Contacts of the helix formed by residues 59 - 75 (chain C) in PDB entry 3UGV
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 ALA 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C PRO* 5.0 3.8 - - + +
56C VAL* 2.8 41.3 + - + +
58C LYS* 1.3 69.1 - - - +
60C MET* 1.3 56.6 + - - +
61C LYS 3.0 5.8 - - - -
62C TYR* 2.9 41.7 + - + +
63C LEU* 3.0 20.9 + - + +
100C LEU* 4.6 12.8 - - + -
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Residues in contact with MET 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PRO* 3.8 25.1 - - + +
15C VAL 4.1 9.2 - - - +
16C LEU* 5.1 2.5 - - + -
34C PRO* 3.9 21.8 - - + -
35C LEU 3.4 26.5 - - - +
36C ILE* 3.7 29.2 - - + -
54C PRO* 4.1 11.9 - - + -
56C VAL 4.6 0.2 - - - +
57C PRO* 2.9 26.1 + - + +
59C ALA* 1.3 77.2 - - - +
61C LYS* 1.3 61.8 + - + +
62C TYR 3.2 0.2 - - - -
63C LEU 3.8 1.1 - - - +
64C VAL* 3.2 29.0 + - + +
366C VAL* 4.3 15.3 - - + -
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PRO 5.4 0.7 - - - +
58C LYS* 3.3 32.8 + - + +
59C ALA 3.0 0.2 - - - -
60C MET* 1.3 81.4 - - - +
62C TYR* 1.3 71.2 + - + +
65C PRO* 2.9 26.5 - - - +
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Residues in contact with TYR 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 6.2 0.2 - - + -
58C LYS* 3.6 24.0 + - - +
59C ALA* 2.9 31.3 + - + +
61C LYS* 1.3 95.1 - - + +
63C LEU* 1.3 64.7 + - + +
65C PRO* 3.7 4.6 - - - +
66C ALA* 3.3 21.7 + - - +
100C LEU* 4.0 30.1 - - + -
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Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.9 22.4 - - + -
52C LEU* 4.8 3.4 - - + -
54C PRO* 3.9 24.5 - - + -
59C ALA* 3.0 18.5 + - + +
60C MET 4.4 0.2 - - - +
61C LYS 3.5 0.2 - - - -
62C TYR* 1.3 77.0 - - - +
64C VAL* 1.3 55.1 + - - +
66C ALA* 3.0 6.5 + - + +
67C LEU* 2.5 46.0 + - + +
100C LEU* 3.6 48.2 - - + +
103C ILE* 3.7 26.7 - - + -
104C ALA* 4.2 10.8 - - + +
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ALA* 3.9 23.6 - - + +
14C PRO* 4.4 22.0 - - + -
36C ILE* 4.6 12.3 - - + -
60C MET 3.2 16.1 + - - +
63C LEU* 1.3 74.9 - - - +
65C PRO* 1.3 67.0 - - + +
67C LEU* 3.1 6.5 + - - +
68C HIS* 2.8 62.1 + - + +
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Residues in contact with PRO 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C LYS* 2.9 31.2 - - - +
62C TYR* 3.7 6.1 - - - +
64C VAL* 1.3 96.8 - - + +
66C ALA* 1.3 56.6 + - - +
68C HIS* 3.6 5.5 + - + +
69C ASP* 2.9 38.5 + - - +
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C TYR 3.3 13.5 + - - +
63C LEU* 3.0 14.6 + - + +
65C PRO* 1.3 76.5 - - - +
67C LEU* 1.3 65.8 + - - +
69C ASP* 3.4 8.9 + - - +
70C MET* 3.2 28.5 + - - +
92C LEU* 5.3 10.9 - - + +
100C LEU 5.8 0.4 - - - +
104C ALA* 4.3 15.0 - - + -
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 4.1 14.3 - - + +
12C ALA* 3.5 31.9 - - + -
36C ILE* 3.9 16.6 - - + -
38C ILE* 4.3 17.0 - - + -
52C LEU* 4.5 8.5 - - + -
63C LEU* 2.5 30.3 + - + +
64C VAL* 3.6 4.3 - - - +
66C ALA* 1.3 73.8 - - - +
68C HIS* 1.3 62.2 + - - +
70C MET* 3.0 16.3 + - - +
71C SER* 3.1 11.4 + - - -
104C ALA* 3.4 36.1 - - + +
108C VAL* 3.7 17.5 - - + -
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Residues in contact with HIS 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 3.4 23.3 - - + -
11C THR* 3.8 8.1 - - + +
12C ALA* 3.1 31.2 + - + -
64C VAL* 2.8 47.1 + - + +
65C PRO* 4.1 4.6 - - + +
67C LEU* 1.3 71.0 - - - +
69C ASP* 1.3 65.4 + - - +
71C SER* 3.0 16.1 + - - -
72C ASP* 3.1 21.2 + - - +
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Residues in contact with ASP 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C PRO* 2.9 25.6 + - - +
66C ALA* 3.5 10.0 - - - +
67C LEU 3.3 0.4 - - - -
68C HIS* 1.3 76.6 - - - +
70C MET* 1.3 60.1 + - + +
72C ASP* 3.9 15.4 + - - +
73C MET* 3.5 19.1 + - - +
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Residues in contact with MET 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU* 6.4 0.2 - - + -
66C ALA 3.2 11.4 + - - +
67C LEU* 3.0 10.8 + - - +
69C ASP* 1.3 75.7 - - + +
71C SER* 1.3 67.3 + - - +
73C MET* 3.2 9.3 + - + +
74C LEU* 2.9 40.2 + - + +
88C THR* 4.0 37.2 - - + +
91C SER* 4.7 8.1 - - - +
92C LEU* 3.6 31.9 - - + -
101C SER 4.2 2.9 - - - +
104C ALA* 3.8 30.1 - - + -
105C ALA 4.1 6.1 - - - +
108C VAL* 4.1 17.3 - - + -
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Residues in contact with SER 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 3.7 12.5 - - - -
8C ARG 4.7 0.2 + - - -
9C LYS* 3.3 13.5 - - - +
10C LEU* 2.7 46.9 + - - +
67C LEU 3.1 8.0 + - - -
68C HIS* 3.0 12.5 + - - -
70C MET* 1.3 75.9 - - - +
72C ASP* 1.3 65.7 + - - +
73C MET 3.1 0.3 + - - -
74C LEU 3.1 1.0 + - - -
75C ALA* 3.0 25.1 + - - +
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Residues in contact with ASP 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C HIS* 3.1 14.8 + - - +
69C ASP* 3.9 18.8 - - - +
70C MET 3.3 0.2 - - - -
71C SER* 1.3 78.8 + - - +
73C MET* 1.3 60.6 + - - +
75C ALA* 3.7 15.0 + - - +
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Residues in contact with MET 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ASP 3.5 12.7 + - - +
70C MET* 3.2 11.2 + - + +
71C SER 3.1 0.6 - - - -
72C ASP* 1.3 82.1 - - - +
74C LEU* 1.3 90.6 + - + +
75C ALA 4.7 0.3 - - - +
77C GLN* 2.9 21.6 + - - +
87C LYS* 3.9 25.8 - - + +
88C THR* 4.5 8.5 - - + +
91C SER* 3.8 27.8 - - - +
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 3.6 36.0 - - + +
10C LEU* 6.1 0.4 - - + -
70C MET* 2.9 24.6 + - + +
73C MET* 1.3 97.6 - - + +
75C ALA* 1.3 66.8 + - - +
76C GLY 3.2 0.3 + - - -
77C GLN* 2.9 29.8 + - + +
84C ILE* 3.7 44.6 - - + -
87C LYS* 4.5 15.7 - - + -
88C THR* 4.3 7.6 - - + -
108C VAL* 4.2 14.8 - - + -
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.8 3.1 - - - -
8C ARG 3.5 22.7 - - - +
71C SER 3.0 14.8 + - - +
72C ASP* 3.7 12.8 - - - +
73C MET 3.4 1.7 - - - +
74C LEU* 1.3 76.4 - - - +
76C GLY* 1.3 59.8 + - - +
77C GLN* 3.3 8.5 + - - -
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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