Contacts of the helix formed by residues 48 - 61 (chain A) in PDB entry 3K6R
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLU 4.9 6.7 - - - -
18A LEU* 3.6 21.8 - - + -
19A PRO* 3.1 29.6 - - + +
22A LEU* 3.4 28.5 - - + -
45A LEU* 2.9 11.7 + - - -
47A PRO* 1.3 104.2 - - + +
49A LYS* 1.3 57.0 + - - +
50A HIS 3.1 2.9 + - - -
51A ARG* 3.2 14.6 + - + -
52A ILE* 2.6 50.3 + - + +
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Residues in contact with LYS 49 (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* 5.8 0.2 - - - +
41A LEU* 5.1 9.2 - - + -
45A LEU 3.1 8.7 + - - +
46A GLU* 3.0 31.7 + - + +
48A TYR* 1.3 77.7 - - - +
50A HIS* 1.3 85.6 + - + +
52A ILE* 3.6 7.1 - - - +
53A ALA* 2.8 32.7 + - - +
67A ARG* 4.1 18.0 - - - +
81A GLU* 2.8 29.0 + - - +
83A LEU* 3.9 28.6 - - + +
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Residues in contact with HIS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLU 5.5 0.2 - - - -
47A PRO 6.5 0.4 - - - -
48A TYR 3.2 0.8 - - - -
49A LYS* 1.3 101.9 - - + +
51A ARG* 1.3 68.3 + - - +
53A ALA* 3.9 1.4 - - - +
54A GLU* 3.0 25.3 + - - +
81A GLU* 5.7 0.2 - - - -
82A LEU 4.7 4.7 - - - -
83A LEU* 3.3 40.2 + - + +
84A TYR* 5.1 1.4 - - - +
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Residues in contact with ARG 51 (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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13A ILE* 4.3 5.3 - - - +
14A LEU* 4.4 11.0 - - + -
17A GLU* 2.9 42.8 + - + +
18A LEU* 6.2 1.1 - - + -
48A TYR* 3.2 20.2 + - + +
50A HIS* 1.3 78.4 - - - +
52A ILE* 1.3 66.3 + - - +
54A GLU* 2.9 46.2 + - - +
55A VAL* 3.4 32.3 + - - +
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Residues in contact with ILE 52 (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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14A LEU* 4.3 8.1 - - + -
18A LEU* 4.4 7.0 - - + -
26A LEU* 4.0 14.8 - - + -
27A PRO* 5.0 4.9 - - + -
39A LEU* 4.1 11.4 - - + -
45A LEU* 3.8 44.4 - - + +
48A TYR* 2.6 41.3 + - + +
49A LYS* 3.6 6.5 - - - +
51A ARG* 1.3 71.0 - - - +
53A ALA* 1.3 66.1 + - - +
55A VAL* 2.9 28.9 + - - +
56A TYR* 3.3 28.8 + - + -
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Residues in contact with ALA 53 (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* 4.2 14.1 - - + -
49A LYS 2.8 19.9 + - - +
50A HIS 3.4 2.4 + - - +
52A ILE* 1.3 73.3 - - - +
54A GLU* 1.3 56.0 + - - +
56A TYR* 3.3 1.6 + - - +
57A ALA* 3.0 31.4 + - - +
65A VAL* 3.5 35.2 - - + +
83A LEU* 3.9 13.0 - - + -
84A TYR* 3.9 12.3 - - + -
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Residues in contact with GLU 54 (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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50A HIS 3.0 13.0 + - - +
51A ARG* 2.9 42.9 + - - +
52A ILE 3.0 0.4 + - - -
53A ALA* 1.3 77.6 - - - +
55A VAL* 1.3 56.5 - - - +
57A ALA* 3.7 2.6 + - - +
58A GLU* 3.1 27.1 + - + +
84A TYR* 3.5 36.0 + - + +
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Residues in contact with VAL 55 (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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10A ILE* 4.4 6.3 - - + -
13A ILE* 3.7 27.8 - - + +
14A LEU* 3.4 37.0 - - + -
51A ARG* 3.6 40.2 - - - +
52A ILE 2.9 23.4 + - - +
54A GLU* 1.3 74.0 - - - +
56A TYR* 1.3 71.0 + - + +
57A ALA 3.2 1.3 - - - -
58A GLU* 3.3 7.2 + - + +
59A VAL* 3.0 28.6 + - - +
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Residues in contact with TYR 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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10A ILE* 3.6 37.8 - - + +
14A LEU* 4.4 5.6 - - + -
26A LEU* 3.5 10.3 - - + +
27A PRO* 2.7 38.0 + - + +
30A TRP* 3.5 30.1 - + - -
37A LEU* 3.9 13.9 - - + -
39A LEU* 3.7 22.2 - - + -
52A ILE* 3.3 34.8 + - + +
53A ALA 3.7 7.2 - - - +
55A VAL* 1.3 81.8 - - + +
57A ALA* 1.3 57.9 + - - +
59A VAL* 3.4 5.9 - - - +
60A LEU* 2.9 50.4 + - + +
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Residues in contact with ALA 57 (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 ALA 3.0 15.6 + - - +
54A GLU 3.8 2.9 - - - +
56A TYR* 1.3 75.1 - - - +
58A GLU* 1.3 59.1 + - - +
61A GLY* 2.9 25.3 + - - -
62A VAL* 3.2 35.4 + - + +
65A VAL* 4.1 2.4 - - + +
84A TYR* 3.4 37.2 - - + -
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Residues in contact with GLU 58 (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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13A ILE* 5.1 10.4 - - + +
54A GLU* 3.1 19.7 + - + +
55A VAL* 3.3 8.7 + - + +
57A ALA* 1.3 78.0 - - - +
59A VAL* 1.3 62.6 + - - +
61A GLY* 3.7 6.1 + - - -
84A TYR* 5.6 0.4 + - - -
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Residues in contact with VAL 59 (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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6A ILE* 4.1 25.0 - - + +
9A ARG* 3.8 39.6 + - + +
10A ILE* 3.3 36.8 - - + -
13A ILE* 5.3 9.9 - - + -
55A VAL 3.0 21.6 + - - +
56A TYR 3.4 5.6 - - - +
58A GLU* 1.3 77.8 + - - +
60A LEU* 1.3 67.6 + - + +
61A GLY 3.6 0.2 + - - -
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Residues in contact with LEU 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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6A ILE* 3.7 27.4 - - + -
10A ILE* 4.3 6.3 - - + -
30A TRP* 3.9 38.1 - - + +
32A ARG* 3.5 28.3 + - + +
37A LEU* 3.7 30.1 - - + -
56A TYR* 2.9 34.1 + - + +
57A ALA 4.6 0.2 - - - +
59A VAL* 1.3 85.2 - - + +
61A GLY* 1.3 60.6 + - - +
62A VAL* 4.6 7.2 - - + +
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Residues in contact with GLY 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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32A ARG* 3.4 11.4 + - - -
35A ASP* 4.8 5.2 - - - +
57A ALA 2.9 13.3 + - - -
58A GLU 3.7 5.1 + - - -
59A VAL 3.3 3.0 - - - -
60A LEU* 1.3 78.9 - - - +
62A VAL* 1.3 57.8 + - - -
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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