Contacts of the helix formed by residues 170 - 181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A GLU* 3.7 24.2 - - + +
143A GLY* 5.1 2.9 - - - +
159A VAL* 4.4 9.0 - - + -
161A VAL* 4.1 14.6 - - + -
166A GLY 3.7 12.3 - - - +
167A ALA* 3.0 26.7 - - - +
169A ASN* 1.3 80.0 - - - +
171A VAL* 1.3 65.5 + - - +
173A PRO* 3.2 14.5 - - + +
174A MET* 3.1 40.1 + - + +
186A VAL* 4.0 19.1 - - + -
188A THR* 4.7 2.0 - - + -
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA 4.0 4.0 - - - +
168A THR* 3.3 30.3 + - - +
169A ASN 3.5 0.2 - - - -
170A VAL* 1.3 77.2 - - - +
172A THR* 1.3 59.2 + - - +
174A MET* 3.2 16.0 + - + +
175A ALA* 2.8 27.2 + - - +
209A ILE* 3.9 20.9 - - + -
213A CYS* 4.2 17.5 - - - -
168B THR* 4.1 27.1 - - + +
171B VAL* 4.3 7.2 - - + -
209B ILE* 4.4 15.9 - - + -
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLN* 4.3 3.8 - - - +
144A HIS* 4.2 6.3 - - + +
168A THR 5.0 0.4 + - - -
169A ASN 4.9 1.5 + - - -
171A VAL* 1.3 79.3 - - - +
173A PRO* 1.3 67.0 - - + +
175A ALA* 3.1 3.8 + - - +
176A ASP* 2.8 28.4 + - - +
522A LEU* 4.0 2.4 - - + +
524A THR* 3.6 34.1 - - + +
165B PRO* 4.7 2.2 - - + -
168B THR* 2.8 28.1 + - - +
169B ASN* 2.5 35.4 + - - +
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Residues in contact with PRO 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 3.6 37.0 - - + +
143A GLY* 3.6 29.6 - - - +
144A HIS* 3.8 7.6 - - + -
147A GLU* 3.5 14.9 - - - +
169A ASN 3.9 4.9 - - - +
170A VAL* 3.2 21.1 - - + +
172A THR* 1.3 96.5 - - + +
174A MET* 1.3 56.2 + - - +
176A ASP* 3.3 1.9 + - - +
177A ALA* 2.9 27.9 + - - +
184A MET* 3.6 6.3 - - + +
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Residues in contact with MET 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA 4.5 1.1 - - - +
170A VAL* 3.1 40.0 + - + +
171A VAL* 3.6 19.1 - - + +
173A PRO* 1.3 73.2 - - - +
175A ALA* 1.3 61.4 + - - +
177A ALA 3.2 0.5 + - - -
178A PHE* 2.9 30.0 + - - +
184A MET* 3.6 9.6 - - + -
186A VAL* 3.9 29.2 - - + -
210A SER* 3.9 13.0 - - - -
213A CYS* 3.4 17.5 - - - +
214A THR* 3.8 18.6 - - + -
244A PRO* 3.5 5.8 - - + +
245A VAL 5.3 0.2 - - - +
246A LEU* 3.7 31.0 - - + -
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL 2.8 20.3 + - - +
172A THR 3.6 4.0 - - - +
174A MET* 1.3 73.3 - - - +
176A ASP* 1.3 60.9 + - - +
178A PHE* 3.5 3.9 + - - +
179A ALA* 3.2 22.9 + - - +
213A CYS* 3.7 21.0 - - + +
522A LEU* 3.8 21.6 - - + +
168B THR* 4.2 19.3 - - + -
209B ILE* 5.7 1.1 - - + -
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Residues in contact with ASP 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A HIS* 4.5 2.0 - - + -
147A GLU* 2.5 29.4 - - - +
172A THR 2.8 16.5 + - - +
173A PRO* 3.5 6.1 - - + +
174A MET 3.1 0.2 - - - -
175A ALA* 1.3 76.3 - - - +
177A ALA* 1.3 63.6 + - - +
179A ALA* 3.4 3.8 + - - +
180A ASP* 3.2 30.5 + - - +
182A ILE* 4.5 1.2 - - - +
519A SER* 2.7 28.9 + - - -
522A LEU* 3.7 12.0 - - - +
524A THR* 2.8 23.3 + - - +
527A TYR* 3.8 11.2 - - - -
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLU* 3.3 14.1 + - + +
173A PRO 2.9 16.9 + - - +
174A MET 3.8 2.2 - - - +
176A ASP* 1.3 74.1 - - - +
178A PHE* 1.3 60.4 + - - +
181A GLY* 2.9 11.1 + - - -
182A ILE* 2.9 51.1 + - + +
184A MET* 3.7 20.2 - - + -
244A PRO* 3.6 7.4 - - + +
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A MET 2.9 17.4 + - - +
175A ALA* 3.6 8.1 - - - +
177A ALA* 1.3 79.5 - - - +
179A ALA* 1.3 63.9 + - - +
180A ASP 3.6 0.2 + - - -
181A GLY* 3.6 3.0 + - - -
212A SER 3.7 22.0 - - - -
213A CYS* 3.6 9.4 - - + +
214A THR* 3.5 41.5 - - - -
215A LYS* 3.7 13.9 - - + -
241A ARG* 3.6 15.1 + - - -
243A GLY* 5.3 0.4 - - - -
244A PRO* 3.5 10.1 - - + +
411A LYS* 6.2 2.7 - - - -
199B ASP* 5.6 5.8 - - - -
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ALA 3.2 13.4 + - - +
176A ASP 3.8 3.4 - - - +
177A ALA 3.3 0.2 - - - -
178A PHE* 1.3 83.8 - - + +
180A ASP* 1.3 56.3 + - - +
241A ARG* 2.7 25.1 + - - +
376A ARG* 3.8 16.2 + - - +
521A GLY* 3.9 7.0 - - - -
522A LEU* 3.8 29.8 - - + +
701A FAD 4.1 0.3 + - - -
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 3.8 21.3 + - - +
176A ASP* 3.2 23.4 + - - +
179A ALA* 1.3 76.2 - - - +
181A GLY* 1.3 66.0 + - - +
182A ILE* 3.4 15.8 + - + +
241A ARG* 3.4 7.2 - - - +
308A ALA* 5.5 0.5 - - - +
336A GLN* 3.3 20.1 + - - +
518A THR 3.8 1.7 - - - +
519A SER* 3.6 10.6 + - - -
520A GLY 3.1 17.5 + - - -
521A GLY* 2.8 27.6 + - - -
522A LEU 5.0 0.4 + - - -
527A TYR* 6.0 0.2 - - - -
701A FAD 3.6 15.4 + - - -
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 5.3 1.9 + - - -
177A ALA 2.9 8.6 + - - -
178A PHE 3.6 2.8 + - - -
179A ALA 3.4 1.2 - - - -
180A ASP* 1.3 79.0 - - - +
182A ILE* 1.3 55.9 + - - +
183A PRO* 3.9 1.4 - - - +
241A ARG* 3.3 23.0 - - - +
242A PRO* 3.0 44.9 - - - +
243A GLY* 4.5 0.2 - - - -
312A ASN* 5.1 3.3 + - - +
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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