Contacts of the helix formed by residues 59 - 69 (chain C) in PDB entry 6PSI
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 ASP 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C GLN* 3.3 6.1 - - - -
58C SER* 1.3 92.4 + - - +
60C PRO* 1.4 71.6 - - + +
61C GLU 3.1 2.3 + - - +
62C LYS* 2.9 38.7 + - + +
63C ARG* 3.0 21.8 + - - +
88C PHE* 5.9 1.2 - - - -
145C VAL* 3.5 15.0 - - - +
146C SER* 2.9 43.4 + - - +
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Residues in contact with PRO 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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351B GLN* 3.7 31.6 - - + +
19C GLN* 3.4 13.2 - - - +
59C ASP* 1.4 83.0 - - + +
61C GLU* 1.3 62.2 + - - +
63C ARG* 3.5 0.5 - - - +
64C ARG* 3.1 32.5 + - + +
137C VAL* 3.9 33.4 - - + -
144C ARG* 4.2 19.5 - - - +
146C SER* 3.6 13.0 - - - +
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Residues in contact with GLU 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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59C ASP 3.2 0.4 - - - -
60C PRO* 1.3 80.7 - - - +
62C LYS* 1.3 63.0 + - + +
64C ARG* 3.1 7.1 + - - +
65C ILE* 2.9 53.6 + - + +
142C GLY 5.8 0.3 - - - +
143C ARG* 4.5 6.1 - - - +
144C ARG* 3.1 67.5 + - + +
145C VAL* 5.2 0.4 - - - -
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Residues in contact with LYS 62 (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 ALA 3.4 23.2 + - - +
56C VAL* 2.8 29.1 - - + +
57C LEU 4.6 0.4 - - - +
59C ASP* 2.9 38.3 + - + +
61C GLU* 1.3 80.5 - - + +
63C ARG* 1.3 61.6 + - - +
65C ILE* 3.2 14.5 + - + +
66C TYR 3.1 17.3 + - - -
84C ASP* 3.0 35.8 + - - -
88C PHE* 6.0 3.4 - - - -
101C PHE* 5.1 4.9 - - + -
143C ARG* 3.3 34.3 - - - +
144C ARG 3.6 17.3 - - - +
145C VAL* 3.5 5.5 - - - +
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Residues in contact with ARG 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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349B ASP* 2.9 28.4 + - - +
351B GLN* 3.5 4.0 - - - +
8C TYR* 2.8 30.9 + - - -
16C ASN 5.3 1.0 - - - -
17C ALA 3.0 17.4 + - - -
19C GLN* 3.3 28.9 - - - +
22C ILE* 3.5 12.6 - - - +
56C VAL 3.2 7.7 + - - -
57C LEU* 3.4 30.2 - - - +
59C ASP 3.0 17.2 + - - +
60C PRO 3.5 5.4 - - - +
62C LYS* 1.3 77.4 - - - +
64C ARG* 1.3 74.3 + - - +
66C TYR* 3.2 6.5 + - - +
67C ASP* 2.9 52.2 + - - +
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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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349B ASP* 2.9 43.0 + - - +
350B LYS* 4.0 5.9 - - - +
351B GLN* 3.1 25.8 + - - +
60C PRO* 3.1 19.2 + - + +
61C GLU* 3.9 5.4 - - - +
63C ARG* 1.3 85.1 - - - +
65C ILE* 1.3 59.1 + - - +
67C ASP* 2.9 38.8 + - - -
68C THR* 2.8 38.8 + - + +
144C ARG* 5.7 4.7 - - - +
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Residues in contact with ILE 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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56C VAL* 5.1 0.4 - - + -
61C GLU* 2.9 43.4 + - + +
62C LYS* 3.2 19.0 + - - +
64C ARG* 1.3 75.5 - - - +
66C TYR* 1.3 58.8 + - - +
68C THR* 3.1 9.1 + - - -
69C TYR* 2.8 27.2 + - - +
76C PRO* 3.7 39.5 - - + -
83C TYR* 5.1 1.1 - - + -
100C LEU* 4.4 19.7 - - + -
101C PHE* 4.8 13.9 - - + -
143C ARG* 4.1 15.5 - - - +
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Residues in contact with TYR 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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4C LYS* 4.3 22.1 - - - -
5C LYS 3.2 18.6 + - - -
6C ASP* 3.3 20.4 + - - -
7C TYR* 3.5 40.2 - + + -
8C TYR* 3.7 33.0 - + - -
56C VAL* 3.8 17.7 - - + -
57C LEU* 3.7 21.1 - - + -
62C LYS 3.1 5.8 + - - +
63C ARG 3.2 8.0 + - - +
65C ILE* 1.3 78.6 - - - +
67C ASP* 1.3 57.0 + - - +
69C TYR* 2.9 37.8 + + + +
96C PHE* 4.6 7.4 - + - -
100C LEU* 4.9 4.9 - - + -
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Residues in contact with ASP 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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8C TYR* 3.2 10.6 + - - -
63C ARG* 2.9 45.9 + - - +
64C ARG* 2.9 41.7 + - - +
65C ILE 3.4 0.2 - - - -
66C TYR* 1.3 77.1 - - - +
68C THR* 1.3 60.5 + - + +
69C TYR 3.9 4.0 - - - +
71C THR* 4.5 5.4 + - - -
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Residues in contact with THR 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 ARG* 2.8 30.7 + - + +
65C ILE* 3.1 11.6 + - - -
67C ASP* 1.3 75.6 - - + +
69C TYR* 1.4 62.3 + - - +
71C THR* 3.1 11.3 + - + -
72C THR* 2.8 44.5 + - - +
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Residues in contact with TYR 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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2C ALA* 5.6 4.7 - - - -
4C LYS* 4.2 30.2 + - + +
65C ILE 2.8 15.6 + - - +
66C TYR* 2.9 29.9 + + + +
67C ASP 3.9 5.2 - - - +
68C THR* 1.4 77.9 - - - +
70C GLY* 1.3 61.7 + - - +
71C THR* 4.8 0.2 + - - -
72C THR* 3.4 11.9 - - - -
73C GLU* 3.6 29.4 + - + +
74C ALA 5.4 2.0 - - - -
75C PRO* 5.4 2.7 - - + -
96C PHE* 3.5 39.4 - + - -
99C GLU* 5.5 4.2 + - - +
100C LEU* 3.7 29.8 - - + -
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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