Contacts of the strand formed by residues 106 - 111 (chain B) in PDB entry 1WZN
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 PHE 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 3.4 48.0 - - + -
45B VAL 3.7 6.5 - - - -
46B LEU* 3.6 45.5 - - + -
67B VAL* 3.8 23.3 - - + -
102B PHE* 3.7 31.4 - + + -
105B GLU* 1.3 92.0 - - + +
107B ASP* 1.3 62.6 + - - +
108B ALA 3.9 11.2 - - - +
109B VAL* 4.3 8.1 - - + -
134B ALA* 3.1 12.5 + - + +
135B LEU* 3.4 4.7 - - - +
136B LYS* 3.0 28.7 + - - +
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Residues in contact with ASP 107 (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 ARG* 2.8 21.2 + - - +
41B GLU 3.4 13.3 - - - +
42B VAL* 3.7 25.3 - - + +
43B ARG* 2.9 24.3 + - - +
44B ARG* 2.9 24.4 + - - +
106B PHE* 1.3 73.0 - - - +
108B ALA* 1.3 62.1 + - - +
135B LEU* 3.9 1.6 - - - -
136B LYS* 2.8 34.4 + - - -
139B GLY* 3.1 24.3 - - - -
140B VAL 3.2 2.8 + - - -
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Residues in contact with ALA 108 (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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34B PHE* 3.6 33.0 - - + -
42B VAL* 3.8 11.9 - - + -
44B ARG 3.4 2.5 + - - +
45B VAL* 3.3 10.7 - - + -
46B LEU 2.9 23.0 + - - -
106B PHE* 3.2 2.7 - - - +
107B ASP* 1.3 83.2 - - - +
109B VAL* 1.3 67.8 + - - +
110B THR* 5.3 0.2 - - + -
135B LEU* 3.7 1.6 - - - -
140B VAL* 3.2 15.7 - - + +
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Residues in contact with VAL 109 (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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46B LEU* 3.2 29.8 - - + +
48B LEU* 3.7 29.6 - - + -
106B PHE* 4.3 7.4 - - + -
108B ALA* 1.3 79.3 - - - +
110B THR* 1.3 66.1 + - - +
131B VAL* 4.0 28.0 - - + +
134B ALA* 4.5 5.2 - - + -
135B LEU* 3.7 21.8 - - + -
140B VAL 2.9 6.3 + - - +
141B PHE* 3.2 9.0 - - + -
142B ILE* 2.9 23.9 + - - +
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Residues in contact with THR 110 (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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30B VAL* 5.0 0.2 - - + -
34B PHE* 4.7 15.0 - - + -
45B VAL* 4.0 16.9 - - + +
46B LEU 2.8 8.0 + - - -
47B ASP* 2.7 31.0 + - - +
48B LEU* 2.8 30.5 + - - +
59B LEU* 4.7 1.5 - - + +
108B ALA* 5.3 0.2 - - + -
109B VAL* 1.3 81.5 - - - +
111B MET* 1.3 63.5 + - - +
112B PHE* 3.3 33.2 - - + -
141B PHE* 4.7 0.9 - - - -
142B ILE* 3.3 20.0 - - + -
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Residues in contact with MET 111 (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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47B ASP* 4.4 0.2 - - - -
48B LEU* 3.6 37.5 - - + +
49B ALA* 4.4 6.3 - - + -
97B VAL* 4.2 17.7 - - + -
110B THR* 1.3 76.4 - - - +
112B PHE* 1.3 59.9 + - - +
114B SER 5.3 0.2 + - - -
115B THR* 3.8 30.5 + - - -
116B ILE* 4.0 23.8 - - - -
119B PHE* 4.2 6.1 - - + -
127B LEU* 3.8 26.5 - - + -
141B PHE* 4.3 8.7 - - + -
142B ILE 3.0 8.0 + - - -
143B THR* 2.7 43.1 + - - +
144B ASP 3.6 2.8 + - - +
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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