Contacts of the helix formed by residues 61 - 76 (chain A) in PDB entry 2PGE
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A PRO* 2.9 24.9 + - - +
60A GLU* 1.3 105.3 + - + +
62A ILE* 1.3 66.1 + - - +
63A GLY 3.2 2.5 - - - -
64A ARG* 3.3 10.5 + - + +
65A GLU* 3.0 31.2 + - + +
118A PHE* 3.9 22.9 - - + -
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TRP* 3.5 49.6 - - + -
48A VAL* 4.1 18.4 - - + -
50A LEU* 4.0 11.4 - - + -
57A ASP* 4.0 15.5 - - + +
58A PRO 3.5 8.9 + - - +
59A GLU 3.4 2.5 + - - +
61A GLN* 1.3 77.2 - - - +
63A GLY* 1.3 64.6 + - - +
65A GLU* 3.1 5.9 + - - +
66A LEU* 3.0 35.2 + - + +
118A PHE* 3.8 26.0 - - + -
121A LEU* 4.6 10.5 - - + -
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 3.8 8.5 + - - -
33A TRP* 4.5 14.3 - - - +
59A GLU 4.8 0.8 + - - -
60A GLU 5.1 1.4 + - - -
61A GLN 3.2 1.0 - - - +
62A ILE* 1.3 81.1 - - - +
64A ARG* 1.3 56.8 + - - +
66A LEU* 3.2 7.7 + - - +
67A ASP* 2.9 35.8 + - - -
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU 5.4 1.9 + - - +
61A GLN* 3.3 14.5 + - + +
63A GLY* 1.3 71.9 - - - +
65A GLU* 1.3 63.7 + - + +
67A ASP* 3.2 9.8 + - + +
68A LEU* 2.8 67.0 + - + +
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLN* 3.0 23.4 + - + +
62A ILE* 3.1 8.5 + - - +
64A ARG* 1.3 79.1 - - - +
66A LEU* 1.3 63.1 + - - +
68A LEU* 3.4 19.1 + - - +
69A LEU* 3.0 23.6 + - - +
111A GLN 5.3 4.5 - - - +
113A SER 6.0 0.2 + - - -
118A PHE* 3.7 40.2 - - + -
121A LEU* 3.7 25.3 - - + +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.7 19.2 - - + +
9A TYR* 3.7 37.6 - - + -
33A TRP* 3.8 29.4 - - + +
35A VAL* 4.0 20.6 - - + -
48A VAL* 4.8 1.1 - - + -
62A ILE* 3.0 25.1 + - + +
63A GLY 3.5 7.4 - - - +
65A GLU* 1.3 75.8 - - - +
67A ASP* 1.3 60.8 + - - +
69A LEU* 3.3 5.2 + - + +
70A ALA* 3.0 28.2 + - - +
121A LEU* 3.6 26.0 - - + -
125A LEU* 5.3 3.6 - - + -
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 2.6 34.4 + - - -
63A GLY 2.9 20.7 + - - +
64A ARG* 3.2 8.4 + - + +
66A LEU* 1.3 77.1 - - - +
68A LEU* 1.3 62.4 + - + +
70A ALA* 3.4 7.2 + - - +
71A ARG* 3.1 35.1 + - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 2.8 68.3 + - + +
65A GLU* 3.7 20.9 - - - +
67A ASP* 1.3 73.4 - - + +
69A LEU* 1.3 62.0 + - - +
71A ARG* 3.4 19.5 + - - +
72A ARG* 3.1 23.5 + - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.6 23.1 - - + -
65A GLU 3.0 17.0 + - - +
66A LEU* 3.7 3.6 - - + +
67A ASP 3.3 0.2 - - - -
68A LEU* 1.3 75.8 - - - +
70A ALA* 1.3 60.2 + - - +
72A ARG* 3.1 8.3 + - - +
73A LEU* 2.8 50.2 + - + +
110A TRP* 3.8 41.1 - - + +
112A VAL* 4.0 7.6 - - + -
121A LEU* 5.7 1.8 - - + -
125A LEU* 3.2 39.7 - - + -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MET 5.1 0.9 - - - +
7A LEU* 3.7 37.1 + - + +
9A TYR* 5.8 3.6 - - + -
66A LEU 3.0 16.7 + - - +
67A ASP* 3.7 9.2 - - - +
68A LEU 3.4 0.2 - - - -
69A LEU* 1.3 75.1 - - - +
71A ARG* 1.3 63.6 + - + +
73A LEU* 3.4 2.2 + - - +
74A ARG* 3.1 25.6 + - - +
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASP* 3.1 26.1 + - - +
68A LEU* 3.6 23.9 - - + +
69A LEU 3.2 0.2 - - - -
70A ALA* 1.3 77.7 - - + +
72A ARG* 1.3 61.8 + - - +
74A ARG* 3.4 8.1 + - - +
75A ALA* 3.3 23.0 + - - +
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU 3.1 14.6 + - - +
69A LEU* 3.5 13.8 - - - +
71A ARG* 1.3 77.3 - - - +
73A LEU* 1.3 64.6 + - + +
75A ALA* 3.2 15.5 + - - +
76A GLU* 3.4 34.5 + - - +
109A SER 4.6 5.4 + - - -
110A TRP* 3.7 33.2 + - - +
111A GLN* 3.9 29.1 - - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLY* 3.5 4.7 - - - -
5A MET* 3.1 45.2 + - + +
7A LEU* 4.1 15.3 - - + +
37A LEU* 3.9 27.1 - - + -
69A LEU* 2.8 33.6 + - + +
70A ALA* 4.0 4.7 - - - +
72A ARG* 1.3 80.4 - - + +
74A ARG* 1.3 60.3 + - - +
76A GLU* 3.6 13.1 - - + +
110A TRP* 3.5 51.4 - - + +
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER* 4.4 5.2 - - - -
4A GLY* 3.6 16.5 + - - +
5A MET 3.7 14.5 + - - +
6A GLU* 6.0 6.1 - - - +
70A ALA 3.1 17.8 + - - +
71A ARG* 3.8 7.2 - - - +
72A ARG 3.2 0.2 - - - -
73A LEU* 1.3 77.9 - - - +
75A ALA* 1.3 59.1 + - - +
76A GLU 3.5 0.2 - - - -
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER* 4.2 8.2 + - - -
71A ARG 3.3 15.9 + - - +
72A ARG* 3.2 7.9 + - - +
74A ARG* 1.3 79.9 - - + +
76A GLU* 1.3 58.3 + - + +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER* 4.2 2.5 - - - -
4A GLY* 3.2 22.5 - - - -
72A ARG* 3.4 37.6 + - - +
73A LEU* 3.6 8.1 - - + +
74A ARG 3.5 0.2 - - - -
75A ALA* 1.3 80.9 - - + +
77A GLU* 1.3 68.5 + - - +
78A PRO* 3.4 6.1 - - + +
109A SER* 5.3 4.0 + - - +
110A TRP* 3.9 24.7 + - - -
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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