Contacts of the helix formed by residues 64 - 79 (chain C) in PDB entry 2C10
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 SER 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ASP 3.3 4.5 + - - -
63C LEU* 1.3 74.1 - - - +
65C ARG* 1.3 66.7 + - - +
66C GLU* 3.9 7.4 + - - +
67C GLU* 2.6 34.2 + - - +
68C LEU* 2.9 24.2 + - - +
414C HIS* 4.8 9.4 - - - -
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Residues in contact with ARG 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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64C SER* 1.3 73.7 - - - +
66C GLU* 1.3 59.3 + - - +
68C LEU* 3.2 9.3 + - - +
69C THR* 2.8 33.1 + - - +
414C HIS* 3.7 29.8 + - + +
422C PRO* 3.3 44.0 + - + +
423C LYS* 3.7 7.5 - - - +
424C THR* 3.3 26.8 + - - +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C SER* 3.3 8.0 + - - +
65C ARG* 1.3 77.3 - - - +
67C GLU* 1.3 59.6 + - - +
69C THR* 3.4 8.2 + - - -
70C ALA* 3.0 28.1 + - + +
73C ARG* 5.3 0.7 + - - -
147C PRO* 5.5 7.9 - - - +
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ASP 4.0 0.5 - - - +
63C LEU* 3.1 5.0 - - + -
64C SER* 2.6 43.2 + - - +
66C GLU* 1.3 78.9 - - + +
68C LEU* 1.3 65.3 + - - +
70C ALA* 3.0 17.6 + - - +
71C VAL* 3.0 19.4 + - - +
122C ARG* 3.0 46.4 + - - +
146C LEU* 3.6 30.7 - - + +
147C PRO* 5.3 9.6 - - + +
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 3.9 35.9 - - + +
64C SER 2.9 23.5 + - - +
65C ARG 3.5 4.9 - - - +
67C GLU* 1.3 71.7 - - - +
69C THR* 1.3 57.2 + - - +
71C VAL* 3.2 8.7 + - - +
72C MET* 3.0 30.1 + - - +
99C VAL* 3.4 29.8 - - + +
100C GLU* 4.6 1.6 - - - -
414C HIS* 4.1 3.8 - - + +
415C PHE* 3.9 33.2 - - - +
416C LEU* 3.8 18.5 - - + +
422C PRO* 4.0 18.2 - - + -
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Residues in contact with THR 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 ARG* 2.8 21.0 + - - +
66C GLU* 3.5 10.2 - - - -
68C LEU* 1.3 76.3 - - - +
70C ALA* 1.3 56.8 + - - +
72C MET* 3.9 6.1 - - + +
73C ARG* 2.9 59.3 + - + +
422C PRO* 3.4 23.3 - - + +
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Residues in contact with ALA 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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66C GLU* 3.0 14.0 + - + +
67C GLU* 3.0 12.1 + - - +
69C THR* 1.3 75.1 - - - +
71C VAL* 1.3 59.7 + - - +
73C ARG* 3.5 16.4 + - - +
74C PHE* 3.0 29.3 + - - +
146C LEU* 4.7 1.3 - - + -
147C PRO 3.8 22.9 - - - +
148C HIS* 5.8 1.1 - - + -
149C PRO* 3.8 16.3 - - + +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 4.6 2.7 - - + -
67C GLU 3.0 15.8 + - - +
68C LEU* 3.2 6.3 + - - +
70C ALA* 1.3 74.8 - - - +
72C MET* 1.3 53.4 + - - +
74C PHE* 3.1 7.1 + - - +
75C LEU* 2.7 48.9 + - + +
99C VAL* 3.6 25.1 - - + -
124C ALA* 3.8 22.4 - - + -
126C ALA* 5.0 2.0 - - + -
143C VAL* 3.7 29.4 - - + -
146C LEU* 4.2 16.8 - - + -
149C PRO* 4.5 0.7 - - - -
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Residues in contact with MET 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU 3.0 16.3 + - - +
69C THR* 3.9 6.7 - - + +
71C VAL* 1.3 74.7 - - - +
73C ARG* 1.3 58.3 + - - +
75C LEU* 3.3 6.5 + - - +
76C THR* 3.0 38.0 + - + +
96C VAL* 4.0 38.4 - - + -
99C VAL* 4.3 2.2 - - + -
416C LEU* 3.5 26.9 - - + +
419C SER 3.3 26.7 - - - +
420C GLN* 3.1 39.7 - - + +
422C PRO* 6.2 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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66C GLU 5.3 0.6 + - - -
69C THR* 2.9 50.8 + - + +
70C ALA* 3.7 17.7 - - - +
72C MET* 1.3 76.5 - - - +
74C PHE* 1.3 60.5 + - - +
76C THR* 2.9 21.6 + - - +
77C GLN* 3.6 28.4 + - - +
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Residues in contact with PHE 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 ALA 3.0 18.0 + - - +
71C VAL 3.4 3.6 - - - +
73C ARG* 1.3 75.8 - - - +
75C LEU* 1.3 66.6 + - + +
77C GLN* 3.3 17.8 + - - +
78C ARG* 3.2 56.1 + - + +
143C VAL* 3.8 19.7 - - + -
149C PRO* 3.8 35.4 - - + -
150C SER* 3.8 21.5 - - - -
151C TYR 3.5 21.8 - - - -
152C MET* 4.1 8.5 - - + -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 2.7 36.0 + - + +
72C MET* 3.3 8.0 + - - +
74C PHE* 1.3 71.4 - - + +
76C THR* 1.3 61.2 + - - +
77C GLN 3.0 5.2 - - - -
78C ARG* 4.6 1.1 - - - +
79C LEU* 3.0 52.2 + - + +
83C LEU* 4.2 2.7 - - + -
96C VAL* 4.3 19.1 - - + -
99C VAL* 4.2 11.9 - - + -
126C ALA* 3.7 25.1 - - + -
128C VAL* 5.2 0.2 - - + -
141C LEU* 4.4 8.1 - - + -
143C VAL* 3.8 21.8 - - + -
152C MET* 4.1 16.4 - - - -
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Residues in contact with THR 76 (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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72C MET* 3.0 23.0 + - + +
73C ARG* 2.9 25.1 + - - +
75C LEU* 1.3 73.9 - - - +
77C GLN* 1.3 60.7 + - - +
79C LEU 4.6 0.7 - - - -
80C GLY 3.9 15.2 - - - +
83C LEU* 3.9 22.4 - - + -
420C GLN* 4.1 19.3 - - + +
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Residues in contact with GLN 77 (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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73C ARG* 3.6 30.3 + - - +
74C PHE* 3.3 20.1 + - - +
75C LEU 3.0 0.4 - - - -
76C THR* 1.3 81.4 - - - +
78C ARG* 1.3 68.2 + - + +
79C LEU 3.3 1.7 + - - -
80C GLY* 3.7 8.8 + - - -
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Residues in contact with ARG 78 (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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74C PHE* 3.2 43.5 + - + +
75C LEU 4.7 0.7 - - - +
77C GLN* 1.3 80.4 - - + +
79C LEU* 1.3 62.1 + - - +
80C GLY 3.3 4.3 + - - -
150C SER 4.7 3.6 + - - -
151C TYR* 4.3 6.7 - - - +
152C MET* 3.4 72.0 + - + +
3K BMA 4.8 11.9 + - - -
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Residues in contact with LEU 79 (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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75C LEU* 3.0 42.7 + - + +
78C ARG* 1.3 80.5 - - - +
80C GLY* 1.3 64.6 + - - +
82C GLY* 4.4 4.5 + - - -
83C LEU* 4.1 34.0 + - + +
94C ASN* 5.7 3.1 + - - -
96C VAL* 4.5 0.9 - - + -
128C VAL* 4.1 22.9 - - + -
130C PHE* 3.7 30.7 - - + -
141C LEU* 4.5 6.7 - - + -
152C MET* 4.5 4.7 - - - -
2K NAG 4.3 15.3 - - - +
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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