Contacts of the helix formed by residues 71 - 88 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLU* 4.0 2.0 + - - +
68A ASP* 3.1 24.5 + - - +
69A GLU 3.5 0.6 - - - -
70A GLY* 1.3 75.0 - - - +
72A ILE* 1.3 64.3 + - - +
73A ALA* 3.3 10.6 + - - +
74A LEU* 3.1 30.6 + - + +
75A GLN* 3.0 24.4 + - - +
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Residues in contact with ILE 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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70A GLY 3.5 8.8 + - - +
71A ASP* 1.3 72.4 + - - +
73A ALA* 1.3 57.2 + - - +
75A GLN* 3.3 6.2 + - - +
76A ILE* 2.8 36.7 + - + +
79B THR* 5.7 1.1 - - + -
80B LEU* 3.6 31.9 - - + -
83B ALA* 4.7 15.5 - - + -
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Residues in contact with ALA 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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71A ASP* 3.3 8.4 + - - +
72A ILE* 1.3 78.4 - - - +
74A LEU* 1.3 63.1 + - - +
76A ILE* 3.3 6.9 + - - +
77A HIS* 3.0 30.6 + - + -
1161A MLA 5.1 19.3 - - + +
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Residues in contact with LEU 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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43A VAL* 4.1 10.8 - - + -
68A ASP* 3.7 31.4 - - + +
71A ASP* 3.1 28.6 + - - +
73A ALA* 1.3 75.5 - - - +
75A GLN* 1.3 67.5 + - - +
77A HIS* 3.1 8.9 + - + +
78A PHE* 2.9 57.5 + - + -
118A HIS* 3.9 34.1 - - + +
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Residues in contact with GLN 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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64A ALA* 4.0 11.3 - - - +
68A ASP 2.7 30.5 + - - +
69A GLU* 3.7 33.8 + - - +
71A ASP 3.0 18.8 + - - +
72A ILE* 3.8 5.6 - - - +
74A LEU* 1.3 82.1 - - - +
76A ILE* 1.3 56.5 + - - +
78A PHE* 3.1 20.1 + - - +
79A THR* 2.8 30.0 + - - -
94A ARG* 3.9 13.0 + - - -
79B THR* 3.5 21.0 - - + +
82B GLN* 4.8 4.3 + - - -
83B ALA* 4.7 5.2 - - + -
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Residues in contact with ILE 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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72A ILE* 2.8 36.2 + - + +
73A ALA* 3.7 6.5 - - - +
75A GLN* 1.3 72.4 - - - +
77A HIS* 1.3 64.5 + - + +
79A THR* 3.1 5.4 + - - -
80A LEU* 3.1 32.4 + - + +
76B ILE* 3.4 41.3 - - + -
79B THR* 3.9 15.3 - - + -
80B LEU* 4.3 10.3 - - + -
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Residues in contact with HIS 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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43A VAL* 3.4 27.8 + - + +
44A TYR* 3.3 32.1 - + - -
47A ALA* 5.1 8.9 - - + +
73A ALA* 3.0 25.9 + - + +
74A LEU* 3.2 12.3 - - - +
76A ILE* 1.3 77.8 - - + +
78A PHE* 1.3 60.3 + - + +
80A LEU* 3.3 15.2 + - + +
81A ILE* 2.9 35.1 + - - +
1161A MLA 2.8 38.0 + - + -
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Residues in contact with PHE 78 (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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43A VAL* 3.9 12.8 - - + -
62A LEU* 3.8 34.3 - - + +
63A ALA 3.5 14.4 - - - -
64A ALA* 3.7 24.7 - - + -
74A LEU* 2.9 41.7 + - + +
75A GLN* 3.2 29.4 - - - +
77A HIS* 1.3 75.1 - - - +
79A THR* 1.3 66.9 + - - +
81A ILE* 4.7 1.8 - - + -
82A GLN* 2.9 29.8 + - - +
94A ARG* 4.0 20.6 - - - +
118A HIS* 3.4 26.9 - - + -
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Residues in contact with THR 79 (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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75A GLN 2.8 14.0 + - - -
76A ILE 3.1 8.9 + - - -
78A PHE* 1.3 75.6 - - - +
80A LEU* 1.3 59.7 + - - +
82A GLN* 4.0 3.8 - - - +
83A ALA* 3.0 28.9 + - + +
94A ARG* 4.8 3.6 + - - +
72B ILE* 4.9 6.7 - - + -
75B GLN* 3.8 28.3 - - + +
76B ILE* 3.5 27.8 - - + -
79B THR* 2.2 36.9 + - - +
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Residues in contact with LEU 80 (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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76A ILE* 3.1 28.1 + - + +
77A HIS* 3.6 18.8 - - + +
78A PHE 3.2 0.2 - - - -
79A THR* 1.3 76.2 - - - +
81A ILE* 1.3 67.2 + - + +
83A ALA* 3.5 4.0 + - - +
84A PHE* 3.1 24.6 + - - +
72B ILE* 4.4 23.6 - - + -
76B ILE* 5.4 3.6 - - + -
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Residues in contact with ILE 81 (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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43A VAL* 4.1 31.4 - - + +
46A SER* 5.0 0.2 - - - -
47A ALA* 4.8 11.4 - - + +
50A LEU* 3.6 27.8 - - + -
60A CYS* 4.0 26.5 - - - -
62A LEU* 4.2 12.8 - - + -
77A HIS* 2.9 25.5 + - + +
78A PHE* 4.2 2.2 - - + +
80A LEU* 1.3 76.1 - - + +
82A GLN* 1.3 57.7 + - - +
84A PHE* 3.3 6.7 + - - +
85A CYS* 2.9 29.4 + - - -
92A ILE* 4.5 0.2 - - + -
119A CYS* 4.0 22.0 - - + -
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Residues in contact with GLN 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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62A LEU* 4.1 4.3 - - + +
78A PHE 2.9 18.4 + - - +
79A THR* 4.0 4.2 - - - +
81A ILE* 1.3 75.6 - - - +
83A ALA* 1.3 65.5 + - - +
85A CYS* 3.4 1.2 + - - +
86A CYS* 2.9 37.2 + - - -
92A ILE* 3.7 26.5 - - + +
94A ARG* 2.9 40.2 + - - +
152A VAL* 3.9 30.1 - - - +
75B GLN* 5.0 10.5 + - - -
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Residues in contact with ALA 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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79A THR* 3.0 21.5 + - + +
80A LEU* 3.8 4.9 - - - +
82A GLN* 1.3 76.3 - - - +
84A PHE* 1.3 53.5 + - - +
86A CYS* 3.2 4.3 + - - +
87A GLU* 2.8 43.5 + - - +
69B GLU 3.8 17.7 - - - +
72B ILE* 3.5 32.1 - - + -
75B GLN* 5.6 2.5 - - + -
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Residues in contact with PHE 84 (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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50A LEU* 3.1 61.9 - - + -
51A ASN* 5.5 1.8 - - - -
54A PRO* 3.6 23.6 - - + -
80A LEU 3.1 18.0 + - - +
81A ILE* 3.5 5.8 - - - +
83A ALA* 1.3 76.9 - - - +
85A CYS* 1.3 58.6 + - - +
87A GLU* 3.3 10.4 + - - -
88A ASN* 2.6 62.9 + - - +
90A ILE* 4.4 4.0 - - + -
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Residues in contact with CYS 85 (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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50A LEU* 4.6 9.2 - - - -
60A CYS* 3.9 18.4 - - - -
81A ILE* 2.9 27.5 + - - +
82A GLN 3.6 4.5 - - - +
84A PHE* 1.3 77.3 - - - +
86A CYS* 1.3 57.6 + - - +
89A ASP* 2.9 9.0 + - - -
90A ILE* 2.8 64.8 + - - +
92A ILE* 3.9 25.4 - - + -
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Residues in contact with CYS 86 (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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82A GLN* 2.9 35.0 + - - +
83A ALA* 3.6 4.7 - - - +
85A CYS* 1.3 74.2 - - - +
87A GLU* 1.3 63.6 + - - +
88A ASN 3.1 0.7 + - - -
89A ASP* 3.2 18.9 + - - +
90A ILE 5.0 0.9 - - - -
92A ILE* 4.6 11.7 - - - -
151A TRP* 5.3 6.7 - - - -
69B GLU* 3.6 47.7 - - + +
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Residues in contact with GLU 87 (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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83A ALA* 2.8 22.4 + - - +
84A PHE* 4.1 10.6 - - - -
86A CYS* 1.3 76.6 - - + +
88A ASN* 1.3 70.1 + - - +
89A ASP* 3.5 7.3 + - - +
69B GLU* 6.3 0.2 - - + -
70B GLY* 3.4 33.8 - - - +
72B ILE* 3.5 19.0 - - - +
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Residues in contact with ASN 88 (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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54A PRO* 5.0 6.0 - - + +
84A PHE* 2.6 56.9 + - + +
85A CYS 3.4 0.9 - - - +
86A CYS 3.1 0.2 - - - -
87A GLU* 1.3 90.4 + - - +
89A ASP* 1.3 69.7 + - - +
90A ILE* 3.1 23.1 + - + +
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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