Contacts of the strand formed by residues 106 - 111 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ARG* 3.5 51.6 - - + -
45A VAL 3.7 3.6 - - - -
46A LEU* 3.6 44.2 - - + -
67A VAL* 3.7 22.2 - - + -
102A PHE* 3.6 35.9 - + + -
105A GLU* 1.3 88.6 - - + +
107A ASP* 1.3 61.6 + - - +
108A ALA 3.7 13.2 - - - +
109A VAL* 4.3 7.0 - - + -
134A ALA* 3.1 12.7 + - + +
135A LEU* 3.5 4.7 - - - +
136A LYS* 2.9 27.7 + - - +
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Residues in contact with ASP 107 (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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40A ARG* 2.9 31.8 + - - +
41A GLU 3.4 12.4 - - - +
42A VAL* 3.7 26.0 - - + +
43A ARG* 2.9 25.5 + - - +
44A ARG* 2.9 23.3 + - - +
106A PHE* 1.3 73.2 - - - +
108A ALA* 1.3 60.5 + - - +
135A LEU* 4.0 1.1 - - - -
136A LYS* 3.2 22.0 + - - +
139A GLY* 3.1 25.3 - - - -
140A VAL 3.1 2.8 + - - -
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Residues in contact with ALA 108 (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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34A PHE* 3.6 33.0 - - + -
42A VAL* 4.0 10.3 - - + -
44A ARG 3.4 2.2 + - - -
45A VAL* 3.3 12.3 - - + -
46A LEU 3.0 22.4 + - - -
106A PHE* 3.2 3.5 - - - +
107A ASP* 1.3 83.8 - - - +
109A VAL* 1.3 68.4 + - - +
110A THR* 5.2 0.4 - - + -
135A LEU* 3.8 1.1 - - - -
140A VAL* 3.1 16.2 - - + +
142A ILE* 5.6 0.2 - - + -
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Residues in contact with VAL 109 (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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46A LEU* 3.2 26.9 - - + +
48A LEU* 3.5 33.7 - - + -
106A PHE* 4.3 7.4 - - + -
108A ALA* 1.3 79.0 - - - +
110A THR* 1.3 66.0 + - - +
131A VAL* 3.9 24.2 - - + -
134A ALA* 4.4 8.3 - - + -
135A LEU* 3.6 22.4 - - + -
140A VAL 2.8 6.3 + - - +
141A PHE* 3.2 7.7 - - + -
142A ILE 2.9 24.3 + - - -
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Residues in contact with THR 110 (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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30A VAL* 5.0 0.2 - - + -
34A PHE* 4.8 9.4 - - + -
45A VAL* 4.0 16.8 - - + +
46A LEU 2.8 7.4 + - - -
47A ASP* 2.7 31.0 + - - +
48A LEU* 2.8 33.4 + - - +
59A LEU* 4.7 2.1 - - + +
109A VAL* 1.3 82.8 - - - +
111A MET* 1.3 61.4 + - - +
112A PHE* 3.2 31.3 - - + -
141A PHE* 4.6 0.7 - - - -
142A ILE* 3.3 25.1 - - + +
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Residues in contact with MET 111 (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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48A LEU* 3.7 34.3 - - + +
49A ALA* 4.2 0.4 - - + -
97A VAL* 4.1 15.0 - - + -
110A THR* 1.3 76.1 - - - +
112A PHE* 1.3 60.7 + - - +
114A SER 5.4 0.2 + - - -
115A THR* 3.7 39.0 + - + -
116A ILE* 4.0 17.0 - - - -
119A PHE* 4.3 5.2 - - + -
127A LEU* 3.9 33.9 - - + -
141A PHE* 4.3 8.5 - - + -
142A ILE 3.0 6.8 + - - -
143A THR* 2.7 43.2 + - - +
144A ASP 3.6 2.9 + - - +
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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