Contacts of the strand formed by residues 39 - 46 (chain A) in PDB entry 1WQ9
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 CYS 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.2 17.3 - - + -
21A VAL 3.3 17.5 - - - +
22A SER* 4.0 7.6 - - - -
23A ILE* 3.7 1.3 - - - -
37A PRO* 3.2 14.4 - - - +
38A SER* 1.3 78.8 - - - +
40A VAL* 1.3 66.0 + - - +
12B SER* 2.8 26.3 + - - -
47B GLY* 4.4 0.4 - - - -
48B CYS* 2.0 56.7 - - + -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR 3.5 1.0 - - - +
20A LEU* 3.4 5.9 - - - -
21A VAL* 2.9 50.9 + - + +
23A ILE* 3.9 14.1 - - + -
37A PRO* 4.7 1.1 - - + -
39A CYS* 1.3 81.4 - - - +
41A ALA* 1.3 59.1 + - - +
42A VAL* 4.0 10.5 - - + -
66A ILE* 4.0 13.5 - - + -
68A ILE* 4.0 18.4 - - + -
85A PHE* 3.7 24.2 - - + -
3B ARG* 4.8 0.2 - - - +
8B VAL* 4.0 17.9 - - + -
12B SER* 3.5 7.2 - - - -
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Residues in contact with ALA 41 (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 GLU* 3.7 27.8 - - + +
19A THR 3.3 6.3 - - - +
20A LEU* 4.2 11.4 - - + -
40A VAL* 1.3 73.3 - - - +
42A VAL* 1.3 63.7 + - - +
3B ARG* 2.7 35.4 + - - +
8B VAL 5.7 0.4 + - - -
11B ARG* 3.8 26.5 - - + -
12B SER* 4.2 3.8 + - - -
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Residues in contact with VAL 42 (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 ARG 3.4 0.2 - - - +
18A GLU* 4.5 0.4 - - - -
19A THR* 2.8 41.3 + - - +
21A VAL* 3.9 21.1 - - + -
40A VAL* 4.0 18.2 - - + -
41A ALA* 1.3 81.5 - - - +
43A LEU* 1.3 65.3 + - - +
44A ARG* 3.8 27.1 - - + +
64A ALA* 5.5 0.2 - - + -
66A ILE* 4.0 13.7 - - + -
85A PHE* 4.0 14.6 - - + -
86A MET 4.1 0.4 - - - +
87A GLU* 3.3 21.3 - - + +
3B ARG* 4.4 0.7 - - - +
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Residues in contact with LEU 43 (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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16A THR* 4.0 22.2 - - - +
17A ARG* 3.5 3.8 - - - +
18A GLU* 3.8 25.4 - - + +
42A VAL* 1.3 72.0 - - - +
44A ARG* 1.3 57.5 + - - +
62A HIS* 5.4 4.5 - - + +
87A GLU* 2.7 33.1 + - - +
88A HIS 2.7 44.7 + - - +
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Residues in contact with ARG 44 (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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16A THR* 3.9 2.9 - - - -
17A ARG* 2.8 32.7 + - - +
19A THR* 3.5 31.4 + - + +
21A VAL* 4.0 7.4 - - + +
26A GLU* 2.8 39.8 + - - +
42A VAL* 3.8 17.9 - - + +
43A LEU* 1.3 81.4 + - - +
45A CYS* 1.3 66.2 + - - +
46A SER* 3.6 1.4 + - - -
85A PHE* 5.3 0.8 - - - +
86A MET* 2.9 53.8 + - - +
88A HIS* 3.5 28.4 - - + +
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Residues in contact with CYS 45 (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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15A GLN 3.4 5.4 - - - -
44A ARG* 1.3 72.2 - - - +
46A SER* 1.3 64.5 + - - +
56A CYS* 3.8 12.9 - - - +
57A THR 4.2 0.9 - - - -
58A PRO* 3.5 24.9 - - + -
88A HIS* 2.9 27.3 + - + +
90A ALA 3.4 12.8 - - - -
91A CYS* 2.0 48.5 - - + -
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Residues in contact with SER 46 (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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15A GLN 3.0 18.7 + - - +
17A ARG* 2.7 56.9 + - - +
19A THR* 5.0 2.0 + - - -
44A ARG 4.2 0.6 + - - -
45A CYS* 1.3 77.6 - - - +
47A GLY* 1.3 58.3 + - - +
56A CYS* 3.5 12.8 - - - -
20B LEU* 4.0 7.2 - - - +
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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