Contacts of the strand formed by residues 166 - 171 (chain B) in PDB entry 1TUB
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 MET 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE* 2.2 69.8 - - + +
137B LEU* 3.8 13.7 - - + -
154B ILE* 4.9 2.9 - - + -
157B ILE* 3.1 28.0 - - + -
164B ARG 3.7 5.6 - - - +
165B ILE* 1.3 74.2 - - - +
167B ASN* 1.3 62.1 + - - +
168B THR* 3.9 5.3 + - + -
197B ASN* 2.5 41.1 + - + +
198B THR* 3.5 12.1 - - + -
199B ASP* 2.8 30.9 + - - +
200B GLU 3.2 4.0 + - - -
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Residues in contact with ASN 167 (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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134B GLY* 3.8 14.3 - - - -
135B PHE 2.4 27.9 + - - +
136B GLN* 3.4 17.9 - - + +
137B LEU 3.5 1.4 + - - -
165B ILE* 4.2 6.2 + - - +
166B MET* 1.3 78.3 - - - +
168B THR* 1.5 65.7 - - - +
169B PHE* 4.2 3.6 - - + -
199B ASP* 5.2 2.3 - - - +
200B GLU* 4.6 16.1 - - - +
202B TYR* 4.6 17.1 + - + -
238B VAL* 5.7 1.6 - - + -
243B ARG* 4.4 2.6 - - - +
252B LEU* 3.6 41.3 - - - +
255B LEU* 4.7 9.6 - - - +
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.7 30.3 - - + -
139B HIS* 5.8 4.7 - - - -
154B ILE* 4.2 5.8 - - + +
166B MET* 4.5 4.0 - - + -
167B ASN* 1.5 59.9 - - - +
169B PHE* 1.5 58.7 + - - +
170B SER* 4.8 1.6 - - - -
193B GLN* 5.9 2.1 - - - +
198B THR* 3.6 30.8 - - + +
200B GLU 3.4 18.5 + - - -
201B THR* 3.3 11.3 - - - +
202B TYR* 2.8 35.5 + - - +
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Residues in contact with PHE 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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16B ILE* 5.8 1.3 - - + -
20B PHE* 3.3 11.7 - + - -
136B GLN* 4.4 20.6 - - + -
137B LEU 3.0 31.7 + - - +
138B THR* 4.2 16.4 - - + -
139B HIS* 3.5 19.5 + - - +
167B ASN* 5.3 3.6 - - + -
168B THR* 1.5 59.9 - - - +
170B SER* 1.3 59.8 + - - +
202B TYR* 3.7 28.7 - + - -
204B ILE* 4.4 20.4 - - + -
231B VAL* 4.9 0.2 - - + -
234B THR* 5.0 4.5 - - + -
235B MET* 2.2 59.9 - - + -
238B VAL* 6.1 0.7 - - + -
239B THR* 4.3 7.0 - - + -
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Residues in contact with SER 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B HIS* 3.5 15.9 - - - -
141B LEU* 5.8 1.8 - - - -
168B THR* 4.8 2.2 - - - -
169B PHE* 1.3 75.0 - - - +
171B VAL* 1.3 68.6 + - - +
172B VAL* 4.6 4.3 - - - -
193B GLN* 5.6 3.1 - - - -
201B THR* 5.3 2.7 - - - -
202B TYR* 1.3 61.5 + - - +
203B CYS* 2.6 14.8 - - - +
204B ILE* 3.0 28.1 - - - +
267B PHE* 6.4 0.7 - - - -
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Residues in contact with VAL 171 (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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12B CYS* 3.8 29.2 - - + -
16B ILE* 5.0 6.3 - - + -
139B HIS* 3.1 20.8 + - - +
140B SER* 4.1 5.8 - - - -
141B LEU* 2.8 38.0 + - - +
170B SER* 1.3 77.2 - - - +
172B VAL* 1.2 65.4 + - - +
204B ILE* 3.8 23.1 - - + +
206B ASN* 3.1 32.1 - - - +
500B GDP 4.2 9.4 - - + +
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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