Contacts of the helix formed by residues 65 - 81 (chain A) in PDB entry 1WMA
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 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ASP* 3.1 21.5 + - + +
64A ASP* 1.3 78.4 - - - +
66A LEU* 1.3 65.4 + - - +
67A GLN* 2.9 24.8 + - - +
68A SER* 3.0 28.7 + - - -
69A ILE* 3.1 12.0 + - - +
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Residues in contact with LEU 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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64A ASP 4.0 2.9 + - - +
65A ASP* 1.3 73.2 + - - +
67A GLN* 1.4 59.7 + - + +
69A ILE* 3.3 10.4 + - + +
70A ARG* 2.9 66.5 + - - +
119A ASP* 3.3 44.9 - - + +
123A GLU* 5.2 5.2 - - + +
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Residues in contact with GLN 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 ASP* 2.9 13.3 + - - +
66A LEU* 1.4 76.2 - - + +
68A SER* 1.3 61.0 + - - +
70A ARG* 3.4 10.0 + - - +
71A ALA* 3.0 29.5 + - - +
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Residues in contact with SER 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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59A HIS* 5.3 0.3 - - - -
60A GLN* 2.7 32.5 + - - +
61A LEU* 3.3 5.4 - - - +
62A ASP* 2.9 26.5 + - - -
65A ASP* 3.0 26.2 + - - -
67A GLN* 1.3 75.8 - - - +
69A ILE* 1.3 65.7 + - - +
71A ALA* 3.3 6.3 + - - +
72A LEU* 3.1 21.8 + - - +
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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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61A LEU* 3.7 20.9 - - + -
62A ASP 4.0 4.0 - - - +
63A ILE* 3.5 23.6 - - - +
65A ASP 3.1 13.0 + - - +
66A LEU* 3.3 14.1 + - + +
68A SER* 1.3 75.1 - - - +
70A ARG* 1.3 58.6 + - - +
72A LEU* 3.1 4.9 + - + +
73A ARG* 2.9 26.0 + - - +
119A ASP* 3.6 29.6 - - + +
120A VAL* 3.9 21.8 - - + +
123A GLU* 3.7 31.2 - - + -
124A LEU* 4.8 6.8 - - + +
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Residues in contact with ARG 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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66A LEU* 2.9 51.0 + - + +
67A GLN* 4.0 8.8 - - - +
68A SER 3.3 0.2 - - - -
69A ILE* 1.3 75.5 - - - +
71A ALA* 1.3 62.2 + - - +
73A ARG* 3.3 35.1 + - - +
74A ASP* 2.9 30.1 + - - +
123A GLU* 3.0 29.5 + - + +
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Residues in contact with ALA 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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59A HIS* 4.3 11.8 + - + -
67A GLN 3.0 17.6 + - - +
68A SER* 3.8 7.2 - - - +
70A ARG* 1.3 75.7 - - - +
72A LEU* 1.3 57.7 + - - +
74A ASP* 3.3 9.3 + - - +
75A PHE* 3.0 27.5 + - - +
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Residues in contact with LEU 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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8A LEU* 3.8 32.3 - - + -
35A THR* 4.6 0.9 - - + -
59A HIS* 3.8 37.4 - - + +
60A GLN 4.6 0.2 - - - +
61A LEU* 3.8 37.9 - - + -
68A SER 3.1 13.1 + - - +
69A ILE 3.5 7.9 - - - +
71A ALA* 1.3 74.3 - - - +
73A ARG* 1.3 65.8 + - - +
75A PHE* 3.1 12.9 + - + +
76A LEU* 2.9 30.3 + - + +
124A LEU* 4.1 17.0 - - + -
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Residues in contact with ARG 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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69A ILE 2.9 12.5 + - - +
70A ARG* 3.4 31.1 + - - +
72A LEU* 1.3 76.5 - - - +
74A ASP* 1.3 92.0 + - - +
76A LEU* 3.3 2.8 + - - +
77A ARG* 2.9 44.1 + - - +
123A GLU* 2.8 59.7 + - + +
124A LEU* 3.7 17.9 - - + +
127A LEU* 3.8 15.3 - - + +
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Residues in contact with ASP 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 ARG* 2.9 19.7 + - - +
71A ALA* 3.7 7.7 - - - +
73A ARG* 1.3 97.3 + - - +
75A PHE* 1.3 58.2 + - - +
77A ARG* 2.8 40.7 + - - +
78A LYS* 3.0 30.9 + - - +
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Residues in contact with PHE 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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33A VAL* 4.8 9.4 - - + -
57A ARG* 3.8 31.6 - - + -
58A PHE 5.2 4.5 - - - -
59A HIS* 3.5 41.5 - + + +
71A ALA 3.0 13.9 + - - +
72A LEU* 3.1 16.4 + - + +
74A ASP* 1.3 77.6 - - - +
76A LEU* 1.4 67.6 + - + +
78A LYS* 3.3 4.6 + - - +
79A GLU* 2.8 70.9 + - + +
80A TYR* 4.2 15.5 - + - -
300A SO4 5.4 0.2 - - - -
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Residues in contact with LEU 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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6A VAL* 4.6 5.8 - - + -
8A LEU* 4.2 17.3 - - + -
33A VAL* 5.0 0.7 - - + -
72A LEU* 2.9 32.9 + - + +
73A ARG 3.3 3.1 + - - +
75A PHE* 1.4 87.6 - - + +
77A ARG* 1.3 68.6 + - - +
80A TYR* 2.9 40.3 + - + +
81A GLY 3.0 5.9 + - - -
82A GLY 3.4 19.0 + - - +
83A LEU* 4.2 29.2 - - + -
124A LEU* 4.1 23.8 - - + -
127A LEU* 3.9 7.4 - - + -
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Residues in contact with ARG 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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73A ARG* 2.9 38.0 + - - +
74A ASP* 2.8 39.8 + - - +
76A LEU* 1.3 78.3 - - - +
78A LYS* 1.3 59.0 + - - +
81A GLY* 3.0 25.2 + - - -
82A GLY 4.1 8.1 - - - +
127A LEU* 4.0 21.5 - - + +
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Residues in contact with LYS 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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74A ASP 3.0 18.6 + - - +
75A PHE* 3.8 5.2 - - - +
77A ARG* 1.3 79.1 - - - +
79A GLU* 1.3 74.3 + - + +
81A GLY 4.8 0.3 + - - -
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Residues in contact with GLU 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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4A ILE* 5.6 1.7 - - - +
57A ARG* 3.0 30.2 + - - +
75A PHE* 2.8 49.1 + - + +
78A LYS* 1.3 87.4 - - + +
80A TYR* 1.3 79.5 + - + +
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Residues in contact with TYR 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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3A GLY* 6.1 0.2 - - - -
4A ILE* 3.8 33.9 - - + +
6A VAL* 3.7 41.6 - - + +
31A ASP* 2.6 33.5 + - + +
33A VAL* 4.6 1.6 - - + +
57A ARG* 2.9 35.9 + - - -
75A PHE* 4.2 12.6 - + - -
76A LEU* 2.9 17.8 + - + +
79A GLU* 1.3 90.0 - - + +
81A GLY* 1.3 60.8 + - - +
82A GLY 3.5 16.6 - - - +
129A LYS* 2.8 26.9 + - - +
306A SO4 4.8 1.4 + - - -
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Residues in contact with GLY 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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76A LEU 3.0 0.4 + - - -
77A ARG* 3.0 25.6 + - - -
78A LYS 4.8 0.4 + - - -
79A GLU 3.9 0.2 - - - -
80A TYR* 1.3 77.0 - - - +
82A GLY* 1.3 54.9 + - - +
127A LEU 4.9 0.3 - - - +
129A LYS* 3.6 11.9 - - - +
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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