Contacts of the helix formed by residues 181 - 190 (chain A) in PDB entry 1TH1
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 LYS 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ASP* 3.4 29.1 + - - -
177A GLN 4.9 6.5 - - - +
178A LEU* 3.3 16.7 + - + +
179A SER 3.4 0.2 - - - -
180A LYS* 1.3 81.8 - - + +
182A GLU* 1.3 64.3 + - - +
183A ALA* 4.4 10.1 - - - +
184A SER* 3.3 25.6 - - - +
185A ARG* 3.1 25.2 + - - +
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Residues in contact with GLU 182 (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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180A LYS 3.9 0.4 + - - -
181A LYS* 1.3 72.2 - - - +
183A ALA* 1.3 61.1 + - - +
185A ARG* 3.4 29.9 + - - +
186A HIS* 3.0 50.1 + - + -
224A HIS* 5.9 0.2 - - + -
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Residues in contact with ALA 183 (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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145A ASP* 3.8 37.0 - - + +
146A ALA* 5.5 4.0 - - + +
181A LYS* 3.5 8.6 - - - +
182A GLU* 1.3 78.7 - - - +
184A SER* 1.3 59.8 + - - +
186A HIS* 3.7 8.7 + - - +
187A ALA* 3.6 15.6 + - - +
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP* 5.4 1.1 - - - -
149A ALA* 4.4 17.9 - - - -
153A ILE* 5.1 1.2 - - - +
178A LEU* 2.6 47.6 + - - +
181A LYS* 3.3 25.2 - - - +
182A GLU 3.4 0.2 - - - -
183A ALA* 1.3 75.6 - - - +
185A ARG* 1.3 62.9 + - - +
186A HIS 3.3 0.7 - - - -
187A ALA* 3.3 9.8 + - - +
188A ILE* 3.2 27.0 + - - +
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Residues in contact with ARG 185 (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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178A LEU 4.0 4.0 - - - -
179A SER* 3.0 24.8 + - - +
180A LYS 3.3 22.8 + - - -
181A LYS 3.1 14.0 + - - +
182A GLU* 3.5 40.9 - - - +
183A ALA 3.4 0.2 - - - -
184A SER* 1.3 74.5 + - - +
186A HIS* 1.3 64.6 + - - +
188A ILE* 3.4 8.3 + - - +
189A MET* 3.1 24.2 + - - +
220A ASN* 3.7 16.8 - - + +
221A LEU* 3.6 18.8 - - + +
224A HIS* 3.2 35.5 + - + +
1516C ILE* 3.5 32.1 - - - +
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Residues in contact with HIS 186 (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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182A GLU* 3.0 46.1 + - + -
183A ALA* 3.7 11.7 - - - +
184A SER 3.3 0.2 - - - -
185A ARG* 1.3 79.5 - - - +
187A ALA* 1.3 56.1 + - - +
189A MET* 3.5 15.9 - - + +
190A ARG* 3.0 61.7 + - - +
224A HIS* 4.0 29.5 + + - -
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Residues in contact with ALA 187 (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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145A ASP 4.9 2.5 - - - +
146A ALA* 6.0 1.1 - - - -
149A ALA* 4.7 11.7 - - + +
150A THR* 4.7 14.1 - - - +
153A ILE* 4.1 22.0 - - + +
183A ALA 3.6 7.8 + - - +
184A SER* 3.3 16.8 + - - +
185A ARG 3.2 0.6 - - - -
186A HIS* 1.3 78.6 - - - +
188A ILE* 1.3 62.2 + - - +
190A ARG* 3.8 8.6 + - - +
191A SER* 3.4 16.8 + - - -
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Residues in contact with ILE 188 (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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153A ILE* 3.8 21.5 - - + -
175A VAL* 3.7 31.0 - - + +
178A LEU* 4.2 6.5 - - + -
179A SER* 4.1 22.4 - - - +
184A SER 3.2 16.4 + - - +
185A ARG* 3.7 6.5 - - - +
187A ALA* 1.3 74.3 - - - +
189A MET* 1.3 63.9 + - - +
191A SER* 3.3 26.2 + - - +
194A MET* 3.8 9.6 - - - +
195A VAL* 3.4 6.0 - - + +
198A ILE* 3.7 29.2 - - + -
217A THR* 4.6 1.8 - - + -
221A LEU* 4.2 16.2 - - + -
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Residues in contact with MET 189 (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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185A ARG 3.2 11.9 - - - +
186A HIS* 3.5 21.3 - - + +
188A ILE* 1.3 81.2 - - - +
190A ARG* 1.3 81.7 + - - +
191A SER 3.4 2.4 + - - -
192A PRO* 5.0 0.3 - - - +
195A VAL* 4.3 5.7 - - - +
221A LEU* 3.8 13.7 - - + +
224A HIS* 3.6 41.7 - - + -
226A GLU* 3.4 38.2 - - + +
227A GLY* 3.6 22.4 - - - +
230A ALA* 4.0 17.3 - - - +
1519C ASP* 5.9 0.9 - - - +
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Residues in contact with ARG 190 (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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186A HIS* 3.0 58.5 + - - +
187A ALA* 4.3 6.5 - - - +
188A ILE 3.4 0.4 - - - -
189A MET* 1.3 83.0 - - - +
191A SER* 1.3 58.3 + - - +
192A PRO* 3.6 9.9 - - - +
226A GLU* 3.0 39.8 + - - +
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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