Contacts of the helix formed by residues 56 - 70 (chain C) in PDB entry 2PGW
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 ASP 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C VAL* 3.1 5.7 + - - +
54C ALA* 3.7 0.2 - - - +
55C PRO* 1.3 83.9 - - - +
57C GLN* 1.3 60.1 + - - +
58C THR* 3.6 10.4 + - - -
59C GLY* 2.9 23.7 + - - -
60C THR* 2.8 30.7 + - - +
376C ARG* 4.7 9.9 + - - -
62H ALA* 3.9 16.6 - - - +
63H ILE* 4.0 20.2 - - + -
66H ARG* 3.1 34.2 + - - +
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Residues in contact with GLN 57 (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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13C PRO* 3.6 1.5 - - + +
14C LEU 2.9 31.5 + - - +
15C VAL* 3.8 6.1 - - - +
33C ALA* 3.5 17.7 - - + +
34C VAL 3.1 12.7 + - - +
35C ASN* 3.0 24.8 + - - +
53C VAL* 3.5 19.4 + - + +
56C ASP* 1.3 73.8 + - - +
58C THR* 1.3 58.1 + - - +
60C THR* 3.3 7.6 + - - -
61C ALA* 2.8 32.6 + - - +
372C TYR* 3.4 31.5 - - + -
375C SER* 5.4 0.2 + - - -
66H ARG* 4.5 3.2 - - - +
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Residues in contact with THR 58 (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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56C ASP* 3.4 10.7 + - - -
57C GLN* 1.3 78.1 - - - +
59C GLY* 1.3 62.9 + - - +
61C ALA* 3.7 3.8 - - - +
62C ALA* 3.1 22.5 + - + +
372C TYR* 2.7 26.8 + - - +
376C ARG* 3.0 40.0 + - - +
62H ALA* 5.5 6.3 - - + -
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Residues in contact with GLY 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASP* 2.9 19.6 + - - -
58C THR* 1.3 76.3 - - - +
60C THR* 1.3 57.7 + - - +
62C ALA* 3.3 4.7 + - - +
63C ILE* 3.1 32.1 + - - +
59H GLY* 3.7 28.5 - - - -
62H ALA* 4.5 3.6 - - - -
63H ILE* 4.6 2.9 - - - -
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Residues in contact with THR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASN* 3.3 11.9 + - - -
52C THR 4.8 0.9 - - - -
53C VAL* 3.0 34.2 + - - +
54C ALA 3.6 16.4 - - - +
55C PRO* 4.3 7.2 - - + -
56C ASP 2.8 17.7 + - - +
57C GLN 3.3 5.0 + - - -
59C GLY* 1.3 70.0 - - - -
61C ALA* 1.3 63.4 + - - +
63C ILE* 3.7 11.1 - - + +
64C LEU* 2.8 30.3 + - - +
104C GLN* 4.4 5.2 - - - +
105C ILE* 4.3 16.5 - - + +
63H ILE* 4.7 7.0 - - + -
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Residues in contact with ALA 61 (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 VAL* 4.0 11.0 - - + +
13C PRO* 3.8 26.0 - - + -
35C ASN* 3.4 16.2 - - - +
57C GLN 2.8 20.6 + - - +
58C THR* 3.7 6.5 - - - +
60C THR* 1.3 77.3 + - - +
62C ALA* 1.3 63.1 + - - +
64C LEU* 3.8 3.2 - - - +
65C TYR* 3.0 25.5 + - - +
372C TYR* 5.3 0.2 - - - +
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Residues in contact with ALA 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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58C THR* 3.1 15.0 + - + +
59C GLY 3.5 9.4 - - - +
60C THR 3.2 0.2 - - - -
61C ALA* 1.3 78.7 - - - +
63C ILE* 1.3 60.1 + - - +
65C TYR* 3.6 6.2 + - - +
66C ARG* 3.2 23.2 + - - +
56H ASP* 4.0 19.3 - - - +
58H THR* 5.5 5.8 - - + -
59H GLY* 4.4 6.7 - - - +
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLY 3.1 16.4 + - - +
60C THR* 3.7 15.0 - - + +
61C ALA 3.2 0.2 - - - -
62C ALA* 1.3 74.4 - - - +
64C LEU* 1.3 64.8 + - - +
66C ARG* 3.3 6.6 + - + +
67C LEU* 3.1 28.1 + - + +
91C TYR* 3.8 12.8 - - - +
105C ILE* 4.2 14.6 - - + -
55H PRO* 3.5 37.0 - - + -
56H ASP* 3.9 20.2 - - + -
59H GLY* 4.7 2.9 - - - -
60H THR* 4.5 12.8 - - + -
63H ILE* 4.7 10.8 - - + -
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Residues in contact with LEU 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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11C VAL* 3.7 20.6 - - + -
35C ASN* 3.8 37.5 - - + +
36C LEU 4.1 0.2 - - - +
37C ILE* 4.0 18.4 - - + -
51C CYS* 3.9 18.6 - - + -
60C THR 2.8 18.0 + - - +
61C ALA 3.8 3.6 - - - +
63C ILE* 1.3 76.3 - - - +
65C TYR* 1.3 63.1 + - - +
67C LEU* 3.5 0.9 + - - +
68C ALA* 3.0 20.4 + - - +
105C ILE* 3.6 23.8 - - + +
109C ILE* 3.8 27.6 - - + -
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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
----------------------------------------------------------
9C VAL* 3.9 32.1 + - + +
10C ARG* 4.8 2.2 - - - -
11C VAL* 3.6 28.3 - - + -
61C ALA 3.0 18.1 + - - +
62C ALA* 3.8 7.0 - - - +
64C LEU* 1.3 77.3 - - - +
66C ARG* 1.3 63.2 + - - +
68C ALA* 3.2 3.1 + - - +
69C LYS* 3.0 68.1 + - + +
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Residues in contact with ARG 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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62C ALA 3.2 15.1 + - - +
63C ILE* 3.3 6.3 + - - +
65C TYR* 1.3 79.3 - - - +
67C LEU* 1.3 65.4 + - + +
69C LYS* 3.3 27.2 + - - +
70C HIS* 3.2 17.2 + - - +
90C GLU* 2.8 37.0 + - - +
94C HIS* 5.4 5.9 + - - -
55H PRO 3.2 24.4 + - - -
56H ASP* 3.0 34.3 + - - +
57H GLN* 4.4 3.2 - - - +
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Residues in contact with LEU 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 ILE* 3.1 21.6 + - + +
64C LEU 3.9 3.6 - - - +
66C ARG* 1.3 78.8 - - + +
68C ALA* 1.3 63.1 + - - +
70C HIS* 3.2 25.4 + - - +
86C ILE* 3.5 31.1 - - + +
90C GLU* 3.8 26.0 - - + -
91C TYR* 3.7 24.0 - - + +
105C ILE* 3.6 26.5 - - + -
106C PHE* 3.9 22.4 - - + -
109C ILE* 4.0 10.3 - - + -
55H PRO* 4.8 6.5 - - + -
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Residues in contact with ALA 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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9C VAL* 3.4 19.7 - - + +
37C ILE* 3.7 28.5 - - + -
64C LEU 3.0 18.5 + - - +
65C TYR* 3.7 4.3 - - - +
67C LEU* 1.3 74.6 - - - +
69C LYS* 1.3 63.9 + - - +
70C HIS 3.0 2.2 - - - -
71C LEU* 2.9 33.0 + - + +
109C ILE* 4.4 10.8 - - + -
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Residues in contact with LYS 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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9C VAL* 4.0 13.9 - - + -
65C TYR* 3.0 63.1 + - + +
66C ARG* 3.3 30.2 - - - +
67C LEU 3.3 0.4 - - - -
68C ALA* 1.3 76.6 - - - +
70C HIS* 1.3 61.6 + - - +
71C LEU 3.1 0.9 + - - -
72C VAL* 3.3 22.1 + - + +
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Residues in contact with HIS 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 ARG* 3.2 24.2 + - - +
67C LEU* 3.2 18.6 + - - +
68C ALA 3.0 0.8 - - - -
69C LYS* 1.3 79.1 - - - +
71C LEU* 1.3 56.4 + - - +
72C VAL 3.6 2.1 + - - +
74C HIS* 3.0 25.3 + - - -
85C ARG* 3.9 17.2 + - - +
86C ILE* 3.6 30.5 - - + -
89C GLN* 3.6 29.9 + - + -
90C GLU* 2.8 28.5 + - - +
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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