Contacts of the helix formed by residues 20 - 33 (chain A) in PDB entry 1W8I
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 HIS 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY* 4.6 1.1 - - - -
18A ASP* 3.0 16.6 + - - +
19A VAL* 1.3 98.6 - - + +
21A HIS* 1.3 64.2 + - - +
22A MSE 3.4 2.2 - - - -
23A ASP* 2.8 29.0 + - - +
24A SER* 2.8 24.6 + - - +
120A TYR* 3.5 57.7 + + + +
131A ARG* 4.8 13.2 - - + -
132A ASP 5.4 0.9 - - - -
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Residues in contact with HIS 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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12A GLY* 2.8 25.6 + - - -
13A PHE 3.0 21.3 + - - -
15A SER 3.4 11.4 + - - +
16A LEU* 3.6 32.6 - - + +
18A ASP* 3.0 18.6 + - - +
19A VAL 3.4 1.6 + - - -
20A HIS* 1.3 78.3 - - - +
22A MSE 1.3 75.6 + - + +
24A SER* 3.2 2.3 + - - -
25A VAL* 2.9 41.1 + - + +
149A LEU* 4.6 4.4 - - - +
155A ASP* 3.3 23.1 + - - -
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Residues in contact with MSE 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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19A VAL 5.1 1.2 + - - -
21A HIS* 1.3 90.2 - - + +
23A ASP* 1.3 66.3 + - - +
25A VAL* 3.8 15.7 - - + +
26A ALA* 3.0 26.5 + - - +
134A TRP* 3.6 64.2 - - + +
145A ILE* 4.5 2.9 - - + -
146A SER* 4.3 8.1 - - - +
149A LEU* 3.7 32.5 - - + -
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Residues in contact with ASP 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 VAL 4.4 3.4 - - - +
20A HIS* 2.8 40.0 + - - +
22A MSE 1.3 77.9 - - - +
24A SER* 1.3 56.7 + - - +
26A ALA* 3.4 2.3 + - - +
27A ILE* 2.9 33.4 + - - +
120A TYR* 3.2 19.1 - - + +
130A GLY 4.2 5.3 - - - +
132A ASP* 4.1 6.8 + - - -
133A TYR* 3.4 12.7 + - + -
134A TRP* 3.0 34.8 + - - +
135A LYS* 4.7 0.7 + - - +
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Residues in contact with SER 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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9A ILE* 2.7 23.7 + - - -
12A GLY* 3.3 15.7 - - - -
13A PHE* 3.2 29.2 - - - -
20A HIS 2.8 9.8 + - - -
21A HIS 3.5 2.5 - - - -
23A ASP* 1.3 69.7 - - - +
25A VAL* 1.3 59.9 + - - +
27A ILE* 4.4 3.8 - - - +
28A VAL* 2.8 35.7 + - - +
120A TYR* 2.7 22.7 + - - -
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Residues in contact with VAL 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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13A PHE* 3.9 12.1 - - + -
21A HIS* 2.9 46.9 + - + +
22A MSE 3.4 17.0 + - + +
24A SER* 1.3 75.2 - - - +
26A ALA* 1.3 57.3 + - - +
28A VAL* 3.3 1.6 + - - +
29A VAL* 2.9 34.8 + - - +
145A ILE* 3.7 20.9 - - + -
149A LEU* 4.1 24.0 - - + -
154A ILE* 4.2 13.7 - - + -
155A ASP* 4.1 11.2 - - - +
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Residues in contact with ALA 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 MSE 3.0 17.0 + - - +
23A ASP* 3.7 4.0 - - - +
25A VAL* 1.3 78.1 - - - +
27A ILE* 1.3 62.0 + - - +
29A VAL* 3.9 1.4 - - - +
30A HIS* 3.0 29.3 + - - -
133A TYR* 3.8 18.6 - - + -
134A TRP* 3.7 20.9 - - + -
137A LEU* 3.9 11.7 - - + -
145A ILE* 4.0 15.5 - - + +
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Residues in contact with ILE 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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5A ILE* 5.6 2.0 - - + -
9A ILE* 3.9 20.4 - - + -
23A ASP 2.9 22.0 + - - +
24A SER* 3.9 4.7 - - - +
26A ALA* 1.3 75.0 - - - +
28A VAL* 1.3 60.1 + - + +
30A HIS 3.4 0.2 + - - -
31A ALA* 2.8 31.4 + - + +
36A TRP* 3.5 17.0 - - + -
118A ILE* 3.8 24.7 - - + -
120A TYR* 3.6 20.4 - - + +
129A ILE* 5.4 0.4 - - + -
130A GLY* 3.8 28.5 - - - +
133A TYR* 3.7 28.5 - - + -
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Residues in contact with VAL 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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5A ILE* 6.6 0.4 - - + -
9A ILE* 4.5 15.5 - - + -
10A PHE* 5.2 4.7 - - + -
13A PHE* 3.6 39.9 - - + -
24A SER 2.8 24.5 + - - +
25A VAL 3.8 2.9 - - - +
27A ILE* 1.3 74.3 - - + +
29A VAL* 1.3 63.9 + - + +
31A ALA* 3.6 5.3 - - - +
32A VAL* 2.9 34.2 + - + +
67A PHE* 3.8 32.1 - - + -
154A ILE* 5.4 2.2 - - + -
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Residues in contact with VAL 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 VAL 2.9 22.4 + - - +
26A ALA 3.9 3.6 - - - +
28A VAL* 1.3 77.6 - - + +
30A HIS* 1.3 57.4 + - - +
32A VAL* 3.4 9.3 - - + +
33A GLU* 3.0 58.9 + - + +
144A ARG* 4.4 1.8 - - - +
145A ILE* 4.3 24.2 - - + -
148A ILE* 4.2 24.5 - - + -
154A ILE* 3.8 26.9 - - + -
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Residues in contact with HIS 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 ALA 3.0 14.0 + - - +
29A VAL* 1.3 75.3 - - - +
31A ALA* 1.3 61.7 + - - +
33A GLU* 3.3 16.2 + - - +
34A GLY 3.1 5.7 + - - -
35A LYS* 3.0 45.2 + - + +
36A TRP* 3.8 14.6 - - + -
133A TYR* 2.8 35.2 - + - -
137A LEU* 3.8 19.2 - - - +
141A GLU* 2.8 30.9 + - - +
144A ARG* 3.9 3.5 + - - -
145A ILE* 3.7 17.0 - - + +
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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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5A ILE* 4.6 10.1 - - + -
27A ILE* 2.8 23.9 + - + +
28A VAL* 3.6 7.9 - - - +
30A HIS* 1.3 73.2 - - - +
32A VAL* 1.3 58.9 + - + +
34A GLY* 2.9 20.8 + - - -
35A LYS 4.7 1.1 - - - +
36A TRP* 3.7 17.2 + - + -
37A GLY 4.6 0.9 - - - +
39A LEU* 3.9 39.9 - - + +
118A ILE* 5.5 0.2 - - + -
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Residues in contact with VAL 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 VAL* 2.9 30.9 + - + +
29A VAL* 3.4 19.5 - - + +
31A ALA* 1.3 77.1 - - + +
33A GLU* 1.3 64.2 + - + +
34A GLY* 3.1 1.5 + - - -
39A LEU* 4.7 3.6 - - + -
67A PHE* 4.9 5.8 - - + -
72A VAL* 4.2 29.4 - - + -
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Residues in contact with GLU 33 (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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29A VAL* 3.0 34.2 + - + +
30A HIS* 3.6 16.6 + - - +
31A ALA 3.1 0.4 - - - -
32A VAL* 1.3 80.1 - - + +
34A GLY* 1.3 58.6 + - - +
35A LYS* 3.6 0.9 - - + +
144A ARG* 3.0 40.3 + - - -
148A ILE* 4.4 3.3 - - - +
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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