Contacts of the helix formed by residues 56 - 70 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B VAL 3.2 4.5 + - - -
55B PRO* 1.3 82.9 - - - +
57B GLN* 1.3 62.4 + - - +
58B THR* 3.5 12.2 + - - -
59B GLY* 2.9 25.1 + - - -
60B THR* 2.8 30.3 + - - +
62F ALA* 3.9 15.9 - - - +
63F ILE* 4.0 19.3 - - + -
66F ARG* 2.8 38.1 + - - +
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO* 3.6 2.9 - - + +
14B LEU 2.9 30.1 + - - +
15B VAL* 3.8 6.2 - - - +
33B ALA* 3.1 24.0 - - + +
34B VAL 3.2 8.7 + - - +
35B ASN* 3.0 24.5 + - - +
53B VAL* 3.5 19.4 + - + +
56B ASP* 1.3 72.3 + - - +
58B THR* 1.3 58.2 + - - +
60B THR* 3.2 7.1 + - - -
61B ALA* 2.8 33.1 + - - +
372B TYR* 3.5 28.4 - - + -
66F ARG* 4.1 5.0 - - - +
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASP* 3.3 10.9 + - - -
57B GLN* 1.3 75.9 - - - +
59B GLY* 1.3 65.1 + - - +
61B ALA* 3.2 4.4 + - - +
62B ALA* 3.0 25.0 + - + +
372B TYR* 2.7 31.0 + - - +
62F ALA* 5.5 5.6 - - + -
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Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASP* 2.9 22.4 + - - -
58B THR* 1.3 78.2 - - - +
60B THR* 1.3 57.7 + - - +
62B ALA* 3.3 4.8 + - - +
63B ILE* 3.1 32.5 + - - +
59F GLY* 3.7 29.1 - - - -
62F ALA* 4.3 3.6 - - - -
63F ILE* 4.7 1.6 - - - -
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN* 3.3 11.5 + - - -
52B THR 4.8 1.6 - - - -
53B VAL* 2.9 35.8 + - - +
54B ALA 3.5 15.9 - - - +
55B PRO* 4.1 8.3 - - + -
56B ASP 2.8 16.0 + - - +
57B GLN 3.2 7.3 + - - -
59B GLY* 1.3 71.6 - - - -
61B ALA* 1.3 59.7 + - - +
63B ILE* 3.6 11.2 - - + +
64B LEU* 2.9 29.1 + - - +
104B GLN* 4.5 3.6 - - - +
105B ILE* 4.2 17.0 - - + +
63F ILE* 4.7 7.2 - - + -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.9 11.8 - - + +
13B PRO* 3.9 21.3 - - + -
35B ASN* 3.2 22.0 - - - +
57B GLN 2.8 19.7 + - - +
58B THR* 3.2 7.4 + - - +
60B THR* 1.3 74.2 - - - +
62B ALA* 1.3 65.5 + - - +
64B LEU* 3.3 3.4 + - - +
65B TYR* 2.9 25.2 + - - +
372B TYR* 5.2 0.7 - - - +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B THR* 3.0 13.9 + - + +
59B GLY* 3.5 9.6 - - - +
60B THR 3.3 0.2 - - - -
61B ALA* 1.3 76.7 - - - +
63B ILE* 1.3 61.6 + - - +
65B TYR* 3.4 7.1 + - - +
66B ARG* 3.0 24.3 + - - +
56F ASP* 3.9 19.1 - - - +
58F THR* 5.4 6.3 - - + -
59F GLY* 4.4 6.3 - - - +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLY 3.1 17.0 + - - +
60B THR* 3.6 16.2 - - + +
61B ALA 3.2 0.4 - - - -
62B ALA* 1.3 77.0 - - - +
64B LEU* 1.3 62.9 + - - +
66B ARG* 3.3 6.0 + - - +
67B LEU* 3.0 27.8 + - + +
91B TYR* 3.8 12.3 - - - +
105B ILE* 3.9 17.0 - - + -
55F PRO* 3.7 40.4 - - + -
56F ASP* 4.0 15.3 - - + -
59F GLY* 4.7 3.6 - - - -
60F THR* 4.6 7.9 - - + -
63F ILE* 4.6 16.8 - - + -
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.9 16.4 - - + -
35B ASN* 3.8 35.9 - - + +
37B ILE* 3.9 21.8 - - + -
51B CYS* 3.8 20.6 - - + -
60B THR 2.9 17.9 + - - +
61B ALA* 3.6 4.9 - - - +
63B ILE* 1.3 76.1 - - - +
65B TYR* 1.3 56.9 + - - +
67B LEU* 3.4 0.7 + - - +
68B ALA* 2.9 32.1 + - - +
105B ILE* 3.5 29.2 - - + -
109B ILE* 3.8 22.2 - - + -
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Residues in contact with TYR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.9 24.5 + - + +
10B ARG* 4.9 1.8 - - - -
11B VAL* 3.6 28.9 - - + +
61B ALA 2.9 17.0 + - - +
62B ALA* 3.7 7.6 - - - +
64B LEU* 1.3 77.2 - - - +
66B ARG* 1.3 64.2 + - - +
68B ALA* 3.3 1.8 + - - +
69B LYS* 3.0 69.4 + - + +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ALA 3.0 17.6 + - - +
63B ILE* 3.3 5.8 + - - +
65B TYR* 1.3 79.6 - - - +
67B LEU* 1.3 65.2 + - + +
69B LYS* 3.6 25.2 + - - +
70B HIS* 3.2 17.4 + - - +
90B GLU* 3.0 37.7 + - - +
94B HIS* 5.3 5.1 + - - -
55F PRO 3.1 25.3 + - - -
56F ASP* 3.0 34.7 + - - +
57F GLN* 4.2 3.8 - - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 3.0 21.0 + - + +
64B LEU 3.9 3.1 - - - +
66B ARG* 1.3 79.9 - - + +
68B ALA* 1.3 63.2 + - - +
70B HIS* 3.3 24.0 + - - +
86B ILE* 3.5 29.0 - - + +
90B GLU* 3.9 26.0 - - + -
91B TYR* 3.7 32.3 - - + +
105B ILE* 3.7 23.6 - - + -
106B PHE* 4.0 16.6 - - + -
109B ILE* 4.0 11.9 - - + -
55F PRO* 4.5 7.4 - - + -
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.6 19.1 - - + +
11B VAL* 5.3 0.2 - - + -
37B ILE* 3.6 28.7 - - + -
64B LEU 2.9 19.9 + - - +
65B TYR* 3.9 4.0 - - - +
67B LEU* 1.3 75.8 - - - +
69B LYS* 1.3 65.4 + - - +
71B LEU* 2.9 35.8 + - + +
109B ILE* 4.1 8.0 - - + +
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.9 11.2 - - + -
65B TYR* 3.0 70.1 + - + +
66B ARG* 4.0 21.9 + - - +
67B LEU 3.3 0.6 - - - -
68B ALA* 1.3 76.4 - - - +
70B HIS* 1.3 62.5 + - + +
71B LEU 3.0 1.4 + - - -
72B VAL* 3.1 23.8 + - + +
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Residues in contact with HIS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG* 3.2 24.5 + - - +
67B LEU* 3.3 17.0 + - - +
68B ALA 3.1 1.0 - - - -
69B LYS* 1.3 77.4 - - + +
71B LEU* 1.3 58.4 + - - +
72B VAL 3.3 2.0 + - - +
74B HIS* 3.1 24.9 + - - -
82B LEU* 5.0 0.4 - - - +
85B ARG* 3.8 19.1 + - - +
86B ILE* 3.6 28.3 - - + -
89B GLN* 3.3 33.2 + - - -
90B GLU* 2.8 27.2 + - + +
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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