Contacts of the helix formed by residues 70 - 85 (chain A) in PDB entry 2PG0
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 70 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 3.4 26.2 + - - -
14A HIS* 3.1 22.2 + - - -
58A PRO* 5.9 0.3 - - - +
59A TRP* 5.3 2.8 - - - +
68A ASN 3.7 1.6 + - - -
69A ALA* 1.3 78.3 - - - +
71A PHE* 1.3 63.5 + - - +
72A ALA* 3.0 12.7 + - - +
73A TYR* 3.2 22.0 + - - +
74A SER* 4.0 2.4 + - - -
313A MET* 3.8 17.5 - - + +
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP* 6.2 0.9 - - - -
70A ASP* 1.3 72.9 - - - +
72A ALA* 1.3 65.0 + - - +
74A SER* 3.0 31.2 + - - +
75A VAL* 3.0 34.5 + - + -
78A ASN* 6.0 1.1 - - - -
96A ASP* 4.7 5.2 - - + -
247A GLN* 3.6 38.8 - - + -
250A LEU* 4.0 29.4 - - + -
251A VAL* 4.8 6.7 - - + -
254A ILE* 4.5 8.1 - - + -
309A ILE* 4.3 6.1 - - + -
312A HIS* 4.0 10.5 - + + -
313A MET* 3.9 30.8 - - + +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.5 32.5 - - + +
10A LEU* 4.2 1.9 - - + +
14A HIS* 3.4 20.6 - - + +
70A ASP* 3.0 13.8 + - - +
71A PHE* 1.3 77.1 - - - +
73A TYR* 1.3 61.7 + - - +
75A VAL* 3.3 12.5 + - - +
76A VAL* 3.0 27.7 + - - +
313A MET* 3.8 10.0 - - + +
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Residues in contact with TYR 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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13A GLU* 2.7 38.6 + - - +
14A HIS* 3.3 25.6 - + - -
17A PHE* 3.6 50.7 - + + -
58A PRO* 4.7 9.6 - - + -
69A ALA* 3.7 31.0 - - + -
70A ASP* 3.2 27.8 + - - +
72A ALA* 1.3 79.2 - - - +
74A SER* 1.3 56.7 + - - +
76A VAL* 3.3 6.5 + - - +
77A ILE* 3.0 33.4 + - - +
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 4.6 8.9 - - - +
59A TRP* 4.2 11.4 - - - +
70A ASP 4.0 1.3 + - - -
71A PHE* 3.0 25.6 + - - -
73A TYR* 1.3 76.9 - - - +
75A VAL* 1.3 65.8 + - - +
77A ILE* 3.3 8.3 + - - +
78A ASN* 2.9 32.0 + - - -
95A ASN* 5.0 1.4 + - - +
96A ASP* 2.5 38.1 + - - -
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 3.8 22.2 - - + +
10A LEU* 5.5 0.2 - - + -
18A ARG* 5.6 0.9 - - - +
71A PHE* 3.0 40.2 + - + +
72A ALA* 3.5 11.4 - - - +
74A SER* 1.3 76.2 - - - +
76A VAL* 1.3 64.1 + - + +
78A ASN* 3.9 3.1 - - - +
79A GLU* 2.9 48.4 + - + +
254A ILE* 4.0 13.9 - - + +
309A ILE* 4.0 23.3 - - + -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.9 15.9 - - + -
14A HIS* 4.2 14.6 - - + +
17A PHE* 3.5 26.9 - - + -
18A ARG* 3.7 55.0 - - + +
21A PHE* 4.9 1.1 - - + -
72A ALA 3.0 18.5 + - - +
73A TYR* 3.6 7.9 - - - +
74A SER 3.3 0.2 - - - -
75A VAL* 1.3 76.1 - - - +
77A ILE* 1.3 64.0 + - - +
79A GLU* 3.7 0.5 - - - +
80A GLU* 2.9 27.7 + - + +
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.7 27.1 - - + -
21A PHE* 3.5 24.8 - - + -
50A MET* 4.7 0.2 - - + -
55A PHE* 3.7 23.8 - - - +
58A PRO* 4.0 22.7 - - + -
73A TYR 3.0 21.4 + - - +
74A SER* 3.3 6.3 + - - +
76A VAL* 1.3 75.5 - - - +
78A ASN* 1.3 66.1 + - - +
80A GLU 3.3 0.2 + - - -
81A LEU* 2.9 48.8 + - + +
91A ILE* 4.6 1.3 - - + -
95A ASN* 4.2 17.3 - - - +
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Residues in contact with ASN 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 6.0 1.2 - - - -
74A SER* 2.9 20.2 + - - +
75A VAL* 4.1 3.7 - - - +
77A ILE* 1.3 84.9 - - - +
79A GLU* 1.3 62.4 + - - +
81A LEU* 3.9 6.8 - - - +
82A GLU* 3.0 24.6 + - - +
92A GLY* 3.3 25.9 + - - -
95A ASN* 5.2 0.3 + - - -
96A ASP* 3.0 26.4 + - - +
251A VAL* 4.0 27.7 - - + +
254A ILE* 4.9 14.5 - - + +
255A ALA* 5.4 6.7 - - + +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TYR* 4.2 1.6 + - - -
18A ARG* 2.9 35.8 + - - +
75A VAL* 2.9 35.4 + - - +
76A VAL 3.7 3.1 - - - +
78A ASN* 1.3 76.2 - - - +
80A GLU* 1.3 57.5 + - - +
82A GLU 3.2 2.1 + - - -
83A LYS* 3.0 36.5 + - - +
254A ILE* 3.7 12.6 - - + +
258A THR* 3.4 28.4 - - + +
302A ARG* 3.0 35.8 + - - -
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 2.9 35.1 + - + +
21A PHE* 3.5 26.5 - - + -
22A ARG* 3.0 44.1 + - - +
25A LEU* 3.5 17.2 - - + +
30A TYR* 4.3 2.6 + - - -
76A VAL* 2.9 21.6 + - + +
79A GLU* 1.3 76.8 - - - +
81A LEU* 1.3 61.9 + - - +
83A LYS* 2.8 42.6 + - - +
84A VAL* 3.4 9.0 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.9 9.4 - - + -
25A LEU* 3.8 28.9 - - + -
46A PHE* 4.6 1.1 - - + -
50A MET* 4.3 2.5 - - + -
77A ILE* 2.9 31.3 + - + +
78A ASN* 3.9 8.7 - - - +
80A GLU* 1.3 74.6 - - - +
82A GLU* 1.3 60.1 + - - +
84A VAL* 3.1 7.5 + - - +
85A GLY 2.9 28.1 + - - +
88A LEU* 3.6 32.5 - - + +
91A ILE* 3.5 50.3 - - + -
92A GLY 4.8 1.1 - - - +
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Residues in contact with GLU 82 (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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78A ASN 3.0 17.8 + - - +
79A GLU 3.2 4.5 + - - +
81A LEU* 1.3 73.9 - - - +
83A LYS* 1.3 66.0 + - - +
85A GLY* 3.1 7.7 + - - +
86A SER* 2.4 43.7 + - - -
89A VAL* 4.2 8.3 - - - +
255A ALA* 3.3 42.6 - - + +
258A THR* 4.0 8.5 - - + -
259A ALA* 3.8 25.0 - - + +
262A VAL* 4.9 0.6 - - - +
358A ARG* 2.9 24.4 + - - -
362A ILE* 5.9 0.2 - - - +
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Residues in contact with LYS 83 (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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18A ARG* 3.9 9.7 - - - +
22A ARG* 3.3 21.3 - - - +
30A TYR* 3.3 26.1 - - - +
79A GLU* 3.0 19.3 + - - +
80A GLU* 2.8 43.5 + - - +
81A LEU 3.2 0.2 - - - -
82A GLU* 1.3 76.3 - - - +
84A VAL* 1.3 52.6 + - - +
258A THR* 3.8 17.3 - - + -
261A GLU* 5.9 1.8 - - - -
262A VAL* 4.1 19.2 - - + +
358A ARG* 2.8 24.3 + - - -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.9 13.5 - - + -
29A ALA* 3.9 28.7 - - + +
30A TYR* 3.6 39.6 - - + +
33A TYR* 3.6 27.6 - - + -
80A GLU 3.4 11.9 + - - +
81A LEU 3.1 7.5 + - - +
82A GLU 3.6 0.2 - - - -
83A LYS* 1.3 75.7 - - - +
85A GLY* 1.3 58.4 + - - +
88A LEU* 3.6 11.2 - - + -
357A ARG* 2.8 22.5 + - - -
358A ARG* 3.3 6.2 + - - -
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 3.3 14.8 - - - -
81A LEU 2.9 18.5 + - - +
82A GLU* 3.1 13.4 + - - +
84A VAL* 1.3 77.9 - - - +
86A SER* 1.3 64.6 + - - -
87A SER 3.2 3.4 - - - -
88A LEU* 3.1 15.8 + - - +
357A ARG* 3.4 10.8 - - - -
358A ARG* 3.8 0.9 - - - -
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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
------------------------------------------------------------
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