Contacts of the helix formed by residues 64 - 79 (chain A) in PDB entry 1UK0
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A SER* 1.3 83.1 + - - +
65A ASP* 1.3 58.4 + - - +
66A SER* 3.1 28.9 + - - -
67A GLN* 2.8 33.5 + - - +
68A ILE* 3.3 4.0 + - - +
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Residues in contact with ASP 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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62A GLY 5.0 1.4 - - - +
63A SER 3.2 10.9 - - - +
64A SER* 1.3 67.9 - - - +
66A SER* 1.4 54.8 + - - +
67A GLN 2.7 13.7 + - - -
68A ILE* 3.1 16.6 + - + +
69A LEU* 3.4 32.5 + - + +
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Residues in contact with SER 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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64A SER* 3.1 16.9 + - - -
65A ASP* 1.4 71.4 - - - +
67A GLN* 1.4 61.2 + - - +
69A LEU* 5.0 5.3 - - - +
70A ASP* 3.9 16.0 - - - +
39B LYS* 6.0 1.2 - - - +
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Residues in contact with GLN 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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58A ALA* 5.2 2.7 - - + -
63A SER* 3.3 16.2 - - - +
64A SER* 2.8 26.1 + - - +
65A ASP 2.7 1.8 + - - -
66A SER* 1.4 80.0 - - - +
68A ILE* 1.3 65.8 - - - +
69A LEU 3.5 0.9 - - - -
70A ASP* 2.8 22.6 + - - +
71A LEU* 2.8 33.8 + - + +
74A ARG* 4.5 16.2 - - - +
43B ARG* 5.9 4.2 - - - +
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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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55A VAL* 3.5 13.6 - - + +
58A ALA* 3.9 17.5 - - + -
59A VAL* 4.2 12.1 - - + -
63A SER* 4.0 12.3 - - - +
64A SER 3.3 9.6 + - - +
65A ASP* 3.1 11.1 + - + +
67A GLN* 1.3 75.2 - - - +
69A LEU* 1.3 61.1 + - + +
71A LEU* 2.6 50.4 + - + +
72A SER* 3.2 12.3 + - - +
91A LEU 3.6 6.5 - - - +
92A ASN* 3.5 37.7 - - + +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 3.4 28.9 + - + +
66A SER* 5.2 3.6 - - - +
68A ILE* 1.3 81.4 - - + +
70A ASP* 1.3 66.6 + - - +
71A LEU 3.1 0.2 + - - -
72A SER* 3.6 2.3 - - - -
73A ASN* 2.9 30.7 + - - +
90A LEU* 3.9 28.7 - - + -
92A ASN* 5.2 0.7 - - - +
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Residues in contact with ASP 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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65A ASP 4.9 0.2 + - - -
66A SER 3.9 17.2 - - - +
67A GLN* 2.8 14.4 + - - +
69A LEU* 1.3 79.6 - - - +
71A LEU* 1.3 62.1 + - - +
73A ASN* 3.6 14.0 + - + +
74A ARG* 2.7 47.3 + - - +
39B LYS* 3.3 41.8 + - - +
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Residues in contact with LEU 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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51A ILE* 3.4 21.4 - - + +
54A GLU* 3.3 40.8 - - + +
55A VAL* 3.4 40.2 - - + +
58A ALA* 5.0 1.6 - - + -
67A GLN* 2.8 27.7 + - + +
68A ILE* 2.6 31.6 + - + +
70A ASP* 1.3 75.3 - - - +
72A SER* 1.3 53.4 - - - +
74A ARG* 3.2 16.4 + - - +
75A PHE* 2.7 30.7 + - - +
91A LEU* 5.3 0.4 - - - -
43B ARG* 5.8 0.9 - - - +
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Residues in contact with SER 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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55A VAL* 4.5 2.4 - - - +
68A ILE 3.2 9.4 + - - -
69A LEU 3.6 8.5 - - - -
71A LEU* 1.3 72.7 - - - +
73A ASN* 1.3 64.0 + - - -
75A PHE* 2.6 20.4 + - - -
76A TYR* 2.8 21.6 + - - -
90A LEU* 3.8 27.3 - - - +
91A LEU* 3.1 44.9 + - - +
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Residues in contact with ASN 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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69A LEU* 2.9 32.2 + - - +
70A ASP* 4.1 14.3 + - + +
72A SER* 1.3 75.0 - - - +
74A ARG* 1.3 62.1 + - - +
76A TYR* 3.5 12.3 + - - +
77A THR* 3.3 25.3 + - - -
90A LEU* 5.6 4.2 - - - +
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Residues in contact with ARG 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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51A ILE* 3.9 20.3 - - + +
54A GLU* 4.6 3.5 + - - -
67A GLN* 4.5 12.5 - - - +
70A ASP* 2.7 46.7 + - - +
71A LEU* 3.3 25.7 - - - +
73A ASN* 1.3 76.6 - - - +
75A PHE* 1.4 63.8 + - - +
76A TYR 3.2 0.5 + - - -
77A THR* 3.5 8.4 + - + -
78A LEU* 3.5 22.7 + - + +
39B LYS* 5.0 7.9 + - - +
41B SER* 4.3 23.7 + - - -
43B ARG* 4.3 28.9 - - - +
44B GLN* 4.6 20.2 + - + +
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Residues in contact with PHE 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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48A ALA* 4.1 20.2 - - + -
51A ILE* 4.2 10.5 - - + -
52A LEU* 3.4 38.6 - - + -
71A LEU 2.7 14.0 + - - +
72A SER 2.6 13.9 + - - +
74A ARG* 1.4 71.7 - - - +
76A TYR* 1.3 93.6 + + - +
78A LEU* 4.2 0.4 - - - +
79A ILE* 3.1 23.2 + - + +
81A HIS* 4.1 11.4 - + - -
91A LEU* 3.7 21.3 - - + -
100A LYS* 3.5 32.5 - - + -
103A MET* 3.9 15.9 - - + -
104A LEU* 4.2 6.3 - - + -
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Residues in contact with TYR 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 SER* 2.8 30.2 + - - +
73A ASN* 4.0 13.5 - - - +
74A ARG 3.1 0.8 - - - -
75A PHE* 1.3 102.1 - + - +
77A THR* 1.3 55.8 + - - +
78A LEU 2.5 16.6 + - - -
79A ILE 2.6 23.0 + - - -
80A PRO* 3.3 3.1 - - + -
81A HIS* 3.4 45.5 - + + +
83A PHE* 3.4 24.6 - + - -
88A PRO* 5.2 5.6 - - + -
89A PRO* 3.3 33.4 + - + +
90A LEU* 5.4 1.8 - - + -
91A LEU* 4.1 7.9 - - + +
100A LYS* 4.5 7.8 - - - +
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Residues in contact with THR 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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73A ASN 3.3 16.2 + - - -
74A ARG* 3.5 10.5 + - + +
76A TYR* 1.3 75.1 - - - +
78A LEU* 1.3 66.9 + - + +
80A PRO* 3.4 17.8 - - - +
47B ALA* 5.7 4.0 - - + -
78B LEU* 3.7 35.6 - - + +
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Residues in contact with LEU 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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44A GLN* 2.9 54.5 + - + +
47A ALA* 3.6 17.5 - - + -
48A ALA* 3.4 40.4 - - + +
51A ILE* 3.8 16.4 - - + -
74A ARG* 3.5 11.6 + - + +
75A PHE* 4.2 1.1 - - - +
76A TYR 2.5 4.4 + - - -
77A THR* 1.3 82.2 - - + +
79A ILE* 1.4 53.7 + - + +
80A PRO* 3.3 5.1 - - - +
47B ALA* 5.7 10.3 - - + -
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Residues in contact with ILE 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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30A ILE* 4.4 11.9 - - + -
35A MET* 3.5 20.9 - - + -
44A GLN* 3.8 24.2 - - - +
45A ILE* 4.7 1.8 - - - -
48A ALA* 3.6 33.2 - - + -
75A PHE* 3.1 20.3 + - + +
76A TYR* 2.6 17.2 + - - +
78A LEU* 1.4 71.2 - - + +
80A PRO* 1.4 55.2 - - - +
81A HIS* 2.7 44.1 + - + -
103A MET* 4.6 6.1 - - + -
104A LEU* 3.8 15.0 - - + -
107A LEU* 4.7 3.1 - - + -
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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