Contacts of the helix formed by residues 63 - 73 (chain C) in PDB entry 2PK2
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 ILE 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C ALA* 4.0 21.3 - - + +
45C LEU* 4.3 10.1 - - + -
59C ILE* 2.8 27.8 - - + +
60C ASN* 2.6 24.7 + - - +
62C ALA* 1.3 73.6 - - - +
64C VAL* 1.3 54.7 + - - +
66C MET* 4.3 3.4 - - - -
67C HIS* 2.8 28.8 + - + +
182C LEU* 2.8 52.9 - - + +
183C HIS* 3.4 36.8 - - + +
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASN 3.1 3.0 + - - -
61C THR 4.2 0.7 - - - +
63C ILE* 1.3 77.1 - - - +
65C TYR* 1.3 63.1 + - + +
66C MET 3.0 5.4 - - - -
67C HIS* 4.0 4.3 - - - -
68C ARG* 3.0 67.2 + - + +
150C ILE* 4.2 15.0 - - + -
152C HIS* 3.3 29.4 - - + +
182C LEU* 4.7 4.0 - - + -
188C SER* 3.7 31.6 - - - +
189C LEU* 5.5 0.2 - - + -
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Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C THR* 2.9 30.7 + - + +
62C ALA* 3.6 2.2 - - - -
63C ILE 3.5 0.6 - - - -
64C VAL* 1.3 89.5 - - + +
66C MET* 1.3 52.3 + - - +
68C ARG* 4.8 6.7 - - - -
69C PHE* 3.3 20.7 - - - +
83C VAL* 5.3 0.3 - - - +
87C ALA* 2.8 57.2 - - + +
90C LEU* 3.8 19.4 - - + +
91C ALA* 3.6 23.1 - - + -
94C VAL* 4.2 13.9 - - + +
140C ILE* 3.8 7.5 - - + +
141C LEU* 5.6 4.1 - - + +
144C LEU* 4.5 21.5 - - + -
147C GLU 4.6 11.1 + - - -
148C LEU* 4.7 6.6 - - - -
150C ILE* 4.5 19.7 - - + +
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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
----------------------------------------------------------
38C ARG* 3.6 25.6 - - - +
41C ALA* 5.0 9.2 - - + -
42C ALA* 3.4 34.3 - - + +
45C LEU* 3.8 17.7 - - + -
62C ALA 3.7 9.8 + - - +
63C ILE* 4.3 3.6 - - - +
64C VAL 3.0 0.2 - - - -
65C TYR* 1.3 81.9 - - - +
67C HIS* 1.3 91.8 + - + +
68C ARG 3.4 0.4 - - - -
69C PHE* 3.7 4.3 - - - -
70C TYR* 2.8 57.7 + - + +
75C PHE* 5.4 3.8 - - + -
80C GLY 6.1 0.4 - - - +
83C VAL* 5.1 6.1 - - + -
84C ALA* 6.0 1.6 - - - +
87C ALA* 4.4 6.1 - - + -
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Residues in contact with HIS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 5.5 0.9 - - + -
38C ARG* 2.7 70.2 + - + +
42C ALA* 4.8 3.0 - - - +
63C ILE* 2.8 27.3 + - + +
64C VAL* 4.2 3.1 - - - -
66C MET* 1.3 105.3 - - + +
68C ARG* 1.3 57.3 + - - +
71C MET* 3.0 14.5 + - - +
182C LEU* 3.2 22.9 + - - -
183C HIS* 4.9 2.4 - - - -
184C LEU 5.0 6.7 - - - -
185C THR 3.9 21.8 + - - -
186C THR* 5.0 2.5 - - + -
188C SER* 4.0 22.1 + - - +
189C LEU* 4.1 0.2 - - - -
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Residues in contact with ARG 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASN 5.1 1.6 + - - -
12C TRP* 3.6 58.8 - - - +
13C TYR* 5.1 6.1 + - - -
64C VAL* 3.0 49.7 + - + +
65C TYR* 4.8 9.1 - - - -
67C HIS* 1.3 76.7 - - - +
69C PHE* 1.3 66.1 + - - +
71C MET* 2.8 20.5 - - - +
72C ILE* 3.5 11.3 - - - +
144C LEU* 3.9 23.8 - - + +
149C THR 5.1 4.4 + - - -
150C ILE* 4.5 16.4 - - - +
188C SER 4.8 6.9 + - - -
189C LEU* 3.4 30.9 - - + +
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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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64C VAL 3.9 0.8 + - - -
65C TYR 3.3 24.5 - - - +
66C MET 3.3 2.7 + - - +
67C HIS 3.3 0.6 - - - -
68C ARG* 1.3 81.6 - - - +
70C TYR* 1.3 76.7 + + - +
71C MET 3.0 0.4 + - - -
72C ILE* 3.3 6.6 + - - +
73C GLN* 3.0 52.2 + - + +
78C PHE* 3.8 19.5 - + - -
83C VAL* 4.5 21.3 - - + -
86C ALA* 6.2 2.0 - - + -
136C LEU* 5.5 1.6 - - + -
139C ILE* 3.1 29.4 - - + -
140C ILE* 3.3 31.0 - - + -
143C THR* 3.8 4.9 - - - -
144C LEU* 3.7 17.3 - - + -
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Residues in contact with TYR 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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22C SER* 5.6 1.0 - - - -
23C PRO* 4.3 2.3 - - - +
24C SER* 4.8 4.3 + - - -
38C ARG* 4.5 5.5 + - - +
66C MET* 2.8 38.2 + - + +
67C HIS 3.8 2.0 - - - +
69C PHE* 1.3 78.8 - + - +
71C MET* 1.3 61.2 + - - +
72C ILE 3.1 0.7 - - - -
73C GLN* 2.5 29.5 - - + +
74C SER 2.8 43.5 - - - -
75C PHE* 3.6 44.2 - + + -
78C PHE* 3.1 10.8 + + + -
80C GLY* 2.9 36.3 + - - -
83C VAL* 3.1 36.1 - - + +
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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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12C TRP* 5.5 0.9 - - + -
14C PHE* 3.7 34.5 - - + -
18C GLN* 4.2 19.4 + - - +
19C LEU* 5.7 6.1 - - - +
22C SER* 4.6 14.4 - - - -
23C PRO* 2.8 30.5 - - - +
38C ARG* 3.6 14.1 - - - +
67C HIS 3.0 20.9 + - - +
68C ARG* 2.8 24.2 - - - +
70C TYR* 1.3 77.7 - - - +
72C ILE* 1.3 53.2 - - + +
189C LEU* 3.5 26.0 - - + -
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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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11C ARG* 5.9 1.8 - - - +
12C TRP* 3.8 23.8 - - + -
23C PRO* 3.4 14.1 - - - +
68C ARG 3.5 11.9 - - - +
69C PHE 3.5 7.0 - - - +
71C MET* 1.3 75.6 - - + +
73C GLN* 1.3 69.7 + - - +
143C THR* 3.2 58.8 - - + +
144C LEU* 4.3 1.8 - - + -
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Residues in contact with GLN 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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23C PRO* 3.1 16.5 - - - +
24C SER* 4.3 1.2 + - - -
69C PHE* 3.0 54.9 + - + +
70C TYR* 2.5 26.8 + - + +
72C ILE* 1.3 108.0 - - - +
74C SER* 1.3 62.7 + - - +
78C PHE* 3.5 24.4 - - + -
139C ILE* 5.1 4.3 - - - +
143C THR* 4.1 10.6 - - + +
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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