Contacts of the helix formed by residues 18 - 32 (chain A) in PDB entry 1WH6
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL* 1.3 76.4 - - - +
19A THR* 1.3 58.0 + - - +
20A LEU* 3.1 5.5 + - + +
21A GLU* 4.1 19.1 - - + +
22A LEU* 2.9 28.6 + - - +
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Residues in contact with THR 19 (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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17A VAL* 3.5 6.3 + - + -
18A ASP* 1.3 72.1 - - - +
20A LEU* 1.3 64.0 + - - +
22A LEU* 3.7 8.0 - - + +
23A THR* 2.8 33.8 + - - +
59A PRO* 4.0 1.9 - - - +
60A LYS 2.8 27.9 + - - +
61A PRO* 3.5 11.3 - - - +
62A TRP* 3.8 40.7 + - + +
65A LEU* 4.1 2.0 - - + -
73A PHE* 3.9 23.8 - - + -
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Residues in contact with LEU 20 (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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18A ASP* 3.1 4.1 + - + +
19A THR* 1.3 84.8 - - - +
21A GLU* 1.3 61.5 + - - +
23A THR* 3.0 15.0 + - - +
24A ARG* 3.3 29.6 + - - +
27A LYS* 5.0 3.7 + - - +
57A SER 5.3 3.1 - - - +
59A PRO* 3.8 41.1 - - + +
60A LYS 5.1 2.7 - - - +
61A PRO* 5.4 2.7 - - + -
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Residues in contact with GLU 21 (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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18A ASP* 3.1 21.0 + - + +
20A LEU* 1.3 74.3 - - - +
22A LEU* 1.3 60.4 + - - +
24A ARG* 3.2 49.7 + - - +
25A GLN* 2.8 61.0 + - + +
28A GLU* 4.8 2.8 - - - +
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Residues in contact with LEU 22 (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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17A VAL* 4.3 9.9 - - + -
18A ASP 2.9 17.6 + - - +
19A THR* 3.7 9.2 - - + +
21A GLU* 1.3 77.4 - - - +
23A THR* 1.3 62.9 + - - +
25A GLN* 3.2 6.2 + - - +
26A VAL* 3.0 28.7 + - + +
73A PHE* 3.6 35.4 - - + +
76A MET* 4.1 11.0 - - + -
77A GLN* 3.5 48.2 - - + +
80A LEU* 3.6 23.1 - - + -
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Residues in contact with THR 23 (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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19A THR 2.8 19.2 + - - +
20A LEU* 3.0 15.9 + - - +
22A LEU* 1.3 74.5 - - + +
24A ARG* 1.3 51.2 + - - +
26A VAL* 3.4 2.0 + - - +
27A LYS* 2.8 55.5 + - - +
55A MET 4.3 0.2 - - - +
56A LEU* 3.8 17.7 - - + -
59A PRO* 3.6 19.6 - - + +
73A PHE* 4.0 13.9 - - + -
76A MET* 3.7 26.9 - - + -
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Residues in contact with ARG 24 (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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20A LEU* 3.3 24.0 + - - +
21A GLU* 3.2 38.7 + - - +
22A LEU 3.2 0.2 - - - -
23A THR* 1.3 76.5 + - - +
25A GLN* 1.3 65.7 + - - +
27A LYS* 3.1 20.3 + - - +
28A GLU* 2.9 38.1 + - - +
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Residues in contact with GLN 25 (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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21A GLU* 2.8 43.7 + - + +
22A LEU* 3.5 7.9 - - - +
24A ARG* 1.3 70.6 - - - +
26A VAL* 1.3 56.5 + - - +
28A GLU* 3.4 13.2 + - - +
29A LYS* 2.9 31.2 + - - +
80A LEU* 3.7 31.7 - - + +
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Residues in contact with VAL 26 (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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22A LEU* 3.0 23.0 + - + +
23A THR 3.5 5.4 - - - +
25A GLN* 1.3 74.6 - - - +
27A LYS* 1.3 62.9 + - - +
29A LYS* 3.2 2.8 + - - +
30A LEU* 2.9 48.2 + - + +
40A PHE* 3.7 23.1 - - + -
56A LEU* 4.5 4.5 - - + -
76A MET* 3.6 35.4 - - + +
79A TRP* 4.2 10.8 - - + -
80A LEU* 3.7 21.1 - - + -
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Residues in contact with LYS 27 (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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20A LEU* 5.0 3.8 + - - +
23A THR* 2.8 44.7 + - - +
24A ARG* 3.1 20.5 + - - +
26A VAL* 1.3 70.8 - - - +
28A GLU* 1.3 58.5 + - + +
30A LEU* 3.7 9.3 - - - +
31A ALA* 2.9 31.7 + - - +
37A GLN* 4.7 16.6 - - - +
56A LEU* 2.9 52.3 + - + +
57A SER* 5.0 2.8 + - - +
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Residues in contact with GLU 28 (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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21A GLU* 4.8 2.6 - - - +
24A ARG* 2.9 36.8 + - - +
25A GLN* 3.6 13.1 + - - +
27A LYS* 1.3 74.1 - - + +
29A LYS* 1.3 60.6 + - - +
31A ALA* 3.1 6.6 + - - +
32A LYS* 2.8 40.6 + - + +
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Residues in contact with LYS 29 (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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25A GLN 2.9 21.3 + - - +
26A VAL 3.8 2.9 - - - +
28A GLU* 1.3 73.5 - - - +
30A LEU* 1.3 60.9 + - - +
32A LYS* 3.8 9.0 - - + +
33A ASN* 3.7 22.1 + - - +
35A ILE* 4.8 0.3 - - - +
79A TRP* 3.8 25.7 - - + -
80A LEU* 3.3 42.0 - - + +
83A GLN* 4.6 19.2 + - - -
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Residues in contact with LEU 30 (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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26A VAL* 2.9 40.7 + - + +
27A LYS* 3.7 4.0 - - - +
29A LYS* 1.3 74.3 - - - +
31A ALA* 1.3 63.6 + - - +
33A ASN* 3.1 9.5 + - - +
35A ILE* 3.0 63.0 + - + +
37A GLN* 3.6 22.9 - - + -
40A PHE* 3.6 29.4 - - + -
56A LEU* 4.8 0.7 - - + -
79A TRP* 3.4 29.6 - - + -
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Residues in contact with ALA 31 (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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27A LYS 2.9 20.5 + - - +
28A GLU* 3.6 5.8 - - - +
30A LEU* 1.3 74.9 - - - +
32A LYS* 1.3 58.3 + - + +
33A ASN 3.0 5.4 + - - -
34A GLY* 3.0 14.9 + - - +
35A ILE 4.6 2.4 + - - +
37A GLN* 5.7 4.4 + - - +
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Residues in contact with LYS 32 (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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28A GLU* 2.8 30.2 + - + +
29A LYS* 3.8 11.0 - - + +
30A LEU 3.3 0.2 - - - -
31A ALA* 1.3 69.1 - - + +
33A ASN* 1.3 66.4 + - - +
34A GLY 3.7 0.2 - - - -
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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