Contacts of the helix formed by residues 71 - 88 (chain B) in PDB entry 2WAL
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 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B GLU 4.8 1.1 + - - +
68B ASP* 3.1 27.0 + - - +
69B GLU 3.4 0.2 - - - -
70B GLY* 1.3 74.9 - - - +
72B ILE* 1.3 57.0 + - - +
73B ALA* 3.5 11.3 + - - +
74B LEU* 3.1 33.5 + - + +
75B GLN* 2.8 31.8 + - - +
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Residues in contact with ILE 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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79A THR* 4.9 4.7 - - + -
80A LEU* 4.4 21.1 - - + -
83A ALA* 3.5 31.6 - - + -
87A GLU* 3.5 17.5 - - - +
69B GLU 4.7 0.4 - - - +
70B GLY* 3.4 10.2 + - - +
71B ASP* 1.3 69.1 + - - +
73B ALA* 1.3 60.4 + - - +
75B GLN* 4.3 3.8 - - + -
76B ILE* 2.8 51.8 + - + +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 5.2 5.6 - - - +
71B ASP* 3.3 8.2 + - - +
72B ILE* 1.3 77.0 - - - +
74B LEU* 1.3 62.2 + - - +
76B ILE* 3.3 5.1 + - - +
77B HIS* 2.8 38.7 + - + +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.8 22.4 - - + -
68B ASP* 3.9 30.7 - - + +
71B ASP* 3.1 27.7 + - - +
73B ALA* 1.3 77.9 - - - +
75B GLN* 1.3 59.5 + - - +
77B HIS* 3.2 6.2 + - - +
78B PHE* 2.8 73.2 + - + -
118B HIS* 3.9 21.1 - - + +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR* 3.8 18.5 - - + +
82A GLN* 5.0 10.4 + - - -
83A ALA* 5.6 2.5 - - + -
64B ALA* 4.9 3.8 - - - +
65B GLY 5.7 0.2 + - - -
68B ASP* 2.9 25.7 + - - +
69B GLU* 3.6 25.7 - - - +
71B ASP 2.8 20.7 + - - +
72B ILE* 3.9 6.7 - - + +
74B LEU* 1.3 78.2 - - + +
76B ILE* 1.3 60.7 + - - +
78B PHE* 3.1 27.4 + - - +
79B THR* 2.8 32.4 + - - -
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 3.4 39.7 - - + +
79A THR* 3.5 23.1 - - + -
80A LEU* 5.4 4.3 - - + -
72B ILE* 2.8 35.8 + - + +
73B ALA* 3.7 6.5 - - - +
75B GLN* 1.3 72.0 - - - +
77B HIS* 1.3 63.6 + - + +
79B THR* 3.2 5.5 + - - -
80B LEU* 2.9 39.7 + - + +
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Residues in contact with HIS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.3 31.3 - - + +
44B TYR* 3.5 38.6 + + - -
47B ALA* 5.5 8.5 - - + -
73B ALA* 2.8 32.1 + - + -
74B LEU* 3.5 8.1 + - - +
76B ILE* 1.3 78.5 - - + +
78B PHE* 1.3 59.6 + - - +
80B LEU* 3.8 16.1 - - + +
81B ILE* 2.8 38.6 + - + +
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Residues in contact with PHE 78 (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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43B VAL* 4.4 3.6 - - + -
62B LEU* 3.7 33.8 - - + +
63B ALA 3.2 26.2 - - - -
64B ALA* 3.3 19.3 - - + -
74B LEU* 2.8 54.4 + - + -
75B GLN* 3.4 29.2 - - - +
77B HIS* 1.3 72.6 - - - +
79B THR* 1.3 58.3 + - - +
81B ILE* 3.8 6.0 - - + +
82B GLN* 2.9 35.8 + - - +
118B HIS* 3.2 24.0 - - + -
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Residues in contact with THR 79 (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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72A ILE* 5.0 0.7 - - + +
75A GLN* 3.5 34.9 - - + +
76A ILE* 3.9 13.0 - - + -
79A THR* 2.2 34.0 + - - +
75B GLN 2.8 11.8 + - - -
76B ILE* 3.3 11.2 - - - -
78B PHE* 1.3 77.6 - - - +
80B LEU* 1.3 64.9 + - + +
82B GLN* 3.9 6.0 - - - +
83B ALA* 3.0 24.5 + - + +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.6 35.7 - - + -
76A ILE* 4.3 11.2 - - + -
76B ILE* 2.9 36.0 + - + +
77B HIS* 3.2 15.7 + - + +
79B THR* 1.3 74.7 - - + +
81B ILE* 1.3 63.7 + - + +
83B ALA* 4.0 3.0 - - + +
84B PHE* 3.2 23.4 + - - +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 3.8 33.2 - - + +
46B SER* 5.2 0.4 - - - -
47B ALA* 5.0 11.7 - - + +
50B LEU* 4.2 24.0 - - + -
60B CYS* 3.9 18.4 - - - -
62B LEU* 3.8 25.8 - - + -
77B HIS* 2.8 23.5 + - + +
78B PHE* 3.8 4.0 - - + +
80B LEU* 1.3 77.4 - - + +
82B GLN* 1.3 62.8 + - - +
84B PHE* 3.2 4.3 + - - +
85B CYS* 3.0 23.5 + - - -
92B ILE* 4.3 2.5 - - + -
119B CYS* 4.1 20.6 - - + -
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 3.2 17.3 + - - +
75A GLN* 4.8 5.1 + - - -
94A ARG* 4.5 16.4 - - - +
62B LEU* 4.4 10.0 - - + +
78B PHE* 2.9 19.7 + - - +
79B THR* 3.9 5.1 - - - +
81B ILE* 1.3 78.4 - - - +
83B ALA* 1.3 62.5 + - - +
85B CYS* 3.4 2.1 + - - +
86B CYS* 3.1 26.4 + - - -
92B ILE* 3.7 20.6 - - + -
94B ARG* 5.1 5.0 - - - +
152B VAL* 3.1 44.5 - - + +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU 3.3 25.8 - - - +
70A GLY* 4.6 5.2 - - - -
72A ILE* 4.7 19.3 - - + -
75A GLN* 4.7 10.5 - - + -
79B THR* 3.0 19.2 + - + +
80B LEU* 4.0 5.4 - - - +
81B ILE 3.4 0.2 - - - -
82B GLN* 1.3 76.8 - - - +
84B PHE* 1.3 57.7 + - - +
86B CYS* 3.7 1.6 + - - +
87B GLU* 3.0 32.7 + - - +
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Residues in contact with PHE 84 (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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50B LEU* 3.3 69.1 - - + -
51B ASN* 5.6 2.9 - - - -
54B PRO* 3.4 22.4 - - + -
80B LEU 3.2 13.7 + - - +
81B ILE 3.4 8.1 - - - +
83B ALA* 1.3 76.6 - - - +
85B CYS* 1.3 56.5 + - - +
87B GLU* 3.1 3.9 + - + -
88B ASN* 2.7 69.2 + - + +
90B ILE* 4.8 1.8 - - + -
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Residues in contact with CYS 85 (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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50B LEU* 4.6 16.2 - - - -
60B CYS* 3.9 22.0 - - - -
81B ILE* 3.0 19.4 + - - +
82B GLN 3.8 4.0 - - - +
84B PHE* 1.3 78.9 - - - +
86B CYS* 1.3 52.8 + - - +
88B ASN 3.2 0.2 + - - -
89B ASP* 2.7 31.4 + - - -
90B ILE* 2.8 44.8 + - + +
92B ILE* 3.9 24.0 - - + -
121B LEU* 5.2 0.2 - - - -
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Residues in contact with CYS 86 (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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66A GLU* 5.5 1.1 - - + +
69A GLU* 3.7 43.1 - - + -
70A GLY 5.0 0.7 - - - +
82B GLN* 3.1 22.4 + - - +
83B ALA 3.9 3.6 - - - +
85B CYS* 1.3 76.3 - - - +
87B GLU* 1.3 68.4 + - - +
88B ASN 3.4 0.2 + - - -
89B ASP* 3.5 13.1 + - - +
90B ILE 4.9 1.1 - - - -
92B ILE* 4.4 17.7 - - - -
151B TRP* 4.8 7.9 - - - -
152B VAL* 4.6 5.2 - - - -
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Residues in contact with GLU 87 (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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67A GLU 4.9 2.3 - - - +
70A GLY* 3.7 30.0 + - - +
83B ALA 3.0 19.5 + - - +
84B PHE* 3.3 5.2 - - + +
86B CYS* 1.3 77.9 - - - +
88B ASN* 1.3 78.1 + - - +
89B ASP* 3.6 8.8 + - - +
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Residues in contact with ASN 88 (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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54B PRO* 5.1 6.2 - - + +
84B PHE* 2.7 60.6 + - + +
85B CYS 3.3 0.2 - - - -
87B GLU* 1.3 89.4 - - - +
89B ASP* 1.3 71.6 + - - +
90B ILE* 3.1 24.4 - - + +
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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