Contacts of the helix formed by residues 61 - 73 (chain C) in PDB entry 3P71
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 GLN 61 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C VAL* 3.3 16.0 + - + +
59C HIS* 2.9 13.0 + - - +
60C GLY* 1.3 73.2 - - - +
62C PHE* 1.3 64.2 + - - +
63C HIS* 3.4 2.9 - - - -
64C ASP* 3.0 31.3 + - + +
65C LEU* 3.0 11.4 + - - +
89C ARG* 5.9 0.2 - - - +
90C GLY* 4.2 2.9 + - - -
92C TYR* 5.3 0.2 - - - -
96C THR* 3.9 0.8 + - - -
262C ALA* 3.5 30.3 - - + +
263C PRO* 2.9 27.0 + - - +
264C ASN 4.5 0.7 - - - -
265C TYR* 3.7 4.7 - - - -
266C CYS* 3.4 24.9 + - - -
267C TYR* 3.7 32.0 - - + +
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Residues in contact with PHE 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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17C LEU 3.0 28.9 - - - -
18C ASN 3.7 12.1 - - - -
20C CYS* 3.6 31.9 - - + -
60C GLY 3.2 5.5 + - - -
61C GLN* 1.3 73.9 - - - +
63C HIS* 1.3 70.1 + + - +
65C LEU* 2.9 24.6 + - + +
66C MET* 3.0 48.1 + - + +
92C TYR* 3.6 23.2 - - + +
95C GLU* 3.9 26.2 - - + -
96C THR* 3.4 17.3 - - - +
99C LEU* 4.0 10.8 - - + -
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Residues in contact with HIS 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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20C CYS* 4.1 15.6 - - + +
61C GLN 3.4 1.0 - - - -
62C PHE* 1.3 87.5 + + - +
64C ASP* 1.3 63.2 + - - +
66C MET* 3.4 10.2 - - + +
67C GLU 3.1 18.4 + - - -
70C ARG* 4.0 0.5 + - - -
92C TYR* 3.4 39.8 - + - -
267C TYR* 5.7 0.4 + - - -
292C ALA* 3.5 19.8 - - + +
299C HIS* 3.3 59.6 + + + -
302C ARG* 5.9 1.8 - - - -
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Residues in contact with ASP 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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58C VAL* 5.8 0.4 - - + -
61C GLN* 3.0 36.2 + - + +
63C HIS* 1.3 78.3 - - - +
65C LEU* 1.3 61.4 + - - +
66C MET 3.3 0.2 - - - -
67C GLU* 3.4 8.1 - - - +
68C LEU* 2.8 25.3 + - - +
261C SER 5.2 2.8 - - - +
263C PRO* 3.7 33.3 - - + +
267C TYR* 4.4 8.8 - - - -
289C PHE* 3.6 6.8 - - - -
291C PRO* 3.1 11.4 - - - +
292C ALA* 3.1 26.0 + - - +
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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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58C VAL* 4.1 15.7 - - + +
61C GLN 3.0 9.3 + - - +
62C PHE* 2.9 13.8 + - + +
64C ASP* 1.3 75.2 - - - +
66C MET* 1.3 59.7 + - + +
68C LEU* 3.1 17.3 - - + +
69C PHE* 3.0 55.5 + - + -
82C PHE* 4.0 24.2 - - + -
96C THR* 3.8 31.4 - - + +
99C LEU* 4.6 10.8 - - + -
100C LEU* 4.0 19.3 - - + -
261C SER 6.1 0.4 - - - -
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Residues in contact with MET 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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18C ASN* 4.0 23.6 - - - +
62C PHE* 3.0 47.9 + - + +
63C HIS* 3.4 11.9 - - + +
64C ASP 3.3 0.2 - - - -
65C LEU* 1.3 79.1 - - + +
67C GLU* 1.3 55.9 + - - +
69C PHE* 3.3 25.7 + - + +
70C ARG* 3.1 49.3 + - - +
74C LYS* 5.4 0.4 - - - -
99C LEU* 3.5 32.1 - - + -
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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
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63C HIS 3.1 13.6 + - - +
64C ASP* 3.4 13.5 - - - +
65C LEU 3.2 0.2 - - - -
66C MET* 1.3 74.2 - - - +
68C LEU* 1.3 67.1 + - - +
70C ARG* 2.9 37.2 + - - +
71C ILE* 3.2 45.7 + - + +
289C PHE* 3.8 10.7 - - + +
290C ASP 3.6 22.8 - - - +
291C PRO 5.1 0.7 - - - -
292C ALA* 3.8 15.8 - - + +
293C PRO* 5.2 2.2 - - - +
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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
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55C CYS* 4.0 15.7 - - + -
58C VAL* 4.7 4.7 - - + -
64C ASP 2.8 13.9 + - - +
65C LEU* 3.1 17.7 - - + +
67C GLU* 1.3 74.1 - - - +
69C PHE* 1.3 70.1 + - + +
71C ILE* 3.1 5.8 + - - +
72C GLY* 2.8 26.7 + - - -
80C TYR* 3.7 32.1 - - + +
82C PHE* 4.3 11.2 - - + -
261C SER* 4.1 17.9 - - - +
275C ILE* 3.8 30.7 - - + +
289C PHE* 4.1 16.4 - - + -
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Residues in contact with PHE 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 46.3 + - + -
66C MET* 3.3 27.8 + - + +
68C LEU* 1.3 81.5 - - + +
70C ARG* 1.3 60.5 + - - +
73C GLY* 2.8 37.8 + - - +
74C LYS* 3.6 37.7 + - + -
75C SER* 4.9 1.6 - - - -
80C TYR* 3.6 38.4 - + - -
82C PHE* 4.3 5.4 - + - -
99C LEU* 4.3 6.5 - - + -
100C LEU* 4.3 9.2 - - + -
103C LEU* 4.0 19.5 - - + -
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Residues in contact with ARG 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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63C HIS 4.0 2.8 + - - -
66C MET* 3.1 27.7 + - - +
67C GLU* 2.9 46.6 + - - +
69C PHE* 1.3 76.3 - - - +
71C ILE* 1.3 64.0 + - + +
73C GLY* 4.2 3.6 + - - -
292C ALA* 3.6 19.6 - - - +
293C PRO* 5.6 0.8 - - - +
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Residues in contact with ILE 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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67C GLU* 3.2 40.5 + - + +
68C LEU* 3.1 4.3 + - - +
70C ARG* 1.3 80.4 - - + +
72C GLY* 1.3 61.7 + - - +
73C GLY 3.3 1.0 + - - -
275C ILE* 4.4 6.5 - - + -
277C GLU* 5.3 0.2 - - - +
287C LEU* 3.8 40.3 - - + +
288C GLN 5.1 2.9 - - - +
289C PHE* 3.6 31.9 - - + -
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Residues in contact with GLY 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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53C THR* 4.7 5.0 + - - -
68C LEU 2.8 14.0 + - - -
71C ILE* 1.3 74.3 - - - +
73C GLY* 1.3 54.6 + - - +
78C THR* 2.7 31.2 + - - +
80C TYR* 3.3 12.1 - - - -
275C ILE* 3.9 15.7 - - - +
277C GLU* 5.1 6.4 - - - +
287C LEU* 4.5 5.2 - - - -
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Residues in contact with GLY 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 PHE* 2.8 17.0 + - - +
70C ARG 4.2 2.8 + - - -
71C ILE 3.3 3.2 + - - -
72C GLY* 1.3 77.9 - - - +
74C LYS* 1.3 62.1 + - - -
77C ASP* 6.1 0.7 - - - -
78C THR* 3.5 7.9 - - - -
80C TYR* 2.6 32.2 + - - -
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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