Contacts of the helix formed by residues 54 - 71 (chain A) in PDB entry 2WJZ
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 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 4.0 9.5 - - - +
14A ASP* 5.9 0.2 - - - +
52A ILE 3.4 5.0 + - - -
53A THR* 1.3 73.8 - - + +
55A SER* 1.3 54.3 - - - +
56A VAL* 2.5 34.3 + - + +
57A GLU* 3.0 12.6 + - - +
58A LYS 3.4 0.9 + - - -
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Residues in contact with SER 55 (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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53A THR 2.9 9.6 + - - -
54A ALA* 1.3 65.2 - - - +
56A VAL* 1.3 70.3 + - - +
57A GLU 3.1 1.2 + - - -
58A LYS* 3.3 13.0 + - - +
59A ARG* 4.3 6.1 + - - +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 2.5 27.7 + - + +
55A SER* 1.3 75.4 + - - +
57A GLU* 1.3 69.8 + - + +
59A ARG* 5.2 0.7 + - - +
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 5.0 3.4 - - - +
53A THR* 3.9 10.3 - - + -
54A ALA 3.0 3.1 + - - +
56A VAL* 1.3 90.2 - - + +
58A LYS* 1.3 67.1 + - - +
59A ARG 3.2 2.0 - - - -
60A LYS* 2.9 16.9 + - - -
61A THR* 2.9 24.0 + - - +
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Residues in contact with LYS 58 (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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51A ASP* 4.4 2.5 - - - -
53A THR* 3.7 30.4 - - - +
54A ALA 3.4 4.8 + - - -
55A SER* 3.3 10.1 + - - +
57A GLU* 1.3 76.8 - - - +
59A ARG* 1.3 56.8 + - - +
61A THR* 4.1 0.4 - - - -
62A MET* 3.0 40.8 + - - +
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Residues in contact with ARG 59 (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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55A SER* 4.3 6.3 + - - +
56A VAL 5.9 0.4 - - - +
57A GLU 2.9 3.6 + - - -
58A LYS* 1.3 74.6 - - - +
60A LYS* 1.3 62.0 + - - +
62A MET* 4.4 4.5 - - - +
63A LEU* 3.6 31.8 + - - +
85A ASP* 4.5 5.3 + - - -
87A GLU* 4.3 4.2 - - - +
88A THR* 3.5 43.2 + - + +
91A GLU* 2.9 36.5 + - - +
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Residues in contact with LYS 60 (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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57A GLU 2.9 7.0 + - - -
59A ARG* 1.3 78.0 - - - +
61A THR* 1.3 59.8 + - - +
63A LEU* 3.4 9.3 + - - +
64A GLU* 3.0 28.4 + - - +
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Residues in contact with THR 61 (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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14A ASP* 3.3 42.4 + - - +
15A GLY* 3.8 4.6 - - - +
51A ASP* 4.3 4.7 - - - +
53A THR* 3.7 14.1 - - - +
57A GLU* 2.9 29.8 + - - +
58A LYS 3.3 8.0 + - - -
60A LYS* 1.3 77.6 - - - +
62A MET* 1.3 56.6 + - - +
64A GLU* 3.2 16.8 + - - +
65A LEU* 2.9 26.3 + - + +
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Residues in contact with MET 62 (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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51A ASP* 3.3 38.4 - - + +
58A LYS 3.0 19.0 + - - +
59A ARG* 4.4 4.3 - - - +
61A THR* 1.3 73.3 - - - +
63A LEU* 1.3 60.4 + - - +
65A LEU* 3.3 10.4 + - + +
66A VAL* 2.8 35.1 + - + +
79A VAL* 4.8 5.6 - - + -
80A GLY 4.2 13.7 - - - +
81A GLY 3.3 26.5 - - - +
82A GLY 5.3 2.9 - - - +
83A ILE* 3.8 14.6 - - + -
88A THR* 5.5 2.5 - - + -
92A LEU* 3.6 34.3 - - + -
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Residues in contact with LEU 63 (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 ARG* 3.6 20.1 + - - +
60A LYS* 3.4 10.0 + - - +
61A THR 3.4 0.2 - - - -
62A MET* 1.3 74.5 - - - +
64A GLU* 1.3 64.5 + - - +
66A VAL* 4.4 1.3 - - - +
67A GLU* 3.1 26.6 + - - +
91A GLU* 3.3 58.8 - - + +
92A LEU* 3.6 19.5 - - + -
95A ARG* 3.7 41.6 + - + +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP 4.7 4.8 - - - +
15A GLY* 6.2 1.8 - - - -
60A LYS 3.0 13.1 + - - +
61A THR* 3.2 24.3 + - - +
62A MET 3.2 0.2 - - - -
63A LEU* 1.3 78.5 - - - +
65A LEU* 1.3 63.1 + - - +
67A GLU* 3.3 5.7 + - - +
68A LYS* 3.1 31.9 + - + +
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Residues in contact with LEU 65 (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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12A VAL* 3.6 29.2 - - + -
15A GLY* 5.2 9.9 - - - -
32A PRO* 4.0 31.2 - - + -
33A VAL* 4.8 2.2 - - + -
49A PHE* 3.9 23.8 - - + -
51A ASP* 5.3 4.7 - - + +
61A THR* 2.9 15.3 + - + +
62A MET* 3.5 11.4 - - + +
64A GLU* 1.3 77.9 - - - +
66A VAL* 1.3 57.7 + - - +
68A LYS* 3.3 3.9 + - - +
69A VAL* 2.9 51.5 + - + +
77A PHE* 6.5 0.2 - - + -
79A VAL* 4.4 12.6 - - + -
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Residues in contact with VAL 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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62A MET 2.8 24.3 + - - +
63A LEU 4.0 3.6 - - - +
65A LEU* 1.3 73.4 - - - +
67A GLU* 1.3 57.8 + - - +
69A VAL* 3.9 4.6 - - - +
70A ALA* 3.0 28.8 + - - +
77A PHE* 4.1 4.8 - - + -
79A VAL* 3.5 35.2 - - + -
92A LEU* 3.5 26.0 - - + +
95A ARG* 3.6 15.7 - - + +
96A GLY 3.9 0.4 - - - -
97A ALA* 3.4 30.7 - - + +
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Residues in contact with GLU 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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63A LEU 3.1 18.4 + - - +
64A GLU* 3.8 6.4 - - - +
65A LEU 3.3 0.2 - - - -
66A VAL* 1.3 77.8 - - - +
68A LYS* 1.3 63.5 + - + +
70A ALA* 4.3 1.2 - - - +
71A GLU* 3.4 25.5 + - - +
95A ARG* 3.8 42.0 + - + +
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Residues in contact with LYS 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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33A VAL* 3.6 28.9 - - + +
64A GLU* 3.1 25.6 + - + +
65A LEU* 3.8 4.5 - - - +
67A GLU* 1.3 80.0 - - + +
69A VAL* 1.3 61.7 + - - +
71A GLU* 3.7 24.2 + - - +
72A GLN* 3.7 5.9 + - - +
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Residues in contact with VAL 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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33A VAL* 3.7 24.9 - - + -
49A PHE* 3.8 23.8 - - + -
65A LEU* 2.9 37.6 + - + +
66A VAL* 3.9 3.1 - - - +
68A LYS* 1.3 74.0 - - - +
70A ALA* 1.3 62.3 + - - +
71A GLU 3.1 1.8 - - - -
72A GLN 3.0 2.1 + - - -
73A ILE* 2.9 57.7 + - + +
77A PHE* 3.6 26.9 - - + -
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Residues in contact with ALA 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 VAL 3.0 18.4 + - - +
67A GLU 4.3 2.7 - - - +
69A VAL* 1.3 76.9 - - - +
71A GLU* 1.3 60.0 + - - +
72A GLN 3.3 0.7 + - - -
73A ILE* 3.9 18.2 - - - +
77A PHE* 4.0 3.6 - - + -
95A ARG 4.2 3.6 - - - +
96A GLY* 3.8 32.8 - - - +
15B ASN* 3.3 25.3 - - - +
18B ARG* 3.8 13.3 + - - +
22B ARG* 5.0 1.6 + - - -
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Residues in contact with GLU 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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67A GLU* 3.4 18.8 + - - +
68A LYS* 3.7 16.9 - - - +
69A VAL 3.1 0.4 - - - -
70A ALA* 1.3 80.2 - - - +
72A GLN* 1.3 73.3 + - + +
18B ARG* 3.6 29.7 - - - +
22B ARG* 4.3 7.1 + - - -
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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
------------------------------------------------------------
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