Contacts of the helix formed by residues 56 - 70 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ALA* 3.9 16.9 - - - +
63A ILE* 4.1 19.5 - - + -
66A ARG* 2.8 37.2 + - - +
53G VAL* 3.1 5.3 + - - +
55G PRO* 1.3 82.6 - - - +
57G GLN* 1.3 63.6 + - - +
58G THR* 3.7 10.7 + - - -
59G GLY* 2.9 23.4 + - - -
60G THR* 2.8 30.3 + - - +
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Residues in contact with GLN 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ARG* 4.2 4.0 - - - +
13G PRO* 3.7 1.5 - - + +
14G LEU 3.0 30.3 + - - +
15G VAL* 3.8 5.5 - - - +
33G ALA* 3.5 19.8 - - + +
34G VAL 3.1 20.6 + - - -
35G ASN* 3.2 15.0 + - - +
53G VAL* 3.5 20.9 + - + +
56G ASP* 1.3 72.3 + - - +
58G THR* 1.3 59.2 + - - +
60G THR* 3.2 8.3 + - - -
61G ALA* 2.8 31.4 + - - +
372G TYR* 3.5 30.2 - - + -
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Residues in contact with THR 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA* 5.6 5.8 - - + -
56G ASP* 3.3 11.1 + - - -
57G GLN* 1.3 78.2 - - - +
59G GLY* 1.3 62.6 + - - +
61G ALA* 3.2 5.0 + - + +
62G ALA* 3.1 23.4 + - + +
372G TYR* 2.9 29.6 + - - +
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Residues in contact with GLY 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY* 3.7 29.0 - - - -
62A ALA* 4.3 5.1 - - - +
63A ILE* 4.7 2.5 - - - -
56G ASP* 2.9 21.1 + - - -
58G THR* 1.3 78.0 - - - +
60G THR* 1.3 60.9 + - - +
62G ALA* 3.2 7.3 + - - +
63G ILE* 3.1 26.8 + - - +
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Residues in contact with THR 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 4.9 6.5 - - + -
35G ASN* 3.3 14.1 + - - -
52G THR 4.8 1.8 - - - -
53G VAL* 2.9 34.7 + - - +
54G ALA 3.4 16.6 - - - +
55G PRO* 4.1 7.9 - - + -
56G ASP 2.8 17.1 + - - +
57G GLN 3.2 7.1 + - - -
59G GLY* 1.3 69.1 - - - -
61G ALA* 1.3 59.8 + - - +
62G ALA 3.3 0.2 - - - -
63G ILE* 3.7 13.1 - - + +
64G LEU* 3.1 28.8 + - - +
104G GLN* 4.3 4.7 - - - +
105G ILE* 4.4 14.9 - - + +
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Residues in contact with ALA 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G VAL* 4.1 11.1 - - + +
13G PRO* 3.9 24.5 - - + -
35G ASN* 3.6 15.5 - - - +
57G GLN 2.8 19.8 + - - +
58G THR* 3.5 8.3 - - - +
59G GLY 3.1 0.2 - - - -
60G THR* 1.3 77.1 + - - +
62G ALA* 1.3 64.7 + - - +
64G LEU* 3.5 2.8 + - - +
65G TYR* 3.1 24.3 + - - +
372G TYR* 5.2 1.3 - - - +
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASP* 3.8 19.5 - - - +
58A THR* 5.3 6.7 - - + -
59A GLY* 4.3 7.0 - - - +
58G THR* 3.1 11.7 + - + +
59G GLY 3.2 10.5 + - - +
61G ALA* 1.3 75.3 - - - +
63G ILE* 1.3 64.9 + - - +
65G TYR* 3.4 6.2 + - - +
66G ARG* 3.1 24.1 + - - +
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Residues in contact with ILE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PRO* 3.5 40.8 - - + -
56A ASP* 4.0 14.8 - - + -
59A GLY* 4.6 3.6 - - - -
60A THR* 4.7 7.6 - - + -
63A ILE* 4.6 17.3 - - + -
59G GLY 3.1 13.4 + - - +
60G THR* 3.8 16.6 - - + +
62G ALA* 1.3 76.3 - - - +
64G LEU* 1.3 63.4 + - - +
66G ARG* 3.1 8.4 + - - +
67G LEU* 3.0 28.6 + - + +
91G TYR* 3.8 12.6 - - - +
105G ILE* 4.1 15.9 - - + -
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Residues in contact with LEU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G VAL* 3.7 21.1 - - + -
35G ASN* 3.9 29.6 - - + +
37G ILE* 4.1 16.2 - - + -
51G CYS* 3.8 25.6 - - + -
60G THR 3.1 17.9 + - - +
61G ALA 3.8 3.8 - - - +
63G ILE* 1.3 77.8 - - - +
65G TYR* 1.3 56.9 + - - +
67G LEU* 3.4 0.7 + - - +
68G ALA* 2.9 30.8 + - - +
105G ILE* 3.6 28.9 - - + +
109G ILE* 3.7 23.8 - - + -
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Residues in contact with TYR 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.6 36.4 + - + +
10G ARG* 4.5 3.6 - - - -
11G VAL* 3.7 27.1 - - + +
61G ALA 3.1 18.1 + - - +
62G ALA* 3.8 6.5 - - - +
63G ILE 3.3 0.2 - - - -
64G LEU* 1.3 76.0 - - - +
66G ARG* 1.3 63.7 + - - +
68G ALA* 3.3 1.9 + - - +
69G LYS* 3.0 65.4 + - + +
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Residues in contact with ARG 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PRO 3.2 24.9 + - - +
56A ASP* 3.0 33.9 + - - +
57A GLN* 4.3 4.2 - - - +
62G ALA 3.1 14.7 + - - +
63G ILE* 3.5 9.4 - - - +
65G TYR* 1.3 81.1 - - - +
67G LEU* 1.3 64.9 + - + +
69G LYS* 3.6 16.4 + - - +
70G HIS* 3.3 14.0 + - - -
90G GLU* 2.8 37.4 + - - +
94G HIS* 5.5 5.9 + - - -
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Residues in contact with LEU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PRO* 4.7 7.2 - - + -
63G ILE* 3.0 21.2 + - + +
64G LEU 3.9 3.1 - - - +
66G ARG* 1.3 79.7 - - + +
68G ALA* 1.3 63.6 + - - +
70G HIS* 3.3 25.0 + - - +
71G LEU 4.3 0.2 + - - -
86G ILE* 3.6 29.5 - - + +
90G GLU* 3.9 25.4 - - + -
91G TYR* 3.8 31.0 - - + +
105G ILE* 3.7 25.6 - - + -
106G PHE* 3.8 16.8 - - + -
109G ILE* 4.1 11.2 - - + -
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Residues in contact with ALA 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.5 19.6 - - + +
11G VAL* 5.3 0.2 - - + -
37G ILE* 3.6 30.1 - - + -
64G LEU 2.9 19.1 + - - +
65G TYR* 3.7 5.2 - - - +
67G LEU* 1.3 78.0 - - - +
69G LYS* 1.3 56.1 + - - +
71G LEU* 2.9 39.7 + - + +
109G ILE* 4.1 8.7 - - + +
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Residues in contact with LYS 69 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.8 14.6 - - + +
65G TYR* 3.0 65.0 + - + +
66G ARG* 3.9 9.9 - - - +
67G LEU 3.3 0.6 - - - -
68G ALA* 1.3 76.2 - - - +
70G HIS* 1.3 61.5 + - + +
71G LEU 3.0 1.7 + - - -
72G VAL* 3.3 25.8 + - + +
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Residues in contact with HIS 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ARG* 3.3 23.1 + - - +
67G LEU* 3.3 17.2 + - - +
68G ALA 3.1 0.6 - - - -
69G LYS* 1.3 77.6 - - + +
71G LEU* 1.3 59.4 + - - +
72G VAL 3.4 2.4 - - - +
74G HIS* 3.1 23.2 + - - -
85G ARG* 3.5 21.2 + - - +
86G ILE* 3.7 29.4 - - + -
89G GLN* 3.5 28.3 - - - -
90G GLU* 2.8 28.3 + - - +
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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