Contacts of the helix formed by residues 59 - 75 (chain C) in PDB entry 6P1A
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 ASN 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A MET* 3.5 32.9 + - - +
58A CYS 4.0 9.9 - - - +
59A ASN* 4.3 13.0 - - + +
26C TRP* 3.8 2.1 - - - -
58C CYS* 1.3 83.8 - - - +
60C ASP* 1.3 63.7 + - - +
61C ASP* 3.0 12.5 + - - +
62C ASP* 2.6 50.6 + - - +
63C GLY* 3.0 20.4 + - - -
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Residues in contact with ASP 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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59A ASN* 5.2 3.2 + - - +
26C TRP* 3.0 19.7 + - + +
31C ARG* 2.9 48.1 + - - +
59C ASN* 1.3 76.1 - - - +
61C ASP* 1.3 66.4 + - - +
63C GLY* 3.8 0.2 - - - -
64C MET* 2.9 33.7 + - + +
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Residues in contact with ASP 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 ASN* 3.0 11.7 + - - +
60C ASP* 1.3 84.3 + - - +
62C ASP* 1.3 69.0 + - - +
64C MET* 3.8 3.9 - - - +
65C LEU* 2.9 23.7 + - - +
152C ARG* 4.3 8.9 + - - +
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Residues in contact with ASP 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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56A PRO* 4.6 8.7 - - - +
57A MET 5.0 0.9 + - - -
19C TRP* 3.6 29.3 - - + -
58C CYS* 4.1 15.4 - - + +
59C ASN* 2.6 33.9 + - - +
61C ASP* 1.3 73.1 - - - +
63C GLY* 1.3 56.3 + - - +
65C LEU* 3.6 2.8 - - - +
66C ILE* 2.9 37.6 + - + +
149C PHE* 4.8 3.8 - - + -
152C ARG* 2.7 42.9 + - - +
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Residues in contact with GLY 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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23C TRP* 3.5 6.5 - - - -
26C TRP* 3.4 20.1 - - - -
58C CYS* 3.5 21.0 - - - -
59C ASN 3.0 16.6 + - - -
60C ASP 3.8 0.2 - - - -
62C ASP* 1.3 78.0 - - - +
64C MET* 1.3 56.8 + - - +
66C ILE* 3.4 0.4 + - - -
67C SER* 2.9 32.4 + - - -
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Residues in contact with MET 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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26C TRP* 3.6 20.6 - - + -
31C ARG 5.0 2.2 - - - +
32C LEU* 3.7 28.5 - - + -
33C GLU* 4.7 16.8 - - + +
36C MET* 4.0 29.2 - - + -
60C ASP* 2.9 18.3 + - + +
61C ASP* 3.8 3.8 - - - +
63C GLY* 1.3 75.1 - - - +
65C LEU* 1.3 57.7 + - - +
67C SER* 3.2 4.3 + - - -
68C GLN* 2.9 49.5 + - + +
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Residues in contact with LEU 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 ASP 2.9 17.0 + - - +
62C ASP* 3.6 5.4 - - - +
64C MET* 1.3 77.6 - - - +
66C ILE* 1.3 64.5 + - + +
68C GLN* 3.2 12.9 + - - +
69C VAL* 3.0 27.1 + - + +
145C LEU* 3.7 25.6 - - + -
148C ALA* 3.9 28.3 - - + +
149C PHE* 4.1 15.5 - - + -
152C ARG* 3.7 40.4 - - + +
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Residues in contact with ILE 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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19C TRP* 3.5 48.7 - - + +
20C LEU* 4.3 10.8 - - + -
23C TRP* 3.4 36.3 - - + -
58C CYS* 4.6 4.5 - - - -
62C ASP 2.9 23.8 + - - +
65C LEU* 1.3 79.8 - - + +
67C SER* 1.3 57.9 + - - +
69C VAL* 3.3 6.1 + - + +
70C VAL* 2.9 36.8 + - + +
141C ILE* 6.4 0.2 - - + -
145C LEU* 4.0 23.6 - - + -
149C PHE* 4.5 3.1 - - + -
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Residues in contact with SER 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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23C TRP* 2.7 29.5 + - - +
26C TRP* 3.2 14.4 - - - -
32C LEU* 4.1 20.5 - - - +
36C MET* 6.1 2.0 - - - -
37C SER* 6.3 0.9 - - - -
40C ILE* 4.6 7.5 - - - +
63C GLY 2.9 18.4 + - - -
64C MET* 3.5 9.0 - - - -
65C LEU 3.2 0.2 - - - -
66C ILE* 1.3 74.2 - - - +
68C GLN* 1.3 61.0 + - - +
70C VAL* 3.4 1.9 + - - +
71C ASP* 2.9 32.7 + - - +
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Residues in contact with GLN 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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36C MET* 5.4 14.0 - - + +
64C MET* 2.9 36.0 + - + +
65C LEU* 3.6 11.4 - - - +
67C SER* 1.3 77.3 - - - +
69C VAL* 1.3 62.7 + - + +
71C ASP* 3.3 5.0 + - - +
72C SER* 2.9 26.7 + - - -
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Residues in contact with VAL 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 LEU* 3.0 24.1 + - + +
66C ILE* 3.6 9.4 - - + +
67C SER 3.3 0.2 - - - -
68C GLN* 1.3 75.8 - - + +
70C VAL* 1.3 64.1 + - + +
72C SER* 2.8 21.8 + - - -
73C VAL* 3.0 14.7 + - + +
141C ILE* 4.0 17.9 - - + -
144C VAL* 3.6 26.9 - - + -
145C LEU* 3.8 22.2 - - + +
148C ALA* 3.9 27.8 - - + -
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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
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20C LEU* 4.1 17.9 - - + -
23C TRP* 4.0 17.3 - - + -
66C ILE* 2.9 35.2 + - + +
67C SER 4.0 2.5 - - - +
69C VAL* 1.3 77.2 - - + +
71C ASP* 1.3 57.5 + - - +
73C VAL* 4.7 2.2 - - - -
74C MET* 2.9 36.0 + - + +
81C PHE* 3.7 25.8 - - + -
84C LEU* 3.8 20.2 - - + -
141C ILE* 4.3 14.4 - - + -
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Residues in contact with ASP 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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36C MET 4.2 8.5 - - - +
37C SER* 2.6 38.8 + - - +
38C SER 4.9 0.7 + - - -
39C VAL* 5.3 2.8 - - - +
40C ILE* 5.3 0.2 - - + -
67C SER 2.9 19.6 + - - +
68C GLN* 3.7 5.6 - - - +
70C VAL* 1.3 77.4 - - - +
72C SER* 1.3 63.5 + - - +
75C TYR* 3.2 34.8 + - - +
81C PHE* 4.0 14.7 - - + -
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Residues in contact with SER 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 GLN 2.9 14.9 + - - -
69C VAL* 2.8 18.9 + - - -
71C ASP* 1.3 79.7 + - - +
73C VAL* 1.3 64.3 + - - +
75C TYR* 3.1 26.1 - - - -
144C VAL* 4.3 7.1 - - - +
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Residues in contact with VAL 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 VAL* 3.0 21.4 + - + +
70C VAL 4.1 0.9 - - - +
72C SER* 1.3 85.8 - - - +
74C MET* 1.3 64.3 + - - +
75C TYR* 3.6 1.3 - - - -
76C ILE* 4.2 17.5 - - - +
140C MET* 3.9 34.5 - - + +
141C ILE* 3.6 27.4 - - + -
144C VAL* 3.6 33.4 - - + -
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Residues in contact with MET 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* 2.9 33.0 + - + +
73C VAL* 1.3 85.3 - - - +
75C TYR* 1.3 58.8 + - - +
76C ILE 3.0 11.1 + - - -
77C ASP* 3.5 19.9 + - + +
78C LYS 4.4 0.2 + - - -
80C ALA* 3.6 35.9 - - + +
81C PHE* 3.3 29.9 - - + +
84C LEU* 4.3 5.8 - - + -
137C SER* 3.2 41.1 - - - +
140C MET* 5.7 0.9 - - - -
141C ILE* 4.0 16.2 - - + -
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Residues in contact with TYR 75 (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* 5.7 1.6 - - + -
71C ASP* 3.2 22.1 + - - +
72C SER* 3.1 30.3 - - - -
73C VAL 4.3 0.9 - - - -
74C MET* 1.3 76.3 - - - +
76C ILE* 1.3 85.8 + - + +
78C LYS* 3.0 31.6 - - - +
81C PHE* 4.1 7.8 - - - -
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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