Contacts of the helix formed by residues 180 - 191 (chain A) in PDB entry 1L6N
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 THR 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A HIS* 4.3 15.9 - - + +
178A GLY 5.4 1.1 - - - +
179A ALA* 1.3 79.6 - - - +
181A PRO* 1.4 69.2 - - - +
182A GLN* 3.1 10.2 + - - +
183A ASP* 3.2 15.7 + - + +
184A LEU* 2.8 40.6 + - - +
243A LEU* 3.2 7.1 - - - +
247A ILE* 3.3 35.2 - - + -
250A MET* 3.8 13.0 - - + -
259A GLY* 4.7 0.7 - - - -
262A TYR* 4.6 0.4 - - - -
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Residues in contact with PRO 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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180A THR* 1.4 93.5 - - - +
182A GLN* 1.3 53.3 + - - +
183A ASP 3.2 0.2 - - - -
185A ASN* 2.6 51.7 + - - +
237A ALA 4.4 10.3 - - - +
238A GLY* 5.2 4.0 - - - -
242A THR 5.5 0.7 - - - +
243A LEU* 3.6 15.7 - - + +
246A GLN* 3.6 36.1 - - + +
259A GLY* 5.5 1.1 - - - -
262A TYR* 3.4 32.5 - - + -
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Residues in contact with GLN 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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146A ALA* 5.9 7.4 - - + -
180A THR* 3.1 1.7 + - - +
181A PRO* 1.3 82.6 - - - +
183A ASP* 1.3 58.7 + - - +
185A ASN* 4.0 8.8 + - - +
186A THR* 3.2 28.4 + - - +
243A LEU* 3.7 34.0 - - + +
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Residues in contact with ASP 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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146A ALA* 5.7 1.1 - - - -
147A ILE* 2.6 47.9 - - + +
175A LEU 4.9 5.2 - - - +
176A SER* 5.6 0.9 - - - -
179A ALA* 2.6 28.7 - - - +
180A THR* 3.2 22.4 + - + +
181A PRO 3.2 0.2 - - - -
182A GLN* 1.3 77.0 - - - +
184A LEU* 1.3 63.0 + - - +
185A ASN 3.1 0.9 - - - -
186A THR* 3.1 6.7 + - - +
187A MET* 2.9 27.2 + - - +
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Residues in contact with LEU 184 (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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172A PHE* 4.2 3.6 - - + -
176A SER* 3.2 39.9 - - - +
179A ALA* 3.3 27.4 - - + +
180A THR 2.8 31.1 + - - +
181A PRO* 4.2 2.7 - - + +
183A ASP* 1.3 73.9 - - - +
185A ASN* 1.3 57.6 + - - +
187A MET* 3.4 4.5 + - - +
188A LEU* 2.8 35.9 + - - +
259A GLY 4.0 10.1 - - - +
262A TYR* 4.0 20.0 - - + -
263A LYS* 4.0 11.7 - - + +
266A ILE* 3.7 26.5 - - + -
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Residues in contact with ASN 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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181A PRO* 2.6 38.9 + - - +
182A GLN* 4.0 11.5 + - - +
184A LEU* 1.3 71.1 - - - +
186A THR* 1.3 59.6 + - - +
188A LEU* 3.3 7.1 + - - +
189A ASN* 2.8 41.3 + - - +
237A ALA 5.4 2.8 + - - -
262A TYR* 2.8 26.6 + - - -
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Residues in contact with THR 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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147A ILE* 3.2 20.6 - - + +
152A LEU* 3.1 42.8 - - + +
182A GLN* 3.2 18.9 + - - +
183A ASP 3.1 4.6 + - - +
185A ASN* 1.3 80.8 - - - +
187A MET* 1.3 57.5 + - - +
189A ASN* 3.0 9.2 + - - +
190A THR* 2.9 24.6 + - - -
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Residues in contact with MET 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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147A ILE* 4.9 6.7 - - + -
152A LEU* 3.4 14.1 - - + -
155A TRP* 3.1 64.3 + - + -
172A PHE* 3.1 41.1 - - + +
175A LEU* 3.5 38.4 - - + +
176A SER* 4.2 4.0 - - - +
183A ASP* 2.9 20.0 + - - +
184A LEU* 3.7 7.4 - - - +
186A THR* 1.3 71.7 - - - +
188A LEU* 1.3 57.6 + - - +
189A ASN 3.0 4.7 - - - -
190A THR* 3.0 6.4 - - - +
191A VAL 3.0 23.9 + - - -
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Residues in contact with LEU 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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172A PHE* 3.3 40.4 - - + -
184A LEU 2.8 20.4 + - - +
185A ASN* 3.8 6.1 - - - +
187A MET* 1.3 76.0 - - - +
189A ASN* 1.3 59.0 + - - +
191A VAL* 2.7 31.7 - - + +
198A MET* 3.4 23.0 - - + +
201A LEU* 3.5 28.3 - - + -
205A ILE* 4.9 3.1 - - + -
262A TYR* 5.8 3.8 - - - +
266A ILE* 3.6 23.1 - - + -
270A LEU* 5.3 0.9 - - + -
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Residues in contact with ASN 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 ASN* 2.8 27.3 + - - +
186A THR* 3.1 13.9 - - - +
187A MET 3.0 0.2 - - - -
188A LEU* 1.3 78.2 - - - +
190A THR* 1.3 62.2 + - - +
191A VAL* 3.0 11.8 + - - +
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Residues in contact with THR 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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152A LEU* 3.3 35.4 + - + +
155A TRP* 3.5 16.6 - - + -
156A VAL* 2.8 39.7 - - + +
159A VAL* 5.9 0.2 - - - +
186A THR 2.9 5.0 + - - -
187A MET 3.0 17.7 - - - +
189A ASN* 1.3 72.6 - - - +
191A VAL* 1.3 71.9 + - - +
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A TRP* 3.6 17.5 - - + +
159A VAL* 3.5 31.9 - - + -
163A ALA* 5.6 1.6 - - + -
187A MET 3.0 11.5 + - - +
188A LEU* 2.7 27.1 - - + +
189A ASN 3.0 8.7 - - - +
190A THR* 1.3 92.5 - - - +
192A GLY* 1.3 65.9 + - - +
193A GLY 5.0 1.1 - - - +
198A MET* 3.3 35.9 - - + -
270A LEU* 6.3 1.1 - - + -
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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