Contacts of the helix formed by residues 70 - 81 (chain C) in PDB entry 6M17
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 PHE 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C PHE* 4.3 28.7 - + - -
61C LEU* 3.7 27.6 - - + -
62C CYS* 3.9 38.8 - - + -
65C HIS* 3.4 33.1 + + + +
68C GLY 3.2 1.4 - - - -
69C ALA* 1.3 77.4 - - - +
71C MET* 1.3 59.5 + - - +
72C ILE 3.4 1.6 - - - -
73C PRO* 4.0 3.6 - - + -
74C PHE* 3.1 27.2 + + - +
267C THR* 4.0 8.3 - - - -
270C ASP 3.4 21.8 - - - -
271C ALA* 3.5 29.6 - - + -
274C GLN* 4.8 4.5 - - + -
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Residues in contact with MET 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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58C PHE* 3.6 36.8 - - + -
62C CYS* 4.4 6.3 - - - -
68C GLY 3.9 10.1 + - - +
69C ALA 3.4 0.8 - - - -
70C PHE* 1.3 77.8 - - - +
72C ILE* 1.3 65.3 + - + +
74C PHE* 4.1 7.9 - - - -
75C LEU* 3.3 41.5 + - + +
254C LEU* 4.1 33.2 - - + +
255C PHE* 4.7 16.4 - - + -
314C SER 5.3 1.1 - - - +
315C VAL* 4.7 22.2 - - + -
318C ALA* 5.0 3.1 - - + -
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Residues in contact with ILE 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 GLY 4.0 6.7 - - - +
69C ALA* 3.7 32.3 - - + +
71C MET* 1.3 81.2 - - + +
73C PRO* 1.4 74.8 - - + +
74C PHE 3.3 0.2 + - - -
75C LEU* 3.9 1.2 - - - +
76C ILE* 2.7 39.0 + - + +
257C PRO* 4.8 10.1 - - + -
262C LEU* 4.2 25.4 - - + -
268C TRP* 5.7 3.4 - - + -
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Residues in contact with PRO 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 ALA 3.3 20.2 - - - +
70C PHE* 4.0 4.9 - - + +
72C ILE* 1.4 92.6 - - + +
74C PHE* 1.3 68.2 + - - +
76C ILE* 3.2 1.7 + - + +
77C LEU* 2.9 23.4 + - - +
262C LEU* 4.9 7.4 - - + -
267C THR* 4.2 13.9 - - + +
268C TRP* 3.8 46.2 - - + +
271C ALA* 3.7 22.0 - - + -
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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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58C PHE* 3.7 36.1 - + + -
70C PHE* 3.1 24.6 + + + +
71C MET* 4.1 7.4 - - - +
72C ILE 3.2 0.4 - - - -
73C PRO* 1.3 80.1 - - - +
75C LEU* 1.3 96.0 + - + +
77C LEU* 3.2 2.0 + - - +
78C LEU* 2.9 39.1 + - + +
271C ALA* 3.9 14.1 - - + +
274C GLN* 3.8 29.2 - - + -
275C VAL* 4.2 18.3 - - + +
278C SER* 5.1 8.1 - - - -
279C PHE* 6.2 0.7 - + - -
310C ASN 5.8 0.9 - - - -
311C GLY* 5.5 2.7 - - - -
314C SER* 4.4 22.2 - - - -
315C VAL* 5.9 1.3 - - + -
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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
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71C MET* 3.3 31.1 + - + +
72C ILE* 4.0 1.6 - - - +
74C PHE* 1.3 101.8 - - + +
76C ILE* 1.3 64.8 + - + +
78C LEU* 3.2 13.2 + - + +
79C VAL* 3.0 29.4 + - + +
311C GLY* 5.3 5.4 - - - +
315C VAL* 5.0 14.1 - - + -
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Residues in contact with ILE 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 ILE* 2.7 38.7 + - + +
73C PRO* 3.8 5.4 - - + +
75C LEU* 1.3 77.1 - - + +
77C LEU* 1.3 73.7 + - + +
78C LEU 3.1 0.3 + - - -
79C VAL* 3.2 6.2 + - - +
80C LEU* 3.0 36.3 + - + +
268C TRP* 4.2 22.7 - - + -
541C LEU* 5.2 4.5 - - + -
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Residues in contact with LEU 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 PRO 2.9 19.8 + - - +
74C PHE 3.7 2.2 - - - +
76C ILE* 1.3 80.0 - - + +
78C LEU* 1.3 62.8 + - - +
80C LEU* 4.4 1.1 - - - +
81C GLU* 2.8 41.8 + - + +
82C GLY 3.7 0.2 + - - -
268C TRP* 3.8 32.5 - - + +
271C ALA* 4.1 4.5 - - + +
272C GLY* 3.5 34.5 - - - +
275C VAL* 4.3 10.8 - - + +
541C LEU* 3.5 33.2 - - + -
545C ILE* 4.5 12.1 - - + -
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Residues in contact with LEU 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* 2.9 32.7 + - + +
75C LEU* 3.2 15.7 - - + +
77C LEU* 1.3 74.7 - - - +
79C VAL* 1.3 94.0 + - + +
80C LEU 2.8 6.9 + - - -
82C GLY* 2.9 25.6 + - - -
83C ILE* 3.3 14.4 + - + +
275C VAL* 3.9 18.1 - - + +
279C PHE* 3.8 30.5 - - + -
307C SER* 4.6 8.7 - - - +
311C GLY* 4.3 21.1 - - - -
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Residues in contact with VAL 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 15.2 + - + +
76C ILE* 3.9 4.9 - - - +
78C LEU* 1.3 96.9 - - + +
80C LEU* 1.3 72.1 + - + +
83C ILE* 4.1 16.0 - - + +
84C PRO* 4.0 10.8 - - - +
529C PHE* 4.2 17.5 - - + -
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Residues in contact with LEU 80 (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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76C ILE* 3.0 24.1 + - + +
77C LEU 3.2 1.8 + - - +
78C LEU 2.8 3.4 + - - -
79C VAL* 1.3 99.4 - - + +
81C GLU* 1.3 59.2 + - - +
84C PRO* 3.9 8.3 - - - +
529C PHE* 5.0 6.7 - - + -
533C THR* 4.8 12.5 - - + +
537C VAL* 3.2 33.7 - - + -
538C SER* 3.2 24.9 - - - -
541C LEU* 3.8 22.2 - - + -
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Residues in contact with GLU 81 (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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77C LEU* 2.8 31.6 + - + +
80C LEU* 1.3 79.5 - - - +
82C GLY* 1.3 69.1 + - - +
83C ILE 3.5 0.7 - - - -
84C PRO* 3.5 3.6 - - - +
85C LEU* 2.9 29.4 + - - +
272C GLY* 5.4 1.7 - - - +
275C VAL* 5.1 2.7 - - + -
276C PHE* 3.8 27.3 - - + -
502C MET* 4.7 1.9 - - - +
538C SER* 4.4 6.9 - - - +
541C LEU* 2.3 47.3 - - - +
542C MET* 3.7 25.2 + - + +
545C ILE* 4.4 7.1 - - - +
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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