Contacts of the helix formed by residues 201 - 213 (chain B) in PDB entry 1LQG
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 ASN 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B GLU* 3.8 6.7 - - - -
99B THR* 3.8 10.8 - - - +
199B GLY 4.8 2.0 - - - +
200B CYS* 1.3 73.8 - - - +
202B HIS* 1.3 65.5 + - - +
203B PHE 3.2 2.9 - - - -
204B VAL* 3.0 24.4 + - + -
205B LEU* 2.8 37.1 + - + +
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Residues in contact with HIS 202 (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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95B GLU* 4.5 1.2 + - - -
162B LEU* 3.7 23.0 - - + +
163B LEU 4.6 0.4 - - - -
164B TRP* 3.2 34.0 + + + +
183B LEU* 3.3 51.7 - - + +
184B LYS 2.9 26.3 + - - -
185B ALA* 3.5 4.0 - - + +
200B CYS* 3.3 34.0 + - + -
201B ASN* 1.3 75.6 - - - +
203B PHE* 1.3 62.9 + - + +
205B LEU* 3.9 2.4 - - + +
206B ALA* 2.9 33.1 + - - +
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Residues in contact with PHE 203 (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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60B ILE* 4.5 2.7 - - + -
92B MET* 4.1 20.2 - - + -
95B GLU* 4.3 13.9 - - + -
96B LEU* 3.2 43.3 - - + -
99B THR* 4.3 12.6 - - + -
100B ILE* 5.4 1.6 - - + -
114B TRP* 4.2 12.6 - + - -
162B LEU* 4.6 3.1 - - + -
164B TRP* 4.0 29.8 - + - -
197B PHE* 5.4 4.0 - + - -
201B ASN 3.2 0.8 - - - -
202B HIS* 1.3 80.1 - - + +
204B VAL* 1.3 62.5 + - - +
206B ALA* 3.8 0.3 + - - +
207B ASN* 3.5 14.0 + - - +
220B TRP* 3.0 70.5 + + + +
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Residues in contact with VAL 204 (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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99B THR* 3.6 25.6 + - + +
100B ILE* 5.6 6.0 - - + +
101B PRO* 5.7 3.1 - - + -
201B ASN* 3.0 32.2 + - + +
203B PHE* 1.3 79.3 - - - +
205B LEU* 1.3 73.4 + - + +
207B ASN* 3.3 7.6 + - + +
208B GLN* 2.9 27.9 + - + +
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Residues in contact with LEU 205 (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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181B HIS* 5.0 4.9 + - - +
183B LEU* 3.8 31.2 - - + -
201B ASN* 2.8 29.5 + - + +
202B HIS* 5.5 2.0 - - + -
204B VAL* 1.3 90.7 - - + +
206B ALA* 1.3 60.7 + - - +
208B GLN* 3.2 27.7 - - - +
209B TRP* 2.9 30.3 + - - +
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Residues in contact with ALA 206 (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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58B VAL* 4.5 8.5 - - + -
160B VAL* 3.9 27.6 - - + -
162B LEU* 4.2 8.3 - - + -
181B HIS* 5.5 0.2 - - - -
183B LEU* 4.8 0.8 - - - +
202B HIS 2.9 19.7 + - - +
203B PHE 4.0 4.3 - - - +
205B LEU* 1.3 76.8 - - - +
207B ASN* 1.3 58.2 + - - +
209B TRP* 3.5 3.0 - - - +
210B LEU* 3.1 35.4 + - - +
220B TRP* 4.3 14.8 - - + -
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Residues in contact with ASN 207 (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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100B ILE* 5.5 3.4 - - - +
203B PHE 3.5 3.7 + - - +
204B VAL* 3.3 10.6 + - + +
206B ALA* 1.3 77.6 - - - +
208B GLN* 1.3 60.3 + - - +
210B LEU* 3.7 4.5 - - - +
211B GLU* 2.8 32.8 + - - +
217B PRO* 3.5 13.3 - - + +
218B ILE* 2.6 55.1 + - - +
220B TRP* 3.0 25.8 - - - +
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Residues in contact with GLN 208 (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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204B VAL* 2.9 14.4 + - + +
205B LEU* 3.2 36.1 - - - +
207B ASN* 1.3 78.8 - - - +
209B TRP* 1.3 60.7 + - - +
211B GLU* 3.4 5.3 + - - +
212B GLN* 2.9 28.5 + - - +
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Residues in contact with TRP 209 (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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158B GLY* 3.0 46.4 - - - -
160B VAL* 4.1 7.9 - - + -
178B GLN 5.4 4.0 - - - -
179B ARG 4.6 2.9 - - - -
180B HIS 4.4 3.1 - - - -
181B HIS* 3.2 68.7 + + + -
205B LEU 2.9 12.1 + - - +
206B ALA* 3.5 9.6 - - - +
208B GLN* 1.3 76.9 - - - +
210B LEU* 1.3 70.9 + - + +
212B GLN* 2.7 21.0 + - + +
213B ARG* 3.0 48.1 + - - +
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Residues in contact with LEU 210 (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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57B LYS* 3.3 49.4 - - + +
58B VAL* 4.8 4.0 - - + -
158B GLY 4.7 2.7 - - - +
160B VAL* 3.4 27.1 - - + -
206B ALA 3.1 18.7 + - - +
207B ASN* 3.7 10.1 - - - +
209B TRP* 1.3 85.5 - - + +
211B GLU* 1.3 65.8 + - - +
213B ARG* 2.9 24.4 + - - +
215B GLU* 3.4 27.2 + - + +
216B THR 4.1 6.7 - - - +
217B PRO* 4.5 10.3 - - + -
218B ILE* 4.7 6.1 - - + -
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Residues in contact with GLU 211 (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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207B ASN 2.8 20.5 + - - +
208B GLN* 3.5 6.3 - - - +
210B LEU* 1.3 76.7 - - - +
212B GLN* 1.3 53.6 + - - +
214B GLY* 2.7 26.9 + - - -
215B GLU 3.9 10.7 + - - -
217B PRO* 5.2 11.1 - - + +
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Residues in contact with GLN 212 (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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208B GLN* 2.9 13.2 + - - +
209B TRP* 2.7 23.1 + - + +
211B GLU* 1.3 71.6 - - - +
213B ARG* 1.3 58.6 + - + +
214B GLY 3.5 0.3 + - - -
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Residues in contact with ARG 213 (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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157B GLU* 5.0 6.3 + - - +
158B GLY* 4.0 21.9 + - - +
179B ARG 5.5 0.6 + - - -
209B TRP* 3.0 53.9 + - - +
210B LEU* 2.9 19.3 + - - +
212B GLN* 1.3 76.1 - - - +
214B GLY* 1.3 55.9 + - - +
215B GLU* 3.0 36.4 + - + +
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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