Contacts of the helix formed by residues 52 - 67 (chain A) in PDB entry 2KAT
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 TYR 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A MET* 3.7 28.7 - - + +
20A LEU* 3.7 29.4 - - + +
23A PHE* 3.6 38.7 - + + -
46A LEU* 5.7 0.2 - - + -
49A ASP* 3.9 10.7 + - - +
50A PRO 3.2 3.4 - - - -
51A THR* 1.3 75.3 - - - +
53A SER* 1.3 68.5 + - - +
54A VAL* 3.4 30.8 - - + +
55A ALA* 3.0 42.3 + - + +
56A TRP* 3.2 10.7 + - - -
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR 3.3 6.4 + - - -
52A TYR* 1.3 72.3 - - - +
54A VAL* 1.3 70.5 + - - +
56A TRP* 3.0 48.3 + - - +
57A LYS* 3.3 10.4 + - - +
86A ARG* 5.6 2.9 - - - -
88A ASP* 4.4 14.2 + - - -
91A VAL* 4.2 21.5 - - - +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.5 21.3 - - + -
27A LYS* 5.6 1.8 - - - +
52A TYR* 3.2 28.4 + - + +
53A SER* 1.3 81.9 - - - +
55A ALA* 1.3 61.1 + - - +
57A LYS* 3.2 16.5 + - + +
58A TRP* 3.1 37.1 + - + +
91A VAL* 5.5 5.6 - - + -
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.8 17.7 - - + -
42A LEU* 5.7 4.3 - - + -
45A ALA* 6.4 1.8 - - + -
46A LEU* 4.0 22.2 - - + -
52A TYR* 3.0 29.6 + - + +
54A VAL* 1.3 76.6 - - - +
56A TRP* 1.3 60.4 + - - +
58A TRP* 3.1 4.4 + - - +
59A LEU* 2.9 38.1 + - + +
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Residues in contact with TRP 56 (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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46A LEU* 4.5 12.3 - - + -
50A PRO 2.7 31.0 + - - -
51A THR* 3.7 17.0 - - + -
52A TYR 3.2 11.8 + - - -
53A SER* 3.0 31.1 + - - +
55A ALA* 1.3 75.2 - - - +
57A LYS* 1.3 62.9 + - - +
59A LEU* 3.2 9.9 + - - +
60A GLY* 3.1 18.9 + - - -
75A ALA 5.6 2.1 - - - +
76A TRP* 5.2 0.9 - - - -
79A GLY* 4.0 18.9 - - - -
82A ALA* 3.5 21.7 - - + +
83A ALA* 3.3 37.9 - - + -
86A ARG* 3.4 29.4 - - + -
91A VAL* 4.7 2.9 - - + -
95A LEU* 4.4 8.9 - - + +
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER 3.3 6.1 + - - +
54A VAL* 3.2 18.5 + - + +
55A ALA 3.2 0.2 - - - -
56A TRP* 1.3 82.4 - - - +
58A TRP* 1.3 71.3 + - + +
60A GLY 3.7 0.9 + - - -
61A LYS* 3.5 34.6 + - + +
91A VAL* 4.5 11.0 - - + -
94A GLU* 3.2 49.4 + - + +
95A LEU* 3.4 32.6 - - + +
98A PHE* 6.0 8.8 - - - -
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Residues in contact with TRP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.3 34.7 - + + -
27A LYS* 3.6 29.6 - - + +
30A ALA* 3.7 29.6 - - + -
31A GLU* 3.9 26.5 - - + -
35A PHE* 5.1 0.5 - - - -
42A LEU* 4.7 14.1 - - + -
54A VAL* 3.1 37.0 + - + +
55A ALA* 3.1 6.9 + - - +
57A LYS* 1.3 83.5 - - + +
59A LEU* 1.3 55.8 + - - +
61A LYS* 3.0 44.2 + - + +
62A THR* 2.7 35.5 + - - +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.5 14.1 - - + +
42A LEU* 3.9 29.4 - - + -
43A ARG* 5.9 1.3 - - - +
46A LEU* 3.8 31.9 - - + -
55A ALA* 2.9 26.8 + - + +
56A TRP* 3.4 12.6 - - - +
58A TRP* 1.3 77.1 - - - +
60A GLY* 1.3 62.9 + - - +
62A THR* 2.9 23.5 + - - +
63A LEU* 3.2 27.1 - - + +
75A ALA* 4.7 5.2 - - + -
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Residues in contact with GLY 60 (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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56A TRP 3.1 8.5 + - - -
57A LYS 3.7 1.3 + - - -
58A TRP 3.2 0.4 - - - -
59A LEU* 1.3 80.7 - - - +
61A LYS* 1.3 59.2 + - - +
62A THR 3.3 0.5 + - - -
63A LEU* 3.5 3.6 + - - +
64A GLN* 3.4 19.4 + - - +
72A ALA* 4.2 2.0 - - - +
75A ALA* 4.1 14.9 - - - +
76A TRP* 3.3 40.1 - - - -
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Residues in contact with LYS 61 (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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30A ALA 5.5 0.8 + - - -
31A GLU* 6.1 0.8 - - - +
35A PHE* 3.5 25.3 - - + -
57A LYS* 3.5 27.3 + - + +
58A TRP* 3.0 46.7 + - + +
60A GLY* 1.3 73.7 - - - +
62A THR* 1.3 60.3 + - - +
64A GLN* 3.1 24.9 - - - +
65A GLY* 3.0 23.6 + - - -
76A TRP* 4.2 1.5 - - + +
95A LEU* 6.1 0.4 - - + -
98A PHE* 4.4 19.9 - - + -
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Residues in contact with THR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 5.1 1.2 - - - +
35A PHE* 3.3 46.1 - - + +
38A ALA* 4.6 2.0 - - + -
39A LEU* 3.5 30.7 - - + +
42A LEU* 3.7 14.3 - - + +
58A TRP* 2.7 23.8 + - - +
59A LEU* 2.9 16.2 + - - -
61A LYS* 1.3 77.6 - - - +
63A LEU* 1.3 60.0 + - - +
65A GLY 3.3 0.9 + - - -
66A GLN* 2.9 30.5 + - - +
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Residues in contact with LEU 63 (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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39A LEU* 4.4 15.9 - - + -
59A LEU* 3.2 25.0 + - + +
60A GLY 4.0 2.2 - - - +
62A THR* 1.3 80.9 - - - +
64A GLN* 1.3 61.3 + - - +
66A GLN* 3.3 22.4 + - - +
67A GLY 3.1 5.4 + - - -
68A ASP* 3.0 33.1 + - + +
71A GLY* 3.7 27.8 - - - +
72A ALA* 3.4 21.8 - - - +
75A ALA* 4.4 7.9 - - + -
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Residues in contact with GLN 64 (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 GLY 3.4 4.7 + - - +
61A LYS* 3.1 44.8 - - - +
63A LEU* 1.3 78.3 - - - +
65A GLY* 1.3 61.1 + - - +
67A GLY* 3.3 12.6 + - - -
68A ASP 4.5 3.8 - - - +
69A ARG* 5.9 0.4 - - - +
72A ALA* 3.8 16.7 - - + +
76A TRP* 3.5 24.8 - - + -
98A PHE* 3.6 14.8 - - - -
101A ARG* 5.8 4.0 - - - +
102A LEU* 5.2 9.7 - - + +
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Residues in contact with GLY 65 (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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33A GLU* 5.5 1.7 - - - +
35A PHE* 3.5 35.5 - - - -
61A LYS 3.0 11.1 + - - -
64A GLN* 1.3 77.7 - - - +
66A GLN* 1.3 64.1 + - - +
67A GLY* 3.4 1.0 + - - -
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Residues in contact with GLN 66 (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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35A PHE* 4.1 9.8 - - + -
36A ASP* 4.5 18.3 + - + +
39A LEU* 3.6 27.8 - - + +
62A THR 2.9 16.8 + - - +
63A LEU* 3.5 26.6 - - - +
64A GLN 3.3 0.2 - - - -
65A GLY* 1.3 76.6 - - - +
67A GLY* 1.3 58.5 - - - +
68A ASP* 4.2 11.6 - - + +
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Residues in contact with GLY 67 (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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63A LEU 3.1 2.6 + - - -
64A GLN 3.3 9.2 + - - -
65A GLY 3.2 3.9 - - - -
66A GLN* 1.3 80.5 - - - +
68A ASP* 1.3 61.8 + - - +
69A ARG 3.9 2.7 + - - -
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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