Contacts of the strand formed by residues 39 - 46 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A SER* 3.3 17.6 - - - -
47A GLY 4.5 1.1 - - - -
48A CYS* 2.0 55.1 - - + -
20B LEU* 4.1 17.5 - - + -
21B VAL 3.2 20.6 - - - +
22B SER* 4.3 3.1 - - - -
23B ILE* 4.3 1.3 - - - -
37B PRO* 3.2 24.3 - - - +
38B SER* 1.3 79.2 - - - +
40B VAL* 1.3 65.8 + - - +
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 5.6 0.2 - - - +
8A VAL* 3.9 22.9 - - + -
12A SER* 4.6 3.8 - - - -
19B THR 3.5 1.4 - - - +
20B LEU* 3.4 6.7 - - - -
21B VAL* 2.9 51.1 + - + +
23B ILE* 4.1 5.4 - - + -
37B PRO* 4.8 0.2 - - + -
39B CYS* 1.3 80.6 - - - +
41B ALA* 1.3 61.7 + - - +
42B VAL* 5.2 1.1 - - + -
66B ILE* 4.4 14.4 - - + -
68B ILE* 4.1 18.2 - - + -
85B PHE* 3.7 37.5 - - + -
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Residues in contact with ALA 41 (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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3A ARG* 2.7 37.9 + - - +
8A VAL* 5.5 1.8 + - - +
11A ARG* 3.8 26.9 - - + +
12A SER* 5.2 2.0 - - - +
18B GLU* 3.7 28.0 - - + +
19B THR 3.4 5.6 - - - -
20B LEU* 4.1 12.5 - - + +
40B VAL* 1.3 74.5 - - - +
42B VAL* 1.3 54.9 + - - +
66B ILE* 4.5 1.0 - - - +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 4.6 4.0 - - - +
18B GLU* 4.5 3.1 - - - -
19B THR* 2.8 38.7 + - - +
21B VAL* 4.1 11.9 - - + -
40B VAL* 3.9 6.9 + - + +
41B ALA* 1.3 75.6 - - - +
43B LEU* 1.3 59.3 + - - +
44B ARG* 3.5 34.1 - - + +
64B ALA* 4.9 3.8 - - + -
66B ILE* 5.1 1.3 - - + -
85B PHE* 4.9 9.2 - - + -
86B MET 3.6 8.7 - - - +
87B GLU* 2.9 45.1 - - + +
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Residues in contact with LEU 43 (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 THR* 4.0 19.1 - - + +
17B ARG* 3.4 27.6 - - - +
18B GLU* 3.9 5.6 - - + +
42B VAL* 1.3 70.9 - - - +
44B ARG* 1.3 65.5 + - - +
62B HIS* 6.0 0.2 - - - +
87B GLU* 3.0 34.9 + - + +
88B HIS 2.9 36.5 + - - +
89B THR* 6.0 1.1 - - + -
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Residues in contact with ARG 44 (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 THR* 4.1 2.5 - - - -
17B ARG* 2.9 30.9 + - - +
19B THR* 3.4 33.3 + - + +
21B VAL* 3.8 13.8 - - - +
26B GLU* 2.9 33.1 + - - -
42B VAL* 3.5 15.1 - - + +
43B LEU* 1.3 81.7 + - - +
45B CYS* 1.3 65.0 + - - +
46B SER* 3.6 1.7 + - - -
85B PHE* 5.7 0.8 - - - +
86B MET* 2.9 53.4 + - - +
88B HIS* 3.6 27.9 - - + +
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Residues in contact with CYS 45 (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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15B GLN 3.4 5.6 - - - -
44B ARG* 1.3 71.5 - - - +
46B SER* 1.3 65.6 + - - +
56B CYS* 3.8 15.7 - - - +
57B THR 4.3 0.7 - - - -
58B PRO* 3.6 22.9 - - + -
88B HIS* 3.0 27.7 + - + +
90B ALA 3.5 12.6 - - - -
91B CYS* 2.0 48.2 - - + -
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Residues in contact with SER 46 (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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20A LEU* 3.7 9.2 - - - +
15B GLN 3.1 18.2 + - - +
17B ARG* 2.7 57.6 + - - +
19B THR* 5.0 2.0 + - - -
44B ARG* 4.2 1.2 + - - -
45B CYS* 1.3 76.2 - - - +
47B GLY* 1.3 59.4 + - - +
56B CYS* 3.4 13.0 - - - -
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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