Contacts of the helix formed by residues 65 - 77 (chain A) in PDB entry 2DSA
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 GLU 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR* 2.6 30.6 + - - -
53A PRO 4.3 3.0 + - - -
64A THR* 1.3 89.3 + - - +
66A GLY* 1.3 68.1 + - - +
67A PRO* 3.3 1.1 - - + -
68A ALA* 3.0 14.9 + - + -
69A ILE* 3.0 11.1 + - - +
1224A GSH 2.8 35.6 + - - -
96B GLN* 3.2 31.4 - - + +
99B ASN* 2.8 34.1 + - + +
100B PHE* 3.7 19.6 - - + -
103B SER* 3.7 1.7 + - - -
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Residues in contact with GLY 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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13A SER* 6.1 0.7 - - - -
14A PRO* 5.2 3.8 - - - -
53A PRO* 4.1 19.0 - - - +
65A GLU* 1.3 70.6 - - - +
67A PRO* 1.4 64.2 - - - +
69A ILE* 3.3 3.2 + - - +
70A VAL* 2.9 40.4 + - - +
157A TYR* 5.5 8.7 - - - -
1224A GSH 3.2 13.0 + - - -
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Residues in contact with PRO 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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65A GLU 3.6 3.4 - - - -
66A GLY* 1.4 87.4 - - - +
68A ALA* 1.3 58.9 + - - +
70A VAL* 3.8 8.0 - - + +
71A GLN* 3.0 36.3 + - - +
98A LEU* 3.7 39.3 - - + +
99A ASN 5.1 0.4 - - - +
102A SER* 4.1 1.3 - - - -
157A TYR* 4.0 17.0 - - + -
1224A GSH 4.3 4.0 - - - +
95B GLN* 5.5 1.1 - - + +
99B ASN* 3.3 37.5 - - + +
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Residues in contact with ALA 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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63A LEU* 4.3 8.0 - - + +
64A THR 3.5 13.5 - - - +
65A GLU* 3.0 10.2 + - + +
67A PRO* 1.3 75.6 - - - +
69A ILE* 1.3 66.5 + - - +
71A GLN* 3.3 3.8 + - - +
72A TYR* 3.0 22.9 + - - +
92B TYR* 3.6 29.0 - - - +
95B GLN* 4.0 14.6 + - + +
96B GLN* 3.6 15.3 - - + +
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Residues in contact with ILE 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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3A LEU* 4.9 0.9 - - + -
14A PRO* 3.5 29.4 - - + -
53A PRO* 3.7 36.6 - - + +
54A CYS 4.3 0.2 - - - -
55A LEU* 3.9 27.6 - - + +
63A LEU* 3.5 39.0 - - + +
64A THR 3.9 7.2 - - - -
65A GLU 3.0 16.1 + - - +
66A GLY* 3.7 6.1 - - - +
68A ALA* 1.3 75.9 - - - +
70A VAL* 1.3 56.5 + - - +
72A TYR* 3.2 4.3 + - - +
73A VAL* 2.9 35.6 + - + +
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Residues in contact with VAL 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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13A SER* 3.8 24.7 - - - +
14A PRO* 3.8 27.6 - - + -
17A ALA* 4.4 3.4 - - + -
66A GLY 2.9 28.3 + - - +
67A PRO* 3.8 8.1 - - + +
69A ILE* 1.3 72.3 - - - +
71A GLN* 1.3 57.7 + - - +
73A VAL* 3.8 6.5 - - - +
74A ALA* 3.0 28.1 + - - +
98A LEU* 4.0 18.8 - - + -
153A VAL* 3.5 38.1 - - + +
156A ILE* 6.1 0.2 - - + -
157A TYR* 5.6 1.6 - - + -
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Residues in contact with GLN 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 PRO* 3.0 28.1 + - - +
68A ALA 3.3 4.6 + - - +
69A ILE 3.2 0.6 - - - -
70A VAL* 1.3 75.2 - - - +
72A TYR* 1.3 65.9 + - - +
74A ALA* 3.4 4.6 + - - +
75A ASP* 3.0 29.6 + - - -
91A ARG* 2.9 39.0 + - - +
94A LEU* 4.3 7.0 - - + -
95A GLN* 2.9 27.5 + - - +
98A LEU* 3.7 23.1 - - + +
153A VAL* 5.0 1.3 - - + -
92B TYR* 3.7 3.4 - - + -
95B GLN* 3.5 29.3 + - - +
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Residues in contact with TYR 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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1A MET* 3.7 22.2 - - + +
55A LEU* 3.5 17.3 - - + -
57A LEU* 3.6 40.2 - - + +
63A LEU* 3.6 24.5 - - + -
68A ALA 3.0 6.8 + - - +
69A ILE 3.6 7.2 - - - +
71A GLN* 1.3 75.2 - - - +
73A VAL* 1.3 68.5 + - + +
75A ASP* 3.2 4.7 + - - +
76A GLN* 2.8 59.3 + - + +
89B PHE* 4.7 5.4 - + + -
92B TYR* 3.4 35.9 - + + -
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Residues in contact with VAL 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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1A MET* 5.7 0.2 - - - -
14A PRO* 5.2 1.1 - - + +
17A ALA* 3.8 38.1 - - + +
18A LEU* 3.8 32.5 - - + +
21A ALA* 4.1 11.6 - - + +
23A LEU* 4.3 4.8 - - + +
55A LEU* 4.5 11.7 - - + -
69A ILE* 2.9 33.2 + - + +
70A VAL* 3.8 8.1 - - - +
71A GLN 3.2 0.2 - - - -
72A TYR* 1.3 79.3 - - + +
74A ALA* 1.3 63.0 + - - +
76A GLN* 3.1 22.3 + - - +
77A VAL 3.9 2.3 + - - -
82A LEU* 5.4 0.7 - - + -
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Residues in contact with ALA 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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70A VAL 3.0 18.5 + - - +
71A GLN* 3.9 3.8 - - - +
73A VAL* 1.3 78.3 - - - +
75A ASP* 1.3 62.2 + - - +
76A GLN 3.1 0.4 - - - -
77A VAL* 3.2 23.4 + - - +
78A PRO* 3.8 3.3 - - - +
82A LEU* 3.7 32.2 + - + +
83A ALA* 3.7 29.7 + - + -
153A VAL* 4.1 4.0 - - + -
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Residues in contact with ASP 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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71A GLN 3.0 13.8 + - - +
72A TYR 3.2 3.8 + - - +
74A ALA* 1.3 76.1 - - - +
76A GLN* 1.3 64.6 + - - +
78A PRO* 3.5 15.1 - - - +
83A ALA* 4.8 1.0 - - - +
86A ASN* 3.0 18.1 + - - -
91A ARG* 2.9 39.9 + - - -
87B GLY* 6.0 0.2 - - - -
92B TYR* 2.4 36.7 + - - +
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Residues in contact with GLN 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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1A MET* 5.6 1.3 - - + -
23A LEU* 4.0 25.5 - - + +
72A TYR* 2.8 70.3 + - + +
73A VAL* 3.3 10.3 - - - +
74A ALA 3.1 0.6 - - - -
75A ASP* 1.3 87.7 + - - +
77A VAL* 1.3 64.3 + - + +
78A PRO* 3.5 5.6 - - - +
92B TYR* 4.5 2.6 + - - -
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Residues in contact with VAL 77 (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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21A ALA* 3.4 31.6 - - + +
23A LEU* 3.7 20.9 - - + -
73A VAL 3.9 1.2 + - - +
74A ALA 3.2 11.3 + - - +
76A GLN* 1.3 85.4 - - + +
78A PRO* 1.3 59.5 - - - +
79A GLY* 3.1 5.8 - - - +
80A LYS* 2.9 57.7 + - + +
81A GLN 3.9 2.4 + - - -
82A LEU* 4.9 2.9 + - + +
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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
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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