Contacts of the strand formed by residues 165 - 170 (chain B) in PDB entry 3ZTX
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 ARG 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B VAL* 3.7 21.5 - - + -
124B LEU 3.2 11.4 - - - +
125B PHE* 3.7 29.9 - - + -
126B LYS* 3.7 0.8 - - - -
161B HIS* 3.1 7.4 - - - +
162B ASP* 2.7 58.8 + - - +
163B ARG* 4.2 16.8 - - - +
164B LYS* 1.3 108.0 - - - +
166B ILE* 1.3 64.1 + - - +
167B TYR* 2.9 26.6 + - + +
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Residues in contact with ILE 166 (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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122B LYS 3.5 0.2 - - - +
123B VAL* 3.6 1.7 - - - +
124B LEU* 2.7 52.3 + - + +
126B LYS* 3.8 22.7 - - + -
129B LEU* 4.2 6.1 - - + -
138B LEU* 4.2 15.3 - - + -
142B ILE* 4.6 5.2 - - + -
159B TYR* 5.7 1.3 - - + -
160B PHE 3.7 7.9 - - - +
161B HIS* 4.0 5.4 - - + -
165B ARG* 1.3 77.5 - - - +
167B TYR* 1.3 63.6 + - - +
168B LEU* 4.0 21.8 - - + -
836C LEU* 3.8 28.5 - - + +
837C PHE* 3.7 30.3 - - + -
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Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.7 35.4 - - + +
121B LEU* 4.0 7.6 - - + -
122B LYS 3.3 4.5 - - - -
123B VAL* 3.8 33.7 - - + -
159B TYR* 3.3 7.8 - - - +
160B PHE* 2.8 78.8 + + + +
161B HIS* 4.0 0.9 - - - -
162B ASP* 2.6 40.0 + - + -
165B ARG* 2.9 30.8 + - + -
166B ILE* 1.3 76.0 - - - +
168B LEU* 1.3 63.8 + - - +
169B MET 4.1 0.2 - - - -
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Residues in contact with LEU 168 (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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121B LEU* 3.4 5.4 - - - -
122B LYS* 2.9 55.5 + - + +
124B LEU* 4.1 22.0 - - + -
138B LEU* 4.4 11.0 - - + -
141B GLU* 6.0 3.4 - - - -
142B ILE* 3.8 24.9 - - + -
156B MET* 3.9 26.7 - - + -
158B ASN 4.1 2.9 - - - -
159B TYR* 3.8 15.0 - - + -
166B ILE* 4.0 9.9 - - + -
167B TYR* 1.3 81.3 - - - +
169B MET* 1.3 62.2 + - - +
170B LEU* 3.4 14.6 + - + +
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Residues in contact with MET 169 (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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88B PHE* 3.6 44.9 - - + -
93B PHE* 3.6 33.9 - - + -
119B MET* 3.8 26.5 - - + -
120B ALA 3.7 4.7 - - - -
121B LEU* 3.9 5.4 - - + -
156B MET* 3.4 5.5 - - - +
157B TYR* 2.7 38.3 + - + -
158B ASN* 2.9 34.6 + - + +
160B PHE* 3.9 18.2 - - + -
168B LEU* 1.3 69.1 - - - +
170B LEU* 1.3 57.7 + - - +
825C TYR* 4.2 5.8 - - + -
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Residues in contact with LEU 170 (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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119B MET* 3.4 6.4 - - - +
120B ALA 2.8 38.6 + - - +
122B LYS* 3.6 36.8 - - + +
145B GLN* 4.0 17.5 - - - +
154B LEU* 4.7 5.6 - - + -
155B ARG 3.4 12.1 - - - +
156B MET* 3.9 28.7 - - + -
157B TYR* 3.5 5.8 - - - -
168B LEU* 3.9 11.4 - - + +
169B MET* 1.3 76.8 - - - +
171B GLU* 1.3 59.0 + - - +
233B ALA 5.7 0.4 - - - +
1356B ZTX 3.5 38.4 - - - +
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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