Contacts of the helix formed by residues 114 - 119 (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 SER 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B PHE* 1.3 83.4 - - - +
115B THR* 1.3 63.6 + - - +
116B ILE* 3.2 4.9 + - - -
117B MET* 3.2 27.4 + - - +
118B TYR* 4.9 2.3 - - - -
144B ASP* 2.9 25.7 + - - -
145B PHE* 4.0 5.7 - - - +
146B PRO* 3.0 32.7 - - - +
242B ARG* 6.1 0.7 - - - -
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.7 25.4 - - + +
111B MET* 3.8 25.0 + - - +
112B PHE 3.4 15.8 + - - -
113B PHE 3.2 2.5 + - - -
114B SER* 1.3 70.7 - - - +
116B ILE* 1.3 65.2 + - - +
117B MET 3.0 3.6 + - - -
118B TYR* 3.1 26.9 + - + +
119B PHE* 3.4 15.9 - - + -
143B THR* 5.4 0.4 + - - -
144B ASP 4.5 0.6 + - - -
1002B SAH 3.5 33.4 - - + +
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B MET* 4.0 12.7 - - - -
114B SER 4.5 0.7 - - - +
115B THR* 1.3 76.8 - - - +
117B MET* 1.3 61.6 + - + +
118B TYR 3.0 0.4 - - - -
119B PHE* 3.0 37.5 + - - +
124B LEU* 4.0 20.9 - - + +
127B LEU* 5.0 0.2 - - + -
128B PHE* 4.8 8.1 - - + -
141B PHE* 5.2 0.2 - - + -
143B THR* 3.6 29.8 + - + +
144B ASP 5.0 0.4 - - - +
145B PHE* 3.5 50.3 - - + -
210B TYR* 4.0 12.8 - - + -
215B VAL* 4.1 21.3 - - + -
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Residues in contact with MET 117 (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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114B SER* 3.4 20.6 - - - +
115B THR 3.0 1.4 - - - -
116B ILE* 1.3 83.4 - - + +
118B TYR* 1.3 56.4 + - + +
119B PHE 3.2 1.8 - - - -
145B PHE* 5.0 5.2 - - + -
146B PRO* 4.1 31.4 - - + +
183B LEU* 4.9 15.5 - - + -
207B LEU* 3.3 38.1 - - + -
208B ASN* 2.7 59.6 + - - +
209B ILE* 4.8 7.6 - - + -
210B TYR* 4.8 4.0 - - + +
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Residues in contact with TYR 118 (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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1B MET* 6.2 0.4 - - + -
2B TYR* 4.0 28.3 - + - +
5B TYR* 2.8 36.5 + + - -
114B SER 4.9 2.5 - - - -
115B THR* 3.1 31.0 + - + +
116B ILE 3.0 1.6 - - - -
117B MET* 1.3 76.6 - - - +
119B PHE* 1.3 74.8 + - + +
120B ASP 4.3 0.5 + - - -
185B PHE* 5.9 0.9 - - - -
205B ASP* 2.8 36.1 + - + +
206B GLU 4.6 8.0 - - - +
207B LEU* 3.9 25.8 - - + +
208B ASN* 3.7 5.0 + - - +
1002B SAH 4.5 16.8 - + + +
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Residues in contact with PHE 119 (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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97B VAL* 3.5 20.2 - - + -
98B LEU* 3.9 34.8 - - + -
111B MET* 4.2 14.6 - - + -
115B THR* 3.4 30.3 - - + -
116B ILE* 3.0 19.9 + - - +
117B MET 3.2 0.4 - - - -
118B TYR* 1.3 87.1 - - + +
120B ASP* 1.3 58.9 - - - +
123B ASP* 4.0 10.1 - - + -
124B LEU* 4.1 11.4 - - + +
127B LEU* 4.3 9.9 - - + -
208B ASN* 3.2 12.2 + - - -
210B TYR* 2.7 23.6 + - - -
1002B SAH 3.7 34.3 - + - -
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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