Contacts of the helix formed by residues 67 - 77 (chain C) in PDB entry 3C3P
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 GLY 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C ASP* 3.0 24.3 + - - -
65C GLY 2.9 3.0 + - - -
66C LEU* 1.3 78.4 - - - +
68C CYS* 1.3 57.5 + - - +
70C SER* 3.3 3.8 + - - -
71C TRP* 2.9 29.5 + - - +
85C MSE 3.8 16.8 - - - -
92C ASN 4.2 2.6 + - - -
96C ALA* 3.8 8.9 - - - +
99C MSE 3.7 5.4 - - - +
100C LEU* 6.1 0.3 - - - +
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Residues in contact with CYS 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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27C MSE 3.7 32.8 - - - -
38C ILE* 4.1 17.3 - - + -
39C VAL* 3.8 34.8 - - + +
64C ASP* 3.3 2.8 + - - +
65C GLY 3.1 14.3 + - - +
66C LEU 3.1 1.8 - - - -
67C GLY* 1.3 74.1 - - - +
69C ALA* 1.3 67.6 + - - +
71C TRP* 3.1 13.2 + - - +
72C TRP* 3.2 30.7 + - - -
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Residues in contact with ALA 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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39C VAL* 5.2 4.0 - - + +
47C LEU* 4.3 11.4 - - + -
61C VAL* 4.3 2.5 - - + -
64C ASP* 2.9 20.2 + - - +
68C CYS* 1.3 75.3 - - - +
70C SER* 1.3 62.5 + - - +
72C TRP* 3.2 6.1 + - - +
73C PHE* 3.1 36.4 + - + -
130C PHE* 3.8 41.5 - - + -
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Residues in contact with SER 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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61C VAL* 4.0 8.4 - - - +
64C ASP* 2.7 23.3 + - - -
67C GLY* 3.5 9.2 - - - -
69C ALA* 1.3 74.9 - - - +
71C TRP* 1.3 55.3 + - - +
73C PHE* 4.0 3.2 - - - +
74C ALA* 2.8 38.4 + - - +
83C VAL* 4.1 15.7 - - - +
85C MSE 3.3 30.5 - - - +
100C LEU* 5.2 7.9 - - - -
109C VAL* 5.1 7.6 - - - -
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Residues in contact with TRP 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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21C ASP* 3.4 28.5 - - + -
23C VAL* 3.7 18.3 - - + +
24C VAL* 3.1 34.5 - - + -
27C MSE 4.6 5.8 - - + -
67C GLY 2.9 14.2 + - - +
68C CYS* 3.1 11.2 + - - +
70C SER* 1.3 76.5 - - - +
72C TRP* 1.3 99.3 + + - +
74C ALA* 3.9 4.3 - - - +
75C ARG* 3.3 46.8 + - - +
99C MSE 3.8 32.5 - - + -
100C LEU* 4.6 8.5 - - + +
103C ASN* 3.4 27.4 - - - +
216C EDO 5.0 0.7 - - - -
218C EDO 4.8 3.8 - - - -
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Residues in contact with TRP 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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24C VAL* 4.3 15.5 - - + -
27C MSE 5.0 2.0 - - - +
39C VAL* 4.6 3.9 + - + +
40C ASP 5.8 0.2 - - - -
41C ARG* 4.4 12.3 - - + -
44C GLY* 3.4 43.4 - - - +
45C ARG* 4.0 22.2 - - + -
47C LEU* 4.3 12.1 - - + -
48C TYR* 3.7 26.7 - + + +
68C CYS* 3.2 42.2 + - - -
69C ALA* 3.2 9.7 + - - +
71C TRP* 1.3 108.0 - + - +
73C PHE* 1.3 63.7 + - - +
75C ARG* 3.5 7.6 + - + +
76C ALA* 3.5 8.8 + - - +
216C EDO 4.2 15.0 - - - -
218C EDO 3.8 26.9 - - - -
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Residues in contact with PHE 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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47C LEU* 4.0 34.8 - - + -
51C ALA* 3.9 19.7 - - + -
59C VAL* 3.9 23.3 - - + -
61C VAL* 4.1 6.7 - - + -
69C ALA* 3.1 32.7 + - + +
70C SER* 4.0 3.6 - - - +
72C TRP* 1.3 73.9 - - - +
74C ALA* 1.3 66.5 + - - +
76C ALA* 3.0 13.6 + - - +
77C ILE* 3.4 17.8 + - - +
83C VAL* 4.0 15.5 - - + -
128C ILE* 4.3 14.1 - - + -
130C PHE* 3.7 40.6 - + + -
156C ILE* 4.1 17.7 - - + -
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Residues in contact with ALA 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 SER 2.8 22.7 + - - +
71C TRP 3.9 2.7 - - - +
73C PHE* 1.3 73.9 - - - +
75C ARG* 1.3 60.6 + - - +
76C ALA 3.3 0.7 + - - -
77C ILE* 3.5 17.4 + - - +
83C VAL* 3.9 9.6 - - + +
100C LEU* 3.9 16.8 - - + -
105C LEU* 4.0 13.9 - - + +
108C ARG* 3.9 11.5 + - + -
109C VAL* 3.6 27.6 - - + -
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Residues in contact with ARG 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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21C ASP* 4.4 12.9 + - - +
48C TYR* 3.5 20.9 + - + -
71C TRP* 3.3 44.6 + - + +
72C TRP* 3.9 7.2 - - + +
73C PHE 3.1 0.8 - - - -
74C ALA* 1.3 78.6 - - - +
76C ALA* 1.3 58.0 + - - +
77C ILE 3.5 0.6 + - - -
103C ASN* 5.0 1.3 - - - +
105C LEU* 3.5 23.1 - - + -
216C EDO 3.2 47.0 + - - +
218C EDO 5.8 2.2 - - - -
223C PEG 3.9 17.7 + - - +
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Residues in contact with ALA 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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48C TYR* 3.6 20.4 - - + +
51C ALA* 3.4 33.2 - - + +
52C ARG* 3.3 33.2 + - - +
55C GLN* 5.9 0.7 - - - -
56C PRO* 5.4 0.9 - - - +
72C TRP 3.5 4.8 + - - +
73C PHE 3.0 7.0 + - - +
75C ARG* 1.3 80.3 - - - +
77C ILE* 1.3 60.0 + - - +
223C PEG 3.6 8.7 - - - -
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Residues in contact with ILE 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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51C ALA* 5.3 1.3 - - + -
56C PRO* 4.0 32.3 - - + +
57C GLN 6.3 0.2 - - - -
59C VAL* 4.5 9.0 - - + -
73C PHE 3.5 12.3 - - - +
74C ALA* 3.5 15.2 - - - +
75C ARG 3.5 0.9 - - - +
76C ALA* 1.3 81.5 - - + +
78C SER* 1.3 58.9 + - - +
81C SER* 3.8 6.7 - - - -
82C ARG 3.7 25.6 - - - +
83C VAL* 3.5 24.0 - - + -
108C ARG* 3.0 46.3 + - + +
223C PEG 3.5 11.9 - - - +
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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