Contacts of the helix formed by residues 192 - 203 (chain B) in PDB entry 4LOU
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 ALA 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LEU 5.0 0.6 - - - +
187B ALA* 3.1 14.1 + - - -
190B PHE* 3.9 14.1 - - + +
191B ASN* 1.3 77.8 - - - +
193B PRO* 1.3 68.9 - - - +
194B LEU 3.2 3.3 + - - -
195B ALA* 3.4 13.2 + - + -
196B GLY 3.1 17.0 + - - -
226B THR* 4.8 0.2 + - - -
411B LEU* 4.0 14.8 - - + -
414B GLU* 3.4 23.1 - - + +
415B MET* 5.2 1.3 - - + -
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Residues in contact with PRO 193 (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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419A TYR* 3.7 6.7 - - - +
422A ILE* 4.4 14.8 - - + -
423A LEU* 4.6 3.4 - - + -
426A ILE* 3.7 28.9 - - + -
187B ALA* 4.2 0.4 - - + -
191B ASN 3.9 4.0 - - - -
192B ALA* 1.3 86.9 - - - +
194B LEU* 1.3 59.9 + - - +
196B GLY 4.0 0.2 - - - -
197B ILE* 3.4 17.8 + - - +
222B VAL* 3.2 36.9 - - + +
223B ILE* 5.6 1.1 - - - +
226B THR* 3.9 25.3 - - + +
230B ARG* 5.2 2.5 - - - +
414B GLU* 3.3 12.3 - - - +
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LEU* 4.1 24.5 - - + -
409A ILE* 4.5 10.5 - - + -
410A ILE* 4.4 15.3 - - + -
413A LEU* 4.1 20.6 - - + -
419A TYR* 4.4 0.4 - - + -
422A ILE* 3.9 24.7 - - + -
426A ILE* 4.4 16.2 - - + -
193B PRO* 1.3 74.7 - - - +
195B ALA* 1.3 61.1 + - - +
196B GLY 3.1 1.3 - - - -
197B ILE* 3.0 5.9 + - + -
198B LEU* 2.8 38.0 + - + +
219B PHE* 5.1 4.5 - - + -
410B ILE* 3.8 14.4 - - + -
414B GLU* 3.1 26.4 + - + +
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Residues in contact with ALA 195 (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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186B LEU* 3.8 8.2 - - + +
192B ALA* 3.4 11.2 + - + -
194B LEU* 1.3 72.8 - - - +
196B GLY* 1.3 57.9 + - - +
198B LEU* 3.8 5.1 - - - +
199B PHE* 2.9 31.5 + - - +
407B THR* 4.2 7.8 - - + +
410B ILE* 4.0 6.7 - - - +
411B LEU* 3.7 37.9 - - + +
414B GLU* 2.7 20.9 + - - +
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Residues in contact with GLY 196 (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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183B ALA* 3.3 37.1 - - - +
186B LEU* 3.8 16.7 - - - +
187B ALA* 4.4 2.7 - - - -
192B ALA 3.1 15.0 + - - -
193B PRO 4.2 2.0 - - - -
194B LEU 3.1 0.2 - - - -
195B ALA* 1.3 79.9 - - - +
197B ILE* 1.3 61.0 + - - +
199B PHE* 3.5 11.3 + - - +
200B ILE 3.7 2.4 + - - -
222B VAL* 4.9 0.4 - - - -
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LEU* 3.8 27.4 - - + -
183B ALA* 4.6 4.0 - - - -
193B PRO 3.4 16.0 + - - +
194B LEU* 3.0 9.7 + - + +
196B GLY* 1.3 72.6 - - - +
198B LEU* 1.3 69.3 + - + +
199B PHE 3.3 0.7 + - - -
200B ILE* 3.4 6.1 + - - +
201B ILE* 3.4 26.7 + - + +
215B ILE* 4.7 9.0 - - + +
218B VAL* 4.6 10.1 - - + -
219B PHE* 3.2 57.2 - - + -
222B VAL* 4.0 15.9 - - + -
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Residues in contact with LEU 198 (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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198A LEU* 3.7 26.2 - - + -
201A ILE* 5.4 0.2 - - + -
406A LEU* 4.2 28.0 - - + -
410A ILE* 4.6 3.4 - - + -
194B LEU* 2.8 26.4 + - - +
195B ALA* 4.0 6.5 - - - +
197B ILE* 1.3 73.6 - - + +
199B PHE* 1.3 53.9 + - - +
201B ILE* 3.2 18.1 + - + +
202B GLU* 2.8 36.8 + - + +
406B LEU* 3.7 20.9 - - + -
407B THR* 3.5 16.2 - - - +
410B ILE* 3.8 26.2 - - + -
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Residues in contact with PHE 199 (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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109B ILE* 4.2 22.0 - - + -
152B VAL* 5.0 4.9 - - + -
182B ALA 5.5 0.9 - - - -
186B LEU* 4.0 35.7 - - + -
195B ALA 2.9 17.5 + - - +
196B GLY 3.6 7.4 - - - +
197B ILE 3.2 0.2 - - - -
198B LEU* 1.3 74.1 - - - +
200B ILE* 1.3 66.8 + - + +
203B GLU* 3.1 33.4 + - + -
204B MET* 3.0 51.6 + - + -
357B PHE* 4.1 20.9 - + - -
402B ILE* 4.3 7.6 - - + -
404B ALA* 5.0 0.7 - - + -
407B THR* 3.4 22.6 + - + -
445B TYR* 4.5 7.4 - + - -
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Residues in contact with ILE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 6.2 0.4 - - + -
179B ALA* 3.5 37.5 - - + +
182B ALA* 4.0 10.8 - - + -
183B ALA* 3.8 32.1 - - + +
196B GLY 3.7 2.7 + - - +
197B ILE 3.4 8.2 + - - +
198B LEU 3.4 0.2 - - - -
199B PHE* 1.3 84.1 - - + +
201B ILE* 1.3 68.8 + - + +
204B MET* 3.4 28.1 + - + -
205B ARG* 2.8 36.5 + - + +
213B ILE* 4.6 12.1 - - + -
218B VAL* 4.7 11.4 - - + -
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 3.5 36.6 - - + -
202A GLU* 6.0 1.3 - - + -
215A ILE* 5.9 1.9 - - + +
406A LEU* 3.9 16.8 - - + -
197B ILE* 3.4 30.9 + - + +
198B LEU* 3.2 18.5 + - + +
200B ILE* 1.3 83.8 - - + +
202B GLU* 1.3 63.9 + - + +
205B ARG* 3.5 25.6 + - - +
207B GLN* 4.3 3.8 + - - -
215B ILE* 4.1 29.6 - - + -
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Residues in contact with GLU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 4.0 6.1 + - - -
201A ILE* 5.9 0.7 - - + -
215A ILE* 4.8 20.7 - - + +
198B LEU 2.8 20.4 + - - +
201B ILE* 1.3 77.1 - - + +
203B GLU* 1.3 58.0 + - - +
207B GLN* 3.4 18.1 + - - +
403B ARG 4.9 2.0 - - - +
404B ALA* 3.0 33.6 - - + -
405B PRO* 3.1 19.8 - - - +
406B LEU* 3.3 24.7 - - + +
407B THR* 2.6 36.5 + - - +
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Residues in contact with GLU 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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28A ARG* 2.9 34.8 + - - +
113B GLU* 3.1 30.4 - - - +
199B PHE* 3.1 34.3 + - + +
201B ILE 3.4 1.2 - - - -
202B GLU* 1.3 83.5 - - + +
204B MET* 1.3 66.0 + - - +
205B ARG 3.4 3.3 - - - +
207B GLN* 3.1 17.1 - - - +
402B ILE* 3.8 21.7 - - + +
403B ARG 4.1 1.9 - - - +
404B ALA* 4.0 9.3 - - + +
443B PRO* 4.9 0.3 - - - +
445B TYR* 3.9 16.9 - - + +
446B SER* 4.3 3.6 + - - -
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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