.6 37.4 + - - +
85A GLN* 4.0 21.7 - - + +
86A THR* 3.4 28.7 - - - +
87A GLY* 4.2 10.5 - - - +
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Residues in contact with LYS 76 (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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58A TYR* 4.4 16.5 - - + +
72A ASP* 3.3 31.5 + - - +
73A THR* 2.7 42.0 + - + +
75A LYS* 1.3 73.2 - - + +
77A MET* 1.3 54.6 + - - +
79A LYS* 3.5 9.5 - - - +
80A PHE* 3.1 26.5 + - - +
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Residues in contact with MET 77 (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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53A TYR* 4.2 4.9 - - + -
54A LEU* 4.0 8.3 - - + -
58A TYR* 3.2 45.2 - - + +
73A THR 3.1 3.8 + - - -
74A LEU* 2.9 12.0 + - - +
76A LYS* 1.3 73.0 - - - +
78A GLN* 1.3 70.5 + - - +
80A PHE* 3.1 2.3 + - - +
81A PHE* 2.9 52.0 + - + -
83A LEU* 4.2 4.5 - - + -
93A THR* 3.7 40.8 - - - +
96A THR* 4.0 14.1 - - + -
97A MET* 4.0 24.9 - - + -
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Residues in contact with GLN 78 (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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74A LEU* 2.8 17.7 + - - +
75A LYS* 3.0 18.8 + - - +
77A MET* 1.3 78.3 - - - +
79A LYS* 1.3 61.3 + - - +
81A PHE 3.2 0.9 + - - -
82A GLY 2.9 5.0 + - - -
83A LEU* 2.8 56.9 + - + +
84A PRO 3.3 22.4 - - - +
85A GLN* 4.5 0.2 - - - -
86A THR* 2.2 35.1 + - - +
88A ASP 2.9 27.5 + - - -
90A ASP* 3.7 0.6 + - - -
93A THR* 3.0 18.9 + - + +
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Residues in contact with LYS 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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75A LYS 2.6 19.4 + - - +
76A LYS* 3.5 9.4 - - - +
78A GLN* 1.3 75.2 - - - +
80A PHE* 1.3 65.7 + - + +
81A PHE 3.3 0.5 + - - -
82A GLY* 3.4 8.4 + - - -
83A LEU 4.6 1.8 - - - -
85A GLN* 3.2 36.5 - - - +
415A GLN* 3.4 13.2 + - - +
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Residues in contact with PHE 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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58A TYR* 3.7 10.8 - + + +
76A LYS 3.1 11.2 + - - +
77A MET 3.1 9.0 + - - +
79A LYS* 1.3 80.6 - - + +
81A PHE* 1.3 78.9 + + - +
82A GLY 3.6 0.3 + - - -
106A ASP* 3.7 31.4 - - + -
413A HIS* 4.1 16.8 - - + -
414A SER 3.6 20.0 - - - -
415A GLN* 2.9 59.2 + - + +
423A PRO* 3.5 32.3 - - + -
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Residues in contact with PHE 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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53A TYR* 3.8 11.0 - + - -
58A TYR* 2.9 21.1 - - - -
77A MET* 2.9 45.5 + - + +
78A GLN 3.2 1.8 + - - +
80A PHE* 1.3 87.8 - + - +
82A GLY* 1.3 61.0 + - - +
83A LEU* 3.3 14.5 + - + +
96A THR* 4.1 21.3 - - + -
101A ARG* 3.0 29.2 - - - -
106A ASP* 3.5 6.3 - - - -
423A PRO* 3.5 22.9 - - + -
424A ILE* 4.1 16.6 - - + -
504A MET* 5.0 7.3 - - - +
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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