Contacts of the strand formed by residues 40 - 45 (chain B) in PDB entry 1W5B
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 ILE 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ALA* 3.3 18.3 + - + +
39B LYS* 1.3 76.2 - - - +
41B THR* 1.3 67.3 + - - +
42B VAL* 4.7 0.2 - - + -
63B GLY 3.7 11.9 + - - +
64B ALA* 3.2 15.0 - - + -
65B LYS* 2.8 24.7 + - - +
123B ASP* 5.3 0.2 - - + -
124B MET* 3.3 39.3 - - + +
126B PHE* 3.9 28.0 - - + -
223B VAL* 4.2 8.3 - - + -
226B ILE* 4.8 5.8 - - + -
227B THR* 3.9 20.0 - - + -
236B PHE* 4.6 9.4 - - + -
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Residues in contact with THR 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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40B ILE* 1.3 76.6 + - - +
42B VAL* 1.3 66.5 + - - +
43B VAL* 4.1 4.7 - - + -
65B LYS* 3.4 23.6 - - + +
67B VAL* 3.7 29.8 - - + -
118B ALA 4.6 0.6 + - - +
119B ILE* 4.0 18.2 - - + -
122B SER* 2.8 25.5 + - - -
124B MET 3.0 7.1 + - - -
125B VAL* 3.3 10.2 - - - +
126B PHE* 2.8 26.3 + - - +
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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
----------------------------------------------------------
40B ILE* 4.7 0.4 - - + -
41B THR* 1.3 76.1 - - - +
43B VAL* 1.3 63.3 + - - +
53B ILE* 3.5 21.7 - - + +
56B LEU* 4.0 14.6 - - + -
61B ILE* 4.2 9.6 - - + -
64B ALA* 4.2 13.9 - - + -
65B LYS 2.7 16.5 + - - +
66B THR* 3.5 4.9 - - + -
67B VAL* 2.8 26.2 + - - +
126B PHE* 3.4 14.4 - - + +
128B THR* 4.3 9.2 - - + -
219B VAL* 4.0 12.6 - - + -
223B VAL* 4.0 26.5 - - + -
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Residues in contact with VAL 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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41B THR* 4.1 8.3 - - + -
42B VAL* 1.3 78.3 - - - +
44B GLY* 1.3 61.7 + - - +
45B CYS* 4.0 13.9 + - - -
53B ILE* 4.1 1.6 - - - -
67B VAL* 3.3 15.3 - - + +
69B ILE* 3.9 28.7 - - + -
119B ILE* 3.9 28.3 - - + -
125B VAL* 4.1 8.5 - - + -
126B PHE 2.6 15.6 + - - +
127B ILE* 3.3 4.7 - - - +
128B THR* 2.7 30.0 + - - +
143B VAL* 4.1 15.9 - - + -
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Residues in contact with GLY 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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43B VAL* 1.3 73.9 - - - +
45B CYS* 1.3 60.9 + - - -
49B GLY 3.6 11.4 - - - -
50B ASN* 3.3 5.9 - - - +
53B ILE* 3.5 20.0 - - - +
67B VAL 2.9 9.3 + - - -
68B ALA* 3.6 1.7 - - - -
69B ILE* 2.9 25.8 + - - +
128B THR* 3.2 11.0 - - - -
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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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43B VAL* 4.0 19.3 - - - -
44B GLY* 1.3 76.5 - - - -
46B GLY* 1.3 66.3 + - - +
49B GLY* 3.5 5.9 + - - -
69B ILE* 3.4 11.0 - - + +
127B ILE* 4.2 11.2 - - - -
128B THR 3.2 6.0 + - - -
129B CYS* 3.3 21.3 - - + +
130B GLY 4.7 0.5 + - - -
136B GLY* 3.8 11.1 - - - -
139B SER* 3.3 26.2 - - - +
140B ALA* 4.2 12.6 - - - +
143B VAL* 4.1 16.8 - - - -
500B GTP 4.6 0.9 + - - -
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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