Contacts of the helix formed by residues 170 - 180 (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 VAL 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B GLU* 4.5 9.0 - - + +
143B GLY* 4.4 7.6 - - - -
159B VAL* 4.4 22.2 - - + -
161B VAL* 4.8 3.8 - - + -
166B GLY 3.8 7.1 + - - +
167B ALA* 2.8 29.7 + - - +
168B THR 3.0 1.0 - - - -
169B ASN* 1.3 77.0 - - - +
171B VAL* 1.3 64.5 + - - +
173B PRO* 3.1 28.0 - - + +
174B MET* 3.2 32.4 + - + +
184B MET* 5.6 0.2 - - + -
186B VAL* 4.1 20.6 - - + -
188B THR* 4.8 1.8 - - + -
246B LEU* 5.3 0.2 - - + -
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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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168A THR* 4.0 26.5 - - + +
171A VAL* 4.3 15.0 - - + -
209A ILE* 4.5 11.0 - - + -
167B ALA 4.0 3.1 - - - +
168B THR* 3.2 28.6 + - - +
169B ASN 3.4 0.2 - - - -
170B VAL* 1.3 77.5 - - - +
172B THR* 1.3 57.2 + - - +
174B MET* 3.2 16.7 + - + +
175B ALA* 2.9 26.9 + - - +
209B ILE* 3.8 23.8 - - + -
213B CYS* 4.4 13.8 - - - -
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Residues in contact with THR 172 (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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165A PRO* 4.7 1.6 - - + -
168A THR* 2.7 32.6 + - - +
169A ASN* 2.5 32.6 + - - +
140B GLN* 4.4 4.3 - - - +
144B HIS* 4.3 6.3 - - - +
168B THR 4.9 0.4 + - - -
169B ASN 4.8 1.5 + - - -
171B VAL* 1.3 77.2 - - - +
173B PRO* 1.3 65.5 - - + +
175B ALA* 3.2 2.9 + - - +
176B ASP* 2.8 27.9 + - - +
522B LEU* 3.8 3.1 - - + +
524B THR* 3.6 33.9 - - + +
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Residues in contact with PRO 173 (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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140B GLN* 3.6 31.9 - - + +
143B GLY* 3.6 29.6 - - - +
144B HIS* 3.9 12.1 - - + -
147B GLU* 3.5 13.4 - - - +
169B ASN 4.0 4.3 - - - +
170B VAL* 3.1 23.6 - - + +
172B THR* 1.3 94.6 - - - +
174B MET* 1.3 55.4 + - - +
176B ASP* 4.2 0.2 - - + -
177B ALA* 2.8 31.2 + - - +
184B MET* 3.5 5.2 - - + +
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Residues in contact with MET 174 (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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167B ALA 4.6 0.7 - - - +
170B VAL* 3.2 35.3 + - + +
171B VAL* 3.6 19.7 - - + +
172B THR 3.2 0.4 - - - -
173B PRO* 1.3 72.5 - - - +
175B ALA* 1.3 61.2 + - - +
178B PHE* 2.8 32.1 + - - +
184B MET* 3.5 21.5 - - + -
186B VAL* 3.8 19.7 - - + -
206B VAL* 5.7 1.1 - - + -
210B SER* 4.0 13.2 - - - -
213B CYS* 3.4 17.2 - - - +
214B THR* 3.8 17.3 - - - -
244B PRO* 3.5 6.0 - - + +
245B VAL 5.3 0.2 - - - +
246B LEU* 3.7 28.9 - - + -
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Residues in contact with ALA 175 (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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168A THR* 4.1 18.8 - - + -
204A ALA* 5.7 2.9 - - + -
209A ILE* 5.6 1.1 - - + -
171B VAL 2.9 17.0 + - - +
172B THR 3.6 4.0 - - - +
174B MET* 1.3 75.5 - - - +
176B ASP* 1.3 58.1 + - - +
178B PHE* 3.4 4.9 + - - +
179B ALA* 3.1 27.0 + - - +
213B CYS* 3.6 20.6 - - + +
522B LEU* 3.7 20.1 - - + +
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Residues in contact with ASP 176 (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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144B HIS* 4.5 3.6 - - + -
147B GLU* 2.5 30.7 - - - +
172B THR 2.8 17.5 + - - +
173B PRO* 3.5 5.6 - - + +
175B ALA* 1.3 74.9 - - - +
177B ALA* 1.3 63.2 + - - +
179B ALA* 3.3 3.3 + - - +
180B ASP* 3.1 30.1 + - - +
182B ILE* 4.5 2.1 - - - +
519B SER* 2.6 31.3 + - - -
522B LEU* 3.4 12.6 - - + +
524B THR* 2.9 21.7 + - - +
527B TYR* 4.1 7.6 - - - -
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Residues in contact with ALA 177 (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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147B GLU* 3.2 15.9 + - + +
173B PRO 2.8 20.9 + - - +
174B MET 3.8 1.3 - - - +
176B ASP* 1.3 73.5 - - - +
178B PHE* 1.3 56.9 + - - +
181B GLY* 3.0 10.0 + - - -
182B ILE* 2.8 51.0 + - + +
184B MET* 3.6 22.0 - - + -
244B PRO* 3.7 6.7 - - + +
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Residues in contact with PHE 178 (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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199A ASP* 5.3 9.2 - - - -
174B MET 2.8 17.8 + - - +
175B ALA* 3.5 7.9 - - - +
177B ALA* 1.3 79.7 - - - +
179B ALA* 1.3 62.5 - - + +
181B GLY* 3.6 2.6 + - - -
212B SER 3.6 18.4 - - - -
213B CYS* 3.5 21.3 - - + +
214B THR* 3.5 29.2 - - - -
215B LYS* 3.7 14.8 - - + -
241B ARG* 3.4 17.0 + - - -
243B GLY* 5.4 0.2 - - - -
244B PRO* 3.6 11.4 - - + +
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Residues in contact with ALA 179 (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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175B ALA 3.1 16.6 + - - +
176B ASP 3.3 3.8 + - - +
178B PHE* 1.3 82.1 - - + +
180B ASP* 1.3 59.5 + - - +
181B GLY 3.3 0.2 - - - -
241B ARG* 2.9 19.7 + - - +
376B ARG* 4.0 15.8 + - - +
521B GLY* 3.9 6.7 - - - -
522B LEU* 3.7 31.4 - - + +
1701B FAD 4.2 0.3 + - - -
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Residues in contact with ASP 180 (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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151B ARG* 3.4 24.7 + - - +
176B ASP* 3.1 20.8 + - - +
179B ALA* 1.3 75.3 - - - +
181B GLY* 1.3 66.1 + - - +
182B ILE* 3.5 11.8 - - + +
241B ARG* 3.4 7.4 - - - +
308B ALA* 5.4 1.0 - - - +
336B GLN* 3.0 19.4 + - - +
518B THR 3.8 1.7 - - - +
519B SER* 3.6 10.2 + - - -
520B GLY 3.1 18.4 + - - -
521B GLY* 2.7 29.5 + - - -
527B TYR* 6.0 0.2 - - - -
1701B FAD 3.5 17.3 + - - -
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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