Contacts of the helix formed by residues 65 - 77 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLN* 3.1 33.4 - - + +
99A ASN* 2.9 27.5 + - + +
100A PHE* 3.6 21.8 + - + +
103A SER* 3.8 0.3 + - - -
51B TYR* 2.6 32.2 + - - -
53B PRO 4.3 2.6 + - - -
64B THR* 1.3 93.8 + - - +
66B GLY* 1.3 66.4 + - - +
67B PRO* 3.4 0.7 - - + -
68B ALA* 3.2 2.9 + - + -
69B ILE* 3.1 19.9 + - - +
2224B GSH 2.7 37.2 + - - -
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Residues in contact with GLY 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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13B SER* 6.0 0.9 - - - -
14B PRO* 4.8 6.7 - - - -
53B PRO* 4.2 18.1 - - - +
65B GLU* 1.3 70.0 - - - +
67B PRO* 1.4 64.4 - - - +
69B ILE* 3.1 4.4 + - - +
70B VAL* 2.8 38.0 + - - +
157B TYR* 5.5 7.0 - - - -
2224B GSH 3.1 13.6 + - - -
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Residues in contact with PRO 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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95A GLN* 5.4 1.3 - - + +
99A ASN* 3.3 39.5 - - + +
65B GLU 3.6 2.5 - - - -
66B GLY* 1.4 88.3 - - - +
68B ALA* 1.3 57.7 + - - +
70B VAL* 3.6 9.9 - - + +
71B GLN* 2.9 35.6 + - - +
98B LEU* 3.7 36.9 - - + +
99B ASN 5.2 0.2 - - - +
102B SER* 4.2 0.7 - - - -
157B TYR* 4.0 17.5 - - + -
2224B GSH 4.3 3.1 - - - +
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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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92A TYR* 3.5 19.2 - - - +
95A GLN* 3.9 14.6 + - + +
96A GLN* 3.5 30.5 - - + +
63B LEU* 4.7 5.4 - - + -
64B THR 3.7 9.9 - - - +
65B GLU* 3.2 10.4 + - + +
67B PRO* 1.3 76.5 - - - +
69B ILE* 1.3 65.6 + - - +
71B GLN* 3.4 3.5 + - - +
72B TYR* 3.0 22.7 + - - +
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Residues in contact with ILE 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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3B LEU* 5.0 0.7 - - + -
14B PRO* 3.7 24.5 - - + -
53B PRO* 3.6 35.0 - - + -
54B CYS 4.2 0.2 - - - -
55B LEU* 3.9 30.1 - - + +
63B LEU* 3.6 35.7 - - + +
64B THR* 3.9 10.8 - - - +
65B GLU 3.1 11.6 + - - +
66B GLY* 3.6 6.7 - - - +
68B ALA* 1.3 79.5 - - - +
70B VAL* 1.3 58.2 + - - +
72B TYR* 3.2 8.4 + - - +
73B VAL* 3.0 30.0 + - + +
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Residues in contact with VAL 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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13B SER* 3.7 24.7 - - - +
14B PRO* 3.8 26.7 - - + -
17B ALA* 4.2 6.5 - - + -
66B GLY 2.8 26.8 + - - +
67B PRO* 3.6 15.0 - - + +
69B ILE* 1.3 74.6 - - - +
71B GLN* 1.3 59.6 + - - +
73B VAL* 3.5 6.6 + - - +
74B ALA* 3.1 23.0 + - - +
98B LEU* 4.2 11.7 - - + -
153B VAL* 3.5 40.6 - - + +
156B ILE* 5.9 0.4 - - + -
157B TYR* 5.8 1.8 - - + -
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Residues in contact with GLN 71 (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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71A GLN* 5.6 0.2 - - - +
92A TYR* 3.7 3.4 - - + -
95A GLN* 3.4 28.6 + - - +
67B PRO* 2.9 26.4 + - - +
68B ALA 3.4 5.1 + - - +
69B ILE 3.2 0.2 - - - -
70B VAL* 1.3 77.1 - - - +
72B TYR* 1.3 64.6 + - - +
74B ALA* 3.5 5.3 + - - +
75B ASP* 3.1 28.6 + - - +
91B ARG* 3.0 37.8 + - - +
94B LEU* 4.0 9.6 - - + -
95B GLN* 3.1 30.1 + - - +
98B LEU* 3.7 20.7 - - + +
153B VAL* 4.9 0.9 - - + -
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Residues in contact with TYR 72 (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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89A PHE* 4.7 6.7 - + + -
92A TYR* 3.5 33.7 - + + -
1B MET* 4.5 9.4 - - - -
55B LEU* 3.7 18.8 - - + -
57B LEU* 3.5 42.5 - - + +
63B LEU* 3.8 24.2 - - + -
68B ALA 3.0 9.6 + - - +
69B ILE* 3.5 7.2 - - - +
71B GLN* 1.3 76.6 - - - +
73B VAL* 1.3 66.2 + - + +
75B ASP* 3.3 4.2 + - - -
76B GLN* 3.0 62.4 + - + +
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Residues in contact with VAL 73 (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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1B MET* 5.8 0.2 - - - -
14B PRO* 5.0 1.3 - - + +
17B ALA* 3.7 37.9 - - + +
18B LEU* 3.7 33.0 - - + +
21B ALA* 4.1 11.5 - - + +
23B LEU* 4.2 5.6 - - + +
55B LEU* 4.4 14.6 - - + -
69B ILE* 3.0 25.0 + - + +
70B VAL* 3.7 10.3 - - - +
72B TYR* 1.3 78.6 - - + +
74B ALA* 1.3 64.7 + - - +
76B GLN* 3.1 22.6 + - - +
77B VAL 3.7 2.6 + - - -
82B LEU* 5.7 1.3 - - + -
153B VAL* 5.8 0.2 - - + -
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Residues in contact with ALA 74 (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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21B ALA* 5.8 0.2 - - - -
70B VAL 3.1 18.3 + - - +
71B GLN* 3.9 3.8 - - - +
73B VAL* 1.3 77.7 - - - +
75B ASP* 1.3 57.4 + - - +
77B VAL 3.2 29.3 + - - +
78B PRO* 3.7 3.3 - - - +
82B LEU* 3.9 30.7 + - + +
83B ALA* 3.6 30.3 - - + +
153B VAL* 4.1 4.2 - - + +
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Residues in contact with ASP 75 (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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87A GLY* 5.8 0.7 - - - -
92A TYR* 2.5 30.6 + - - +
71B GLN 3.1 15.3 + - - +
72B TYR 3.3 3.3 + - - +
73B VAL 3.2 0.4 - - - -
74B ALA* 1.3 76.7 - - - +
76B GLN* 1.3 66.5 + - - +
77B VAL 3.4 0.2 - - - -
78B PRO* 3.8 13.6 - - - +
83B ALA* 4.5 3.3 - - - +
85B ALA* 5.9 0.3 - - - -
86B ASN* 3.1 14.5 + - - -
91B ARG* 2.8 42.1 + - - -
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Residues in contact with GLN 76 (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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92A TYR* 4.8 2.6 + - - -
1B MET* 6.0 0.9 - - - -
23B LEU* 4.1 22.6 - - + +
72B TYR* 3.0 68.8 + - + +
73B VAL* 3.1 11.2 + - - +
75B ASP* 1.3 87.7 + - - +
77B VAL* 1.3 63.6 + - + +
78B PRO* 3.5 7.2 - - - +
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Residues in contact with VAL 77 (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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21B ALA* 3.4 34.5 - - + +
23B LEU* 3.8 23.8 - - + -
73B VAL 3.7 1.0 + - - -
74B ALA* 3.2 12.5 + - - +
76B GLN* 1.3 85.3 - - + +
78B PRO* 1.4 64.5 - - - +
79B GLY* 3.2 4.0 - - - +
80B LYS* 2.9 48.3 + - + +
81B GLN 4.0 1.4 + - - -
82B LEU* 5.1 1.6 + - + +
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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