Contacts of the helix formed by residues 17 - 29 (chain B) in PDB entry 1WYI
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 ARG 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A THR* 2.7 33.1 + - - +
71A ASN* 2.9 30.2 + - - +
79A SER* 3.2 10.3 + - - -
81A GLY* 3.7 26.0 + - - -
82A MET* 3.0 22.1 - - - +
85A ASP* 3.4 15.9 - - - +
16B GLY* 1.3 87.4 + - - -
18B LYS* 1.3 71.0 + - - +
19B GLN* 3.3 5.4 - - + +
20B SER* 3.2 10.2 + - - +
21B LEU* 2.7 24.9 + - - +
47B TYR* 3.6 19.3 - - - -
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 2.8 41.4 + - - -
53A GLN* 4.1 8.5 + - - +
85A ASP* 2.6 41.9 + - - +
86A CYS* 4.6 5.8 + - - +
17B ARG* 1.3 67.7 - - - +
19B GLN* 1.3 54.3 + - - +
22B GLY* 2.5 38.6 + - - -
47B TYR* 3.9 13.9 - - + -
50B PHE* 3.7 43.7 - - + -
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Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 5.0 1.8 + - - +
17B ARG* 3.3 4.4 - - + +
18B LYS* 1.3 78.7 - - - +
20B SER* 1.3 65.0 + - - +
22B GLY* 3.1 1.8 + - - -
23B GLU* 2.6 64.1 + - - +
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY* 3.5 15.7 - - - -
17B ARG* 3.2 20.6 + - - +
19B GLN* 1.3 78.4 - - - +
21B LEU* 1.3 61.5 + - - +
23B GLU* 3.0 31.7 + - - +
24B LEU* 3.1 11.9 + - - +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TRP* 3.8 35.0 - - + -
15B ASN 3.6 6.3 - - - +
16B GLY* 3.2 33.9 - - - -
17B ARG 2.7 16.7 + - - +
18B LYS 3.9 1.1 - - - +
20B SER* 1.3 78.3 + - - +
22B GLY* 1.3 56.0 + - - +
24B LEU* 3.7 9.0 - - + +
25B ILE* 2.8 37.6 + - + +
44B PRO* 4.1 4.0 - - + -
47B TYR* 3.3 46.2 - - + -
50B PHE* 4.5 9.2 - - + -
51B ALA* 5.7 0.9 - - + -
236B LEU* 5.2 7.9 - - + -
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LYS 2.5 23.0 + - - -
19B GLN* 3.5 1.8 - - - -
21B LEU* 1.3 74.2 - - - +
23B GLU* 1.3 56.6 + - - +
25B ILE* 3.7 4.7 - - - +
26B GLY* 2.9 28.1 + - - -
50B PHE* 4.2 13.4 - - - -
54B LYS* 6.0 1.6 - - - -
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLN* 2.6 48.7 + - - +
20B SER* 3.0 14.3 + - - +
22B GLY* 1.3 75.9 - - - +
24B LEU* 1.3 61.3 + - - +
26B GLY* 3.7 1.1 + - - -
27B THR* 3.2 24.4 + - - -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TRP* 4.0 28.7 - - + -
20B SER 3.1 11.9 + - - +
21B LEU* 3.7 12.6 - - + +
23B GLU* 1.3 76.2 - - - +
25B ILE* 1.3 64.6 + - + +
27B THR* 3.2 17.9 + - - -
28B LEU* 3.2 29.8 + - + +
235B SER 3.7 17.7 - - - +
236B LEU* 3.5 41.7 - - + +
237B LYS 4.7 7.4 - - - +
238B PRO* 5.1 5.6 - - + -
240B PHE* 5.6 0.2 - - + -
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Residues in contact with ILE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TRP* 4.2 13.9 - - + -
21B LEU* 2.8 34.9 + - + +
22B GLY* 3.7 4.7 - - - +
24B LEU* 1.3 72.7 - - - +
26B GLY* 1.3 65.5 - - - +
27B THR 3.1 0.2 + - - -
28B LEU* 3.4 3.4 + - - +
29B ASN* 3.1 24.2 + - - +
50B PHE* 4.2 11.2 - - + -
51B ALA* 3.4 35.9 - - + -
54B LYS* 3.5 44.0 - - + +
55B LEU* 3.6 21.9 - - + +
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Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLY 2.9 16.9 + - - -
23B GLU* 4.1 2.0 - - - -
25B ILE* 1.3 78.6 - - - +
27B THR* 1.3 62.5 + - - +
29B ASN* 3.5 10.5 - - - +
30B ALA* 3.5 15.8 + - - +
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU 3.2 14.4 + - - -
24B LEU* 3.2 16.4 + - + +
25B ILE 3.1 0.4 - - - -
26B GLY* 1.3 73.1 - - - +
28B LEU* 1.3 59.8 + - + +
29B ASN 3.0 1.1 - - - -
30B ALA* 2.5 33.6 + - - +
31B ALA* 3.1 7.2 + - + +
238B PRO* 5.2 13.8 - - + +
241B VAL* 4.1 21.3 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TRP* 4.5 10.3 - - + -
24B LEU* 3.2 27.0 + - + +
25B ILE* 4.0 4.7 - - - +
27B THR* 1.3 77.8 - - + +
29B ASN* 1.3 57.2 + - - +
31B ALA* 2.9 33.9 + - + +
41B CYS* 3.5 31.4 - - - -
55B LEU* 4.4 10.3 - - + -
56B ASP* 5.0 3.2 - - - +
59B ILE* 3.8 22.8 - - + +
235B SER 5.7 0.2 - - - +
240B PHE* 3.6 24.9 - - + -
241B VAL* 3.4 28.3 - - + -
244B ILE* 4.9 3.4 - - + -
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Residues in contact with ASN 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ILE* 3.1 22.4 + - - +
26B GLY* 3.5 10.4 - - - +
27B THR 2.9 0.8 + - - -
28B LEU* 1.3 76.8 - - - +
30B ALA* 1.3 57.9 + - - +
31B ALA 3.3 2.2 - - - +
54B LYS 2.8 26.4 + - - -
55B LEU* 3.3 7.1 - - - +
56B ASP* 2.6 45.4 + - + +
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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