Contacts of the strand formed by residues 184 - 190 (chain B) in PDB entry 1T9A
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 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B GLY* 3.9 23.3 - - - +
146B ALA* 4.5 4.7 - - + +
147B GLU* 4.1 9.6 - - - -
157B GLY* 3.3 16.4 - - - +
159B VAL* 4.4 11.2 - - + -
173B PRO* 3.5 10.8 - - + +
174B MET* 3.5 42.8 - - + +
177B ALA* 3.6 10.5 - - + -
182B ILE* 4.0 8.5 - - + +
183B PRO* 1.3 76.1 - - - +
185B VAL* 1.3 64.5 + - - +
186B VAL* 3.9 15.5 - - + -
237B ALA* 3.9 2.8 - - - +
243B GLY 3.2 7.8 + - - +
244B PRO* 3.2 9.8 - - + +
245B VAL* 2.8 30.7 + - - +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B PRO* 4.6 5.8 - - + -
157B GLY 2.9 10.1 + - - +
158B VAL* 3.5 4.7 - - + -
159B VAL 3.0 23.6 + - - +
184B MET* 1.3 75.2 - - - +
186B VAL* 1.3 63.9 + - - +
187B PHE* 3.3 38.1 - - + -
233B ALA* 4.1 10.8 - - + -
234B PHE* 4.1 35.9 - - + -
237B ALA* 4.0 12.3 - - + -
245B VAL* 3.6 22.4 - - + +
247B VAL* 4.8 2.2 - - + -
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Residues in contact with VAL 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 3.7 22.9 - - + -
161B VAL* 4.8 0.2 - - + -
170B VAL* 4.1 19.5 - - + -
174B MET* 3.8 27.4 - - + -
184B MET* 3.9 22.0 - - + -
185B VAL* 1.3 74.1 - - - +
187B PHE* 1.3 62.8 + - - +
188B THR* 3.7 23.1 - - + -
244B PRO* 5.5 0.7 - - + -
245B VAL 2.8 16.8 + - - +
246B LEU* 3.2 8.0 - - + +
247B VAL* 2.8 27.5 + - - +
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Residues in contact with PHE 187 (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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98B PHE* 3.6 34.5 - + - -
102B MET* 4.1 13.9 - - + -
158B VAL* 3.9 16.2 - - + -
159B VAL 2.7 20.2 + - - +
160B LEU* 3.4 18.9 - - + +
161B VAL* 2.9 29.2 + - - +
185B VAL* 3.3 31.2 - - + -
186B VAL* 1.3 71.7 - - - +
188B THR* 1.3 60.4 + - - +
230B ILE* 4.1 22.2 - - + -
234B PHE* 4.1 8.1 - + - -
247B VAL* 3.5 30.3 - - + -
249B LEU* 4.0 15.0 - - + -
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Residues in contact with THR 188 (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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118B ILE* 4.8 1.1 - - - -
161B VAL* 3.4 22.4 - - + -
162B THR 4.3 0.2 - - - -
167B ALA* 4.0 23.1 - - + -
170B VAL* 4.8 0.9 - - + -
186B VAL* 3.7 16.6 - - + -
187B PHE* 1.3 77.0 - - - +
189B GLY* 1.3 65.4 + - - +
206B VAL* 4.0 2.3 - - - +
246B LEU* 3.9 20.5 - - + +
247B VAL 3.2 5.7 + - - -
248B ASP* 2.7 31.6 + - - +
249B LEU* 2.8 30.5 + - - +
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Residues in contact with GLY 189 (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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117B ALA* 4.0 1.1 - - - -
118B ILE* 3.8 31.2 - - - +
161B VAL 2.8 16.4 + - - -
162B THR 3.8 0.6 - - - +
163B SER* 2.9 28.4 - - - -
167B ALA* 5.4 0.2 - - - +
188B THR* 1.3 78.0 - - - +
190B GLN* 1.3 59.8 + - - +
206B VAL* 5.7 0.5 - - - +
248B ASP* 4.1 1.6 - - - +
249B LEU 3.6 7.2 - - - -
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Residues in contact with GLN 190 (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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117B ALA* 3.6 12.7 - - - +
163B SER* 3.7 6.3 - - - -
189B GLY* 1.3 75.4 - - - -
191B VAL* 1.3 97.6 + - - +
196B ILE* 4.0 20.4 - - + +
203B GLU* 4.0 13.3 - - - +
204B ALA 3.1 24.3 + - - -
205B ASP* 5.3 0.2 - - - +
206B VAL* 4.5 4.6 - - - +
219B MET* 5.3 0.6 - - - -
248B ASP* 2.9 38.9 + - - +
249B LEU 2.9 16.6 + - - +
250B PRO* 3.9 4.3 - - + -
251B LYS* 2.7 28.2 + - - +
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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
------------------------------------------------------------
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