Contacts of the helix formed by residues 66 - 79 (chain B) in PDB entry 2W50
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 ALA 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B TYR* 5.0 2.4 + - - -
60B GLY* 3.6 7.6 - - - -
65B ALA* 1.3 74.2 - - - +
67B THR* 1.3 64.8 + - - +
68B LYS* 4.2 7.9 - - + +
69B ILE* 3.0 40.7 + - + +
70B LEU 3.2 8.1 + - - -
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Residues in contact with THR 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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38B GLU* 5.3 0.5 - - - +
60B GLY 4.7 1.5 + - - +
65B ALA 3.7 6.6 + - - +
66B ALA* 1.3 67.6 - - - +
68B LYS* 1.3 66.7 + - - +
70B LEU* 3.4 21.5 - - + +
71B SER* 3.1 23.4 + - - -
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Residues in contact with LYS 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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66B ALA* 3.1 7.8 - - + +
67B THR* 1.3 80.0 + - - +
69B ILE* 1.3 67.4 + - + +
71B SER* 3.4 7.8 + - - -
72B GLU* 3.3 39.2 + - + +
93B LEU* 6.2 4.2 - - - +
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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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57B TYR* 5.4 5.8 - - + +
58B TYR* 3.2 30.1 - - - +
59B LEU* 3.7 12.1 - - - -
60B GLY* 3.8 1.8 - - - +
66B ALA* 3.0 27.3 + - + +
68B LYS* 1.3 80.1 - - + +
70B LEU* 1.3 64.1 + - - +
72B GLU* 3.0 17.2 + - + +
73B VAL* 3.1 11.5 + - + +
90B LEU* 4.2 15.0 - - + -
93B LEU* 4.1 24.0 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLU* 4.1 28.9 - - + +
41B LEU* 3.9 26.9 - - + -
42B ILE* 4.1 25.4 - - + -
59B LEU 3.5 14.5 + - - +
60B GLY 3.5 26.5 - - - +
61B ALA* 4.2 5.4 - - + -
66B ALA 3.2 5.7 + - - -
67B THR* 3.4 25.4 - - + +
69B ILE* 1.3 76.1 - - - +
71B SER* 1.3 55.9 + - - +
73B VAL* 3.1 3.5 + - - +
74B THR* 2.8 39.3 + - + +
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLU* 4.1 8.0 + - - -
67B THR 3.1 11.9 + - - -
68B LYS* 3.5 11.7 - - - -
70B LEU* 1.3 74.3 - - - +
72B GLU* 1.3 63.3 + - - +
73B VAL 3.1 0.4 - - - -
74B THR* 3.6 8.3 - - - -
75B ARG* 3.1 58.1 + - - +
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LYS* 3.4 33.7 + - - +
69B ILE* 3.0 17.1 + - + +
71B SER* 1.3 80.3 + - - +
73B VAL* 1.3 58.4 + - - +
75B ARG* 5.9 3.4 - - - +
76B PRO* 3.1 12.8 - - - +
86B ILE* 5.0 1.2 - - - +
89B LYS* 2.6 61.7 + - - +
90B LEU* 4.7 10.3 - - + +
93B LEU* 5.6 7.0 - - + -
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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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41B LEU* 3.9 16.6 - - + -
59B LEU* 3.6 25.1 - - + +
69B ILE 3.1 12.8 + - - +
70B LEU 3.6 6.3 - - - +
71B SER 3.1 0.2 - - - -
72B GLU* 1.3 79.6 - - - +
74B THR* 1.3 65.0 + - - +
75B ARG 3.3 1.6 - - - -
76B PRO* 3.3 6.6 - - - +
77B MET* 3.1 51.9 + - + +
86B ILE* 4.3 12.9 - - + +
90B LEU* 3.6 33.4 - - + -
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Residues in contact with THR 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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34B LEU* 3.7 16.0 - - - +
37B ILE* 3.9 24.0 - - + +
38B GLU* 3.3 44.0 + - + +
41B LEU* 4.6 7.2 - - + -
70B LEU* 2.8 31.7 + - + +
71B SER* 3.6 5.5 - - - -
73B VAL* 1.3 76.7 - - - +
75B ARG* 1.3 65.6 + - - +
77B MET* 3.2 9.2 + - - +
78B SER* 2.9 19.1 + - - -
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 3.5 39.3 - - + +
71B SER* 3.1 39.6 + - - +
72B GLU* 5.3 3.6 - - - +
74B THR* 1.3 79.2 + - - +
76B PRO* 1.4 66.7 - - + +
78B SER* 2.7 22.9 + - - -
79B VAL* 3.8 5.0 + - - +
89B LYS* 5.9 0.4 - - - +
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Residues in contact with PRO 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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72B GLU 3.1 30.5 - - - +
73B VAL* 3.3 7.2 - - - +
75B ARG* 1.4 93.9 - - + +
77B MET* 1.3 59.0 + - - +
79B VAL* 3.2 18.7 - - + +
81B MET* 3.0 55.7 + - + -
86B ILE* 4.0 9.2 - - + -
89B LYS* 3.8 18.4 - - + +
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Residues in contact with MET 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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18B LEU* 3.6 37.0 - - + -
21B PHE* 3.6 27.8 - - + -
22B TYR* 3.4 27.6 - - + +
32B PHE* 3.4 16.9 - - + -
37B ILE* 3.6 29.4 - - + -
41B LEU* 4.3 7.6 - - + -
73B VAL* 3.1 33.8 + - + +
74B THR* 3.2 9.2 + - - +
76B PRO* 1.3 75.2 - - - +
78B SER* 1.3 58.3 + - - +
80B HIS* 2.9 18.0 + - - -
86B ILE* 3.7 6.1 - - + -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.8 22.4 - - - +
34B LEU* 3.9 20.6 - - - +
37B ILE* 3.6 11.8 - - - +
74B THR 2.9 12.0 + - - -
75B ARG* 2.7 19.7 + - - +
77B MET* 1.3 75.8 - - - +
79B VAL* 1.3 65.8 + - - +
80B HIS* 3.4 10.5 + - - -
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG 4.2 2.0 - - - +
76B PRO* 3.2 22.2 - - + +
77B MET 3.1 0.2 - - - -
78B SER* 1.3 86.1 + - - +
80B HIS* 1.3 76.8 + - - +
81B MET* 3.3 11.3 + - + +
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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