Contacts of the helix formed by residues 62 - 74 (chain C) in PDB entry 5DPS
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 62 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C ASP 4.2 7.2 - - - +
61C LEU* 1.3 80.6 - - - +
63C VAL* 1.3 63.7 + - - +
64C GLY* 3.6 2.9 + - - -
65C GLN* 3.0 49.6 + - - +
66C PHE* 3.1 18.5 + - - +
93C THR 3.9 8.4 + - - -
94C SER* 4.3 13.7 - - - +
95C ALA 3.3 8.7 - - - +
96C THR* 3.9 7.9 - - + +
97C MET* 4.4 1.6 - - - -
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Residues in contact with VAL 63 (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 THR* 1.3 68.9 - - - +
64C GLY* 1.3 61.3 + - - +
66C PHE* 3.1 2.9 + - - +
67C TYR* 2.9 47.8 + - + -
84C PHE* 4.3 8.2 - - + -
91C PRO* 4.1 15.5 - - + -
92C PRO 3.4 24.5 - - - +
93C THR* 3.6 2.7 + - - -
95C ALA 2.8 21.1 + - - +
96C THR 4.6 1.3 - - - +
97C MET* 4.1 15.5 - - - -
100C LEU* 3.8 35.2 - - + -
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Residues in contact with GLY 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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62C THR* 3.2 2.8 + - - -
63C VAL* 1.3 75.9 - - - +
65C GLN* 1.3 59.6 + - - +
67C TYR* 3.3 20.6 + - - +
68C PHE* 3.3 12.5 + - - +
93C THR* 2.9 35.0 + - - -
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Residues in contact with GLN 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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60C ASP 4.4 1.6 - - - +
61C LEU* 3.3 27.7 - - + +
62C THR* 3.0 52.2 + - - +
64C GLY* 1.3 75.5 - - - +
66C PHE* 1.3 61.4 + - - +
68C PHE* 3.5 8.1 + - - +
69C LEU* 3.2 22.5 + - - +
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Residues in contact with PHE 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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37C VAL* 4.3 4.3 - - + -
39C VAL* 3.9 29.4 - - + -
55C TYR* 4.4 14.4 - + + -
57C VAL* 3.9 20.2 - - + -
61C LEU* 3.9 20.6 - - + +
62C THR 3.1 13.0 + - - +
63C VAL* 3.1 7.4 + - - +
65C GLN* 1.3 74.4 - - - +
67C TYR* 1.3 64.7 + - - +
69C LEU* 3.5 21.9 + - + +
70C ILE* 3.1 43.1 + - + +
84C PHE* 3.7 20.9 - + + -
97C MET* 3.8 25.8 - - + -
113C ILE* 4.0 14.8 - - + -
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Residues in contact with TYR 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 VAL* 2.9 33.8 + - + -
64C GLY* 3.3 13.2 - - - +
66C PHE* 1.3 73.6 - - - +
68C PHE* 1.3 57.3 + - - +
70C ILE* 3.1 2.3 + - - +
71C ARG* 2.8 45.2 + - + +
82C LEU* 3.4 37.2 + - + -
83C PHE* 3.5 6.2 - - - +
84C PHE* 2.7 64.3 + + + +
90C ILE* 4.2 14.0 - - - +
91C PRO* 4.8 5.1 - - - +
93C THR* 4.4 13.0 - - - -
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Residues in contact with PHE 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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64C GLY 3.3 9.3 + - - +
65C GLN* 3.8 10.8 - - - +
66C PHE 3.4 0.2 - - - -
67C TYR* 1.3 79.3 - - - +
69C LEU* 1.3 62.7 + - - +
71C ARG* 3.5 11.8 + - - +
72C LYS* 3.1 24.4 + - - +
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Residues in contact with LEU 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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55C TYR* 4.6 8.7 - - + -
57C VAL* 6.0 2.2 - - + -
61C LEU* 5.0 9.9 - - + -
65C GLN 3.2 11.8 + - - +
66C PHE* 3.6 28.5 - - + +
67C TYR 3.2 0.2 - - - -
68C PHE* 1.3 78.7 - - - +
70C ILE* 1.3 75.2 + - + +
72C LYS* 3.3 7.8 + - - +
73C ARG* 3.1 64.4 + - + +
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Residues in contact with ILE 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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39C VAL* 4.4 5.4 - - + -
50C LEU* 4.1 31.4 - - + -
55C TYR* 4.4 11.2 - - + -
66C PHE* 3.1 43.6 + - + +
67C TYR 3.8 2.0 - - - +
69C LEU* 1.3 82.1 - - + +
71C ARG* 1.3 67.1 - - - +
73C ARG* 3.0 14.6 + - + +
74C ILE* 3.2 22.8 + - + +
82C LEU* 4.1 14.1 - - + -
84C PHE* 3.8 22.4 - - + -
115C TYR* 4.8 9.2 - - + -
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Residues in contact with ARG 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 TYR* 2.8 38.5 + - - +
68C PHE* 3.6 10.1 - - - +
70C ILE* 1.3 73.1 - - - +
72C LYS* 1.3 60.9 + - - +
74C ILE* 3.4 5.6 + - - +
75C HIS 3.1 17.5 + - - -
76C LEU* 3.2 28.9 + - + +
77C ARG 2.7 31.9 + - - -
78C ALA* 3.4 14.8 + - - +
80C ASP 3.0 23.2 + - - -
81C ALA* 4.4 0.4 - - - +
82C LEU* 3.4 41.7 + - + +
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Residues in contact with LYS 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 PHE 3.1 17.0 + - - +
69C LEU* 3.7 6.3 - - - +
70C ILE 3.2 0.2 - - - -
71C ARG* 1.3 76.1 - - - +
73C ARG* 1.3 66.2 + - + +
75C HIS* 3.4 22.7 + - - +
76C LEU 6.0 0.2 - - - -
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Residues in contact with ARG 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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49C ASP 4.6 4.0 - - - +
50C LEU* 3.5 24.8 - - + +
51C ASP* 5.4 6.1 + - - +
55C TYR* 4.6 17.3 + - - +
69C LEU* 3.1 51.9 + - + +
70C ILE* 3.0 10.1 + - + +
72C LYS* 1.3 79.9 - - - +
74C ILE* 1.3 61.4 + - - +
75C HIS* 3.4 14.3 + - - -
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Residues in contact with ILE 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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47C ILE* 4.1 16.8 - - + -
48C GLY* 4.2 15.5 - - - +
49C ASP 3.9 13.9 - - - +
50C LEU* 3.7 26.7 - - + -
70C ILE* 3.2 20.8 + - + +
71C ARG 3.6 7.4 - - - +
73C ARG* 1.3 80.2 - - - +
75C HIS* 1.3 78.5 + - - +
76C LEU* 3.7 30.1 - - + +
82C LEU* 4.2 12.6 - - + -
115C TYR* 4.1 20.0 - - + +
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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