Contacts of the helix formed by residues 61 - 74 (chain C) in PDB entry 1S5H
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 THR 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A TYR* 4.6 4.6 + - - +
91A SER* 4.6 11.1 + - - +
96A PHE* 4.6 5.2 - - + -
101B GLY 3.2 11.7 - - - +
102B ASP* 3.5 7.6 - - - +
103B GLY* 3.4 34.5 - - - +
48C VAL* 3.9 4.2 - - - +
52C ARG* 4.0 3.1 - - - +
60C ILE* 1.3 82.1 - - + +
62C TYR* 1.3 64.5 + - - +
63C PRO* 3.5 4.6 - - - +
64C ARG* 3.2 34.0 + - - +
65C ALA* 3.1 21.0 + - - +
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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
----------------------------------------------------------
31B SER* 3.2 43.1 - - - -
33B TRP* 2.8 26.6 + - - -
52B ILE* 3.4 17.5 - - - +
100B ARG 4.1 2.0 - - - -
101B GLY* 3.1 26.2 + - - -
44C SER* 4.2 5.6 - - - -
45C TYR* 3.9 33.3 + + + -
48C VAL* 3.6 29.7 - - + +
49C LEU* 5.4 0.5 + - - +
61C THR* 1.3 68.0 - - - +
63C PRO* 1.3 71.1 - - + +
65C ALA* 3.5 4.7 - - - +
66C LEU* 2.9 24.4 + - - +
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Residues in contact with PRO 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 5.8 1.1 - - - +
101B GLY 4.1 7.0 - - - +
102B ASP* 4.5 16.6 - - + -
61C THR* 3.6 7.9 - - - -
62C TYR* 1.3 96.5 - - + +
64C ARG* 1.3 61.6 + - - +
66C LEU* 3.2 14.4 + - + +
67C TRP* 3.2 11.1 + - - +
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Residues in contact with ARG 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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32A ASP* 2.7 44.3 + - - -
50A TYR* 3.7 18.2 + - - -
91A SER 5.1 3.1 + - - -
92A ASN* 4.0 13.1 + - - +
58C GLN* 3.9 20.9 + - - +
59C LEU* 5.4 1.3 - - + -
60C ILE* 5.2 1.1 - - - +
61C THR* 3.2 29.4 + - - +
63C PRO* 1.3 77.5 - - - +
65C ALA* 1.3 58.4 + - - +
67C TRP* 3.2 10.7 + - + +
68C TRP* 2.7 34.5 + - - +
81C LEU* 3.6 30.0 - - + +
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C SER* 3.4 30.6 + - - +
47C ALA* 5.1 0.9 - - + -
48C VAL* 3.8 11.0 - - + -
59C LEU* 3.7 22.9 - - + -
61C THR 3.1 20.2 + - - +
62C TYR* 3.5 5.4 - - - +
63C PRO 3.2 0.2 - - - -
64C ARG* 1.3 77.5 - - - +
66C LEU* 1.3 58.6 + - - +
68C TRP* 3.2 6.8 + - - +
69C SER 2.8 24.3 + - - -
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 4.0 15.3 - - + +
41C LEU* 4.1 26.7 - - + -
44C SER* 2.9 26.2 + - - +
62C TYR 2.9 12.2 + - - +
63C PRO* 3.2 11.2 + - + +
65C ALA* 1.3 77.0 - - - +
67C TRP* 1.3 61.3 + - - +
69C SER* 2.4 30.3 + - - +
70C VAL* 3.1 15.9 + - + +
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Residues in contact with TRP 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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63C PRO 3.2 8.7 + - - +
64C ARG* 3.2 15.6 + - + +
66C LEU* 1.3 75.5 - - - +
68C TRP* 1.3 67.3 + - - +
70C VAL* 3.2 19.3 + - + +
71C GLU* 3.0 40.0 + - + +
78C TYR* 3.5 38.4 - + - -
80C ASP* 3.0 23.7 + - - -
81C LEU* 4.2 8.5 - - + -
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Residues in contact with TRP 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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43C GLY 4.2 10.8 - - - -
47C ALA* 3.7 22.7 - - + -
59C LEU* 3.4 29.4 - - + -
64C ARG 2.7 18.0 + - - +
65C ALA* 3.2 12.8 + - + +
67C TRP* 1.3 75.2 - - - +
69C SER* 1.3 79.1 - - - +
71C GLU* 3.4 15.3 - - + +
72C THR* 2.7 51.5 + - + -
81C LEU* 3.2 35.4 + - + -
82C TYR* 3.8 2.1 - - - +
83C PRO* 3.7 21.4 - - + +
88C GLY 4.6 1.8 - - - -
91C VAL* 4.3 4.5 - - + -
92C ALA* 3.5 43.3 - - + -
95C VAL* 4.5 7.0 - - + -
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Residues in contact with SER 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.4 23.6 + - - +
44C SER* 3.3 16.3 + - - -
65C ALA 2.8 13.4 + - - -
66C LEU* 2.4 28.3 + - - +
68C TRP* 1.3 95.5 - - - +
70C VAL* 1.3 55.5 + - - +
72C THR* 4.3 2.5 - - - -
73C ALA* 2.9 26.3 + - - +
95C VAL* 3.3 15.2 - - - +
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Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 4.1 23.6 - - + -
66C LEU* 3.1 21.2 + - + +
67C TRP* 3.2 19.5 + - + +
69C SER* 1.3 80.7 + - - +
71C GLU* 1.3 61.7 + - - +
72C THR 3.0 4.7 + - - -
73C ALA* 3.2 2.5 + - + +
74C THR* 3.0 39.8 + - + +
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Residues in contact with GLU 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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67C TRP* 3.0 45.8 + - + +
68C TRP* 3.4 15.5 - - + +
70C VAL* 1.3 77.5 - - - +
72C THR* 1.3 58.4 + - - +
74C THR* 3.4 8.5 - - - -
75C CYS 3.7 0.2 - - - -
76C VAL* 2.9 35.8 + - + -
77C GLY* 3.1 10.8 + - - -
78C TYR* 3.0 41.3 + - + -
79C GLY 4.2 0.5 + - - -
80C ASP* 2.6 27.4 - - - +
81C LEU* 4.7 8.0 + - - +
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Residues in contact with THR 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C TRP* 2.7 50.2 + - + -
69C SER* 3.6 5.6 - - - -
71C GLU* 1.3 78.3 - - - +
73C ALA* 1.3 61.5 + - - +
74C THR 3.2 1.8 - - - -
75C CYS* 2.8 27.1 + - - +
77C GLY* 5.2 2.7 - - - +
92C ALA 4.0 5.8 - - - +
95C VAL* 4.0 14.1 - - + -
96C MET* 3.5 37.9 - - + +
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Residues in contact with ALA 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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36C LEU* 4.2 10.3 - - + -
40C LEU* 3.7 19.5 - - + -
69C SER 2.9 17.7 + - - +
70C VAL* 3.2 5.1 + - + +
72C THR* 1.3 77.5 - - - +
74C THR* 1.3 60.4 + - + +
75C CYS* 3.1 5.0 + - - -
95C VAL* 3.8 21.5 - - + +
96C MET* 4.4 0.6 - - - +
99C GLY* 3.3 31.8 - - - -
100C ILE* 3.9 2.1 + - - -
103C PHE* 4.0 4.5 - - + -
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Residues in contact with THR 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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70C VAL* 3.0 30.3 + - + +
71C GLU* 3.4 7.3 + - - -
73C ALA* 1.3 75.5 - - + +
75C CYS* 1.3 68.3 + - - +
76C VAL* 3.1 28.2 + - - +
103C PHE* 4.2 27.4 - - + -
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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