Contacts of the helix formed by residues 18 - 31 (chain A) in PDB entry 1W2I
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 GLY 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLY 3.7 1.6 - - - -
17A VAL* 1.3 79.1 - - - +
19A PHE* 1.3 55.8 + - - +
21A TRP* 3.6 7.3 + - - +
22A SER* 2.7 37.3 + - - -
66A PRO* 3.9 0.8 - - - +
1092A FMT 3.2 21.9 + - - -
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Residues in contact with PHE 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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10A ILE* 4.0 13.7 - - + -
14A VAL* 3.4 40.8 - - + +
16A GLY 5.8 0.2 - - - +
17A VAL* 3.4 4.6 - - + +
18A GLY* 1.3 78.1 - - - +
20A ARG* 1.3 59.4 + - + +
22A SER* 3.3 5.0 + - - -
23A MET* 2.9 56.3 + - + +
38A ASN* 5.8 0.2 - - - +
44A VAL* 4.5 13.2 - - + -
61A TRP* 3.8 12.3 - + - -
62A ALA* 3.5 23.3 - - - -
65A GLY* 3.9 14.6 - - - -
66A PRO* 3.8 10.8 - - + -
69A ALA* 3.9 8.5 - - + -
71A VAL* 3.8 20.4 - - + -
1092A FMT 3.3 3.4 + - - +
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Residues in contact with ARG 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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19A PHE* 1.3 76.4 - - + +
21A TRP* 1.3 65.4 + - - +
23A MET* 3.4 2.3 + - - +
24A GLN* 3.0 24.4 + - - +
36A VAL* 3.9 27.4 - - + +
37A ARG* 4.2 1.3 - - - +
38A ASN* 3.4 38.6 + - - +
44A VAL* 5.1 1.1 - - + -
89A ILE* 3.8 30.1 - - + +
91A GLY* 2.8 41.5 + - - -
1092A FMT 2.8 34.9 + - - +
1093A FMT 3.0 40.0 + - - -
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Residues in contact with TRP 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 GLY* 4.1 7.0 - - - +
20A ARG* 1.3 76.0 - - - +
22A SER* 1.3 59.1 + - - +
24A GLN* 3.3 20.2 + - - +
25A ARG* 3.0 45.6 + - + +
89A ILE* 3.8 23.3 - - + +
1092A FMT 3.1 34.2 + - - +
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Residues in contact with SER 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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18A GLY 2.7 23.7 + - - -
19A PHE 3.3 4.9 + - - -
21A TRP* 1.3 73.1 - - - +
23A MET* 1.3 67.7 + - - +
25A ARG* 3.2 27.5 + - - +
26A GLU* 2.9 28.3 + - - +
61A TRP* 3.4 12.0 - - - -
66A PRO* 3.4 28.8 - - - +
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Residues in contact with MET 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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8A LEU* 5.5 0.2 - - + -
10A ILE* 3.7 19.7 - - + -
19A PHE* 2.9 49.6 + - + +
20A ARG* 3.8 4.7 - - - +
22A SER* 1.3 77.1 + - - +
24A GLN* 1.3 58.1 + - - +
26A GLU* 3.3 1.4 + - - +
27A ALA* 2.8 28.6 + - - +
36A VAL* 3.7 23.6 - - + -
46A ALA* 3.8 16.6 - - + -
48A LEU* 4.6 7.2 - - + -
58A LEU* 4.2 11.2 - - + +
61A TRP* 3.6 20.9 - - + -
62A ALA* 4.3 6.5 - - + -
87A PHE* 3.8 19.3 - - + -
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Residues in contact with GLN 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 ARG 3.0 16.6 + - - +
21A TRP* 3.6 20.6 - - - +
22A SER 3.2 0.2 - - - -
23A MET* 1.3 77.8 - - - +
25A ARG* 1.3 63.1 + - + +
27A ALA* 3.4 1.6 + - - +
28A ARG* 3.0 64.3 + - - +
87A PHE* 2.9 45.1 + - + +
88A ARG* 3.9 1.6 - - - +
89A ILE* 3.8 34.9 - - + +
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Residues in contact with ARG 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 TRP* 3.0 36.2 + - + +
22A SER* 3.2 28.8 + - - +
24A GLN* 1.3 77.9 - - + +
26A GLU* 1.3 67.5 + - + +
28A ARG* 3.3 9.4 + - - +
29A LYS* 3.0 23.2 + - - +
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Residues in contact with GLU 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 SER* 2.9 22.7 + - - +
23A MET 3.8 0.4 - - - +
25A ARG* 1.3 81.2 + - - +
27A ALA* 1.3 64.1 + - - +
29A LYS* 3.3 27.0 + - - +
30A LEU* 3.0 33.0 + - + +
58A LEU* 3.7 21.5 - - + -
61A TRP* 3.5 38.1 + - + +
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Residues in contact with ALA 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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23A MET 2.8 17.6 + - - +
24A GLN 3.7 1.3 - - - +
26A GLU* 1.3 77.2 - - - +
28A ARG* 1.3 57.0 + - - +
30A LEU* 3.2 1.9 + - - -
31A GLY 2.8 25.1 + - - -
32A VAL* 2.9 21.5 + - + +
58A LEU* 3.7 20.1 - - + +
87A PHE* 3.4 38.6 - - + -
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Residues in contact with ARG 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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24A GLN* 3.0 61.2 + - + +
25A ARG* 3.7 7.1 - - - +
27A ALA* 1.3 75.3 - - - +
29A LYS* 1.3 63.4 + - - +
30A LEU 3.4 0.2 + - - -
31A GLY* 3.4 10.7 + - - +
32A VAL 5.1 0.9 - - - -
86A GLY* 6.1 0.4 - - - -
87A PHE* 3.6 21.4 + - + +
88A ARG* 6.0 0.8 - - - +
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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 ARG 3.0 13.8 + - - +
26A GLU* 3.5 28.9 + - - +
28A ARG* 1.3 77.3 - - - +
30A LEU* 1.3 69.7 + - + +
31A GLY 3.7 0.3 + - - -
54A ARG* 4.9 2.6 + - - -
53B GLU* 4.5 15.2 + - - -
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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 GLU* 3.0 24.7 + - + +
27A ALA 3.2 2.9 + - - +
29A LYS* 1.3 87.5 - - + +
31A GLY* 1.3 62.1 + - - +
32A VAL* 4.0 9.9 - - + -
54A ARG* 2.9 53.6 + - + +
57A ALA* 3.9 18.4 - - + -
58A LEU* 3.7 44.4 - - + +
61A TRP* 5.8 1.3 - - + -
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Residues in contact with GLY 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 ALA 2.8 4.5 + - - -
28A ARG* 3.4 8.3 + - - -
29A LYS 3.4 4.2 + - - -
30A LEU* 1.3 79.0 - - - +
32A VAL* 1.3 62.3 + - - +
33A ASN* 4.0 11.1 + - - -
49A GLU 4.6 1.4 - - - +
50A GLY* 5.0 5.4 - - - -
51A ASP 5.6 0.3 + - - -
54A ARG* 4.8 4.0 - - - +
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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