Contacts of the helix formed by residues 67 - 83 (chain A) in PDB entry 1KHM
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 GLN 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PRO 5.6 0.2 + - - -
14A ILE* 4.0 27.0 - - + +
65A GLY 3.8 0.4 + - - -
66A THR* 1.3 72.6 - - - +
68A ASP* 1.3 58.7 + - - +
70A ILE* 3.3 12.8 + - + +
71A GLN* 2.9 42.4 + - - +
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Residues in contact with ASP 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 THR* 3.1 5.4 - - - +
67A GLN* 1.3 77.7 - - - +
69A GLN* 1.3 70.9 + - + +
71A GLN* 3.1 10.7 + - - +
72A ASN* 2.8 56.0 + - - +
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Residues in contact with GLN 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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43A SER* 2.8 39.9 + - - +
44A GLY* 4.0 20.6 + - - +
45A ALA* 3.7 11.1 - - + +
65A GLY* 3.8 6.7 - - - -
66A THR* 2.7 44.6 + - - +
68A ASP* 1.3 81.1 - - + +
70A ILE* 1.3 61.5 + - - +
72A ASN* 3.6 4.2 + - - +
73A ALA* 3.1 9.9 + - - +
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Residues in contact with ILE 70 (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 ILE* 3.6 32.5 - - + +
16A THR* 4.0 13.9 - - + -
45A ALA* 5.6 0.2 - - + -
63A ILE* 3.9 21.8 - - + +
65A GLY* 3.2 30.7 - - - +
66A THR 2.8 15.7 + - - +
67A GLN* 3.5 9.0 - - + +
69A GLN* 1.3 75.8 - - - +
71A GLN* 1.3 55.6 + - - +
73A ALA* 2.9 7.7 + - - +
74A GLN* 2.7 62.5 + - + +
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Residues in contact with GLN 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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67A GLN* 2.9 33.4 + - - +
68A ASP* 3.1 10.9 + - - +
70A ILE* 1.3 74.3 - - - +
72A ASN* 1.3 68.5 - - - +
74A GLN* 3.8 10.7 - - + +
75A TYR* 2.9 26.8 + - + +
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Residues in contact with ASN 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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43A SER* 4.1 15.8 + - - +
68A ASP* 2.8 41.9 + - - +
69A GLN* 3.8 7.0 - - - +
71A GLN* 1.3 80.5 - - - +
73A ALA* 1.3 59.5 + - - +
75A TYR* 4.1 4.5 - - - +
76A LEU* 3.0 35.5 + - + +
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Residues in contact with ALA 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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39A ILE* 4.6 4.1 - - + +
43A SER* 3.6 15.2 + - - +
45A ALA* 4.1 11.7 - - + -
47A ILE* 4.7 11.2 - - + -
63A ILE* 4.2 13.5 - - + -
69A GLN 3.1 14.1 + - - +
70A ILE* 2.9 10.9 + - - +
72A ASN* 1.3 77.5 - - - +
74A GLN* 1.3 65.7 + - - +
76A LEU* 3.0 7.1 + - - +
77A LEU* 3.0 27.2 + - - +
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Residues in contact with GLN 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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16A THR* 3.7 15.0 + - - +
18A VAL* 5.4 5.4 - - + -
63A ILE* 3.5 18.6 - - + -
70A ILE* 2.7 43.4 + - - +
71A GLN* 3.8 8.9 - - + +
73A ALA* 1.3 72.0 - - - +
75A TYR* 1.3 61.4 + - - +
77A LEU* 3.2 11.2 + - + +
78A GLN* 3.1 23.1 + - - +
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Residues in contact with TYR 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 GLN* 2.9 20.2 + - + +
72A ASN* 4.1 5.4 - - - +
74A GLN* 1.3 78.4 - - - +
76A LEU* 1.3 71.2 + - + +
78A GLN* 3.5 14.9 + - + +
79A ASN* 3.1 37.4 + - + +
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Residues in contact with LEU 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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35A ARG* 4.6 8.5 + - - +
39A ILE* 4.0 39.3 - - + +
42A GLU* 4.9 12.6 - - + -
43A SER* 4.4 10.3 - - - +
72A ASN* 3.0 23.7 + - + +
73A ALA 3.0 6.5 + - - +
75A TYR* 1.3 86.3 - - + +
77A LEU* 1.3 58.7 + - - +
79A ASN* 4.0 5.7 - - + +
80A SER* 3.1 26.7 + - - -
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Residues in contact with LEU 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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18A VAL* 5.1 12.3 - - + -
20A ILE* 5.8 0.4 - - + -
28A ILE* 3.8 32.4 - - + +
36A ILE* 4.7 12.6 - - + -
39A ILE* 4.9 10.3 - - + -
47A ILE* 4.9 9.9 - - + -
61A ILE* 4.4 23.8 - - + -
63A ILE* 3.8 29.2 - - + -
73A ALA 3.0 17.1 + - - +
74A GLN* 3.5 9.6 - - - +
75A TYR 3.1 0.2 - - - -
76A LEU* 1.3 78.6 - - - +
78A GLN* 1.3 66.9 + - - +
80A SER* 3.2 13.2 + - - -
81A VAL* 3.3 14.4 + - - +
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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 GLN 3.1 13.7 + - - +
75A TYR* 4.0 14.8 - - + +
77A LEU* 1.3 79.7 - - - +
79A ASN* 1.3 59.7 + - - +
81A VAL* 3.1 26.9 - - + +
82A LYS* 4.3 3.3 + - - +
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Residues in contact with ASN 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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35A ARG* 4.6 8.4 + - - +
75A TYR* 3.1 36.6 + - + +
76A LEU* 4.4 6.3 - - + +
78A GLN* 1.3 74.4 - - - +
80A SER* 1.3 67.8 + - - +
81A VAL 3.1 2.0 + - - -
82A LYS* 3.3 39.3 + - - +
83A GLN 4.2 0.3 + - - -
87A LYS* 4.6 15.1 - - - +
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Residues in contact with SER 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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27A SER* 4.7 0.5 + - - -
28A ILE* 3.3 34.7 + - - +
35A ARG* 3.6 33.8 + - - +
39A ILE* 5.1 1.6 - - - -
76A LEU 3.1 19.8 + - - -
77A LEU* 3.2 6.7 + - - -
79A ASN* 1.3 76.8 - - - +
81A VAL* 1.3 53.1 + - - +
83A GLN* 2.5 44.2 + - - +
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Residues in contact with VAL 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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20A ILE* 5.7 2.2 - - + -
24A LEU* 3.9 37.0 - - + -
27A SER* 4.2 4.3 + - - -
28A ILE* 3.7 23.1 - - + +
77A LEU 3.3 12.6 - - - +
78A GLN* 3.1 24.7 - - + +
80A SER* 1.3 77.7 + - - +
82A LYS* 1.3 53.2 + - + +
83A GLN 2.6 0.2 + - - -
84A TYR* 2.6 40.2 + - + +
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Residues in contact with LYS 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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78A GLN 5.3 2.2 - - - +
79A ASN* 3.3 34.8 + - - +
80A SER 2.9 0.6 + - - -
81A VAL* 1.3 79.1 - - + +
83A GLN* 1.3 54.7 + - - +
84A TYR* 2.5 13.3 + - - -
86A GLY* 2.8 28.5 + - - -
87A LYS* 3.4 28.7 + - + +
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Residues in contact with GLN 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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27A SER* 2.7 36.5 + - - +
28A ILE 4.7 0.2 - - - +
35A ARG* 4.5 20.8 + - - +
79A ASN 4.2 0.4 + - - -
80A SER* 2.5 36.2 + - - +
82A LYS* 1.3 72.4 - - - +
84A TYR* 1.3 48.2 + - - +
85A SER* 2.4 19.4 + - - -
87A LYS* 5.2 7.9 - - - +
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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