Contacts of the helix formed by residues 67 - 81 (chain A) in PDB entry 3UKD
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 SER 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A VAL 3.3 3.5 + - - -
66A PRO* 1.3 71.2 - - - +
68A ILE* 1.3 57.9 + - - +
70A THR* 3.6 5.2 - - - +
71A VAL* 2.8 36.9 + - - +
96A GLU* 2.8 33.2 + - - -
97A ASN* 3.0 37.3 + - - +
100A SER* 3.5 25.4 - - - -
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Residues in contact with ILE 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 PRO* 3.1 14.6 + - + +
67A SER* 1.3 78.3 - - - +
69A VAL* 1.3 76.3 + - + +
71A VAL* 5.0 1.1 - - - +
72A LYS* 3.5 19.6 + - - +
100A SER* 5.1 3.6 - - - -
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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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41A LEU* 4.0 20.4 - - + -
44A GLU* 5.1 4.0 - - + +
51A ASP* 4.0 31.4 - - + +
54A MET* 4.6 6.7 - - + -
55A ILE* 4.2 15.5 - - + -
65A VAL* 3.9 11.9 - - + -
66A PRO* 3.0 12.1 + - + +
67A SER 3.0 0.6 - - - -
68A ILE* 1.3 88.4 - - + +
70A THR* 1.3 64.6 + - - +
72A LYS* 3.3 15.0 + - - +
73A LEU* 3.2 27.8 + - + +
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Residues in contact with THR 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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37A ALA* 4.2 19.7 - - + -
40A LEU* 6.5 0.7 - - + -
41A LEU* 3.9 30.2 - - + +
65A VAL* 4.0 10.4 + - - +
66A PRO 3.5 9.6 + - - -
67A SER* 3.1 7.4 + - - -
69A VAL* 1.3 77.0 - - - +
71A VAL* 1.3 63.3 + - - +
73A LEU* 3.1 8.4 + - + +
74A LEU* 3.0 24.3 + - + +
91A PHE* 3.8 31.0 - - + -
97A ASN* 5.0 1.7 + - - -
196A C5P 4.2 8.6 + - - +
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Residues in contact with VAL 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 SER* 2.8 20.6 + - - +
68A ILE* 5.0 1.3 - - - +
70A THR* 1.3 70.7 - - - +
72A LYS* 1.3 57.4 + - - +
74A LEU* 3.3 8.4 + - - +
75A LYS* 2.8 29.7 + - + +
91A PHE* 3.8 24.7 - - + -
100A SER* 3.2 36.8 - - - +
101A TRP* 4.7 5.8 - - + -
104A ASN* 4.0 29.6 - - + +
105A MET* 4.6 14.4 - - + -
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Residues in contact with LYS 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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44A GLU* 4.3 14.4 + - - -
51A ASP* 5.7 3.4 - - - -
68A ILE 3.5 18.7 + - - +
69A VAL* 3.3 12.5 + - - +
70A THR 3.2 0.4 - - - -
71A VAL* 1.3 79.2 - - - +
73A LEU* 1.3 80.0 + - - +
75A LYS* 3.3 6.3 + - - +
76A ASN* 3.0 54.3 + - - +
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Residues in contact with LEU 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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40A LEU* 3.6 49.8 - - + +
41A LEU* 3.9 23.1 - - + +
44A GLU* 3.4 33.7 - - + +
69A VAL* 3.2 15.2 + - + +
70A THR* 3.1 9.5 + - + +
72A LYS* 1.3 94.6 - - - +
74A LEU* 1.3 62.7 + - - +
76A ASN* 3.7 9.5 + - - +
77A ALA* 3.4 19.9 + - - +
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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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35A LEU* 4.1 23.9 - - + +
37A ALA* 4.7 9.2 - - + -
40A LEU* 3.7 23.1 - - + -
70A THR* 3.0 23.5 + - + +
71A VAL* 3.6 6.7 - - - +
73A LEU* 1.3 74.0 - - - +
75A LYS* 1.3 64.5 + - - +
77A ALA* 3.3 4.9 + - - +
78A ILE* 3.0 31.1 + - + +
88A VAL* 4.4 12.3 - - + -
91A PHE* 3.8 45.1 - - + -
101A TRP* 4.3 19.3 - - + -
105A MET* 6.4 0.2 - - - -
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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 VAL* 2.8 23.3 + - + +
72A LYS* 3.3 6.5 + - - +
74A LEU* 1.3 72.5 - - - +
76A ASN* 1.3 59.7 + - - +
78A ILE* 3.1 6.3 + - + +
79A ASP* 2.8 67.0 + - - +
104A ASN* 5.0 18.1 + - + +
105A MET* 4.0 28.3 - - + +
108A PHE* 4.2 27.8 - - - -
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Residues in contact with ASN 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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72A LYS* 3.0 49.5 + - - +
73A LEU* 3.9 9.7 - - - +
74A LEU 3.4 0.2 - - - -
75A LYS* 1.3 79.0 - - - +
77A ALA* 1.3 61.1 + - - +
79A ASP* 3.5 7.7 + - - +
80A ALA* 3.2 22.7 + - - +
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Residues in contact with ALA 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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35A LEU* 3.6 28.7 - - + -
40A LEU* 5.1 8.7 - - + -
73A LEU 3.4 10.1 + - - +
74A LEU* 3.3 7.7 + - - +
75A LYS 3.3 0.4 - - - -
76A ASN* 1.3 76.0 - - - +
78A ILE* 1.3 64.7 + - - +
80A ALA* 3.4 3.7 + - - +
81A ASN* 2.8 34.5 + - - +
86A PHE* 4.4 1.9 - - - -
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Residues in contact with ILE 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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6A PRO* 4.8 5.4 - - + +
8A VAL* 4.9 3.4 - - + -
35A LEU* 3.6 21.5 - - + -
74A LEU* 3.0 23.4 + - + +
75A LYS* 3.6 5.4 - - - +
77A ALA* 1.3 77.0 - - - +
79A ASP* 1.3 67.1 + - - +
81A ASN 3.1 21.8 + - - +
82A GLN* 4.0 1.7 + - - +
86A PHE* 3.8 35.4 - - + -
88A VAL* 4.9 1.6 - - + -
101A TRP* 3.9 18.2 - - + -
105A MET* 3.7 30.5 - - + -
108A PHE* 6.5 0.2 - - + -
109A VAL* 4.6 10.1 - - + -
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Residues in contact with ASP 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* 2.8 58.8 + - - +
76A ASN* 4.0 6.5 - - - +
77A ALA 3.3 0.2 - - - -
78A ILE* 1.3 81.9 - - - +
80A ALA* 1.3 59.8 + - - +
81A ASN 3.4 0.7 + - - -
82A GLN* 3.6 26.8 + - - +
108A PHE* 5.1 6.8 - - - -
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Residues in contact with ALA 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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76A ASN 3.2 17.8 + - - +
77A ALA* 3.8 7.2 - - - +
78A ILE 3.2 0.2 - - - -
79A ASP* 1.3 78.1 - - - +
81A ASN* 1.3 66.8 + - - +
82A GLN* 3.7 2.1 + - - -
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Residues in contact with ASN 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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6A PRO* 5.5 0.5 - - - +
33A VAL* 4.3 20.2 - - + +
35A LEU* 5.9 0.2 - - - +
77A ALA* 2.8 27.8 + - - +
78A ILE 3.1 7.6 + - - +
80A ALA* 1.3 88.1 + - - +
82A GLN* 1.3 63.7 + - - +
84A LYS* 3.4 24.8 + - + +
86A PHE* 3.3 33.1 - - + -
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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