Contacts of the helix formed by residues 183 - 197 (chain B) in PDB entry 4L6V
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 PHE 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B HIS* 2.9 26.0 + - + +
179B LEU* 3.4 20.0 - - + +
181B GLY 3.9 0.2 - - - -
182B LEU* 1.3 98.5 - - + +
184B GLY* 1.3 66.1 + - - +
186B SER* 3.9 0.7 - - - -
187B SER* 2.9 27.1 + - - -
284B PHE* 3.2 36.8 - + + -
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Residues in contact with GLY 184 (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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179B LEU 3.1 11.8 + - - -
180B ALA 3.1 9.2 + - - -
183B PHE* 1.3 78.3 - - - +
185B VAL* 1.3 51.9 + - - +
187B SER 3.0 2.9 + - - -
188B LEU* 2.8 31.1 + - - -
281B ALA* 3.2 31.4 - - - +
284B PHE* 3.8 7.6 - - - +
285B ILE* 4.1 4.0 - - - -
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Residues in contact with VAL 185 (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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180B ALA 2.8 18.4 + - - +
181B GLY* 3.3 17.0 + - - +
184B GLY* 1.3 71.5 - - - +
186B SER* 1.3 55.1 + - - +
188B LEU* 3.4 16.0 - - + +
189B ALA* 2.7 37.7 + - + +
285B ILE* 4.5 10.5 - - + +
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Residues in contact with SER 186 (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 GLY 3.1 9.1 + - - -
182B LEU* 2.8 36.9 + - - +
183B PHE 3.9 1.1 - - - -
184B GLY 3.2 0.6 - - - -
185B VAL* 1.3 78.8 - - - +
187B SER* 1.3 61.3 + - - +
189B ALA* 3.7 6.9 + - - +
190B TRP* 3.4 19.1 + - - +
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Residues in contact with SER 187 (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 PHE 2.9 19.7 + - - -
184B GLY 3.4 3.1 - - - -
186B SER* 1.3 75.1 - - - +
188B LEU* 1.3 66.0 + - - +
190B TRP* 3.2 5.6 + - - +
191B ALA 3.1 17.8 + - - -
276B HIS* 5.7 0.2 - - - -
277B HIS* 3.1 40.8 + - - +
280B ILE* 3.3 24.7 - - - +
281B ALA* 4.1 0.9 - - - -
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Residues in contact with LEU 188 (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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184B GLY 2.8 13.1 + - - +
185B VAL* 3.1 19.9 + - + +
187B SER* 1.3 78.6 - - - +
189B ALA* 1.3 57.0 + - - +
191B ALA* 3.3 6.9 + - - +
192B GLY* 3.0 22.9 + - - -
278B LEU* 3.4 32.1 - - + -
281B ALA* 3.5 14.9 - - + +
282B VAL* 6.0 1.8 - - + -
285B ILE* 4.8 13.2 - - + -
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B VAL* 2.7 25.3 + - + +
186B SER* 3.9 7.9 - - - +
187B SER 3.2 0.2 - - - -
188B LEU* 1.3 75.8 - - - +
190B TRP* 1.3 56.3 - - - +
192B GLY* 3.2 3.9 + - - -
193B HIS* 3.0 23.7 + - - +
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Residues in contact with TRP 190 (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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123B TRP* 5.0 6.1 - + - -
127B ILE* 3.5 41.5 - - + -
186B SER 3.4 10.7 + - - +
187B SER* 3.2 9.3 + - - +
189B ALA* 1.3 74.7 - - - +
191B ALA* 1.3 66.0 + - - +
192B GLY 3.0 1.6 - - - -
193B HIS* 3.0 40.8 + + + +
194B LEU* 2.9 53.0 + - + +
273B ILE* 5.1 2.2 - - - +
277B HIS* 3.3 34.4 + + + -
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Residues in contact with ALA 191 (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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187B SER 3.1 7.5 + - - +
188B LEU* 3.5 10.1 - - + +
190B TRP* 1.3 75.7 - - - +
192B GLY* 1.3 59.7 + - - +
194B LEU* 3.5 9.3 + - - +
195B VAL* 3.4 29.2 + - + +
255B LEU* 6.1 0.4 - - + -
274B ALA* 3.6 20.8 - - - +
277B HIS* 3.7 10.0 - - + +
278B LEU* 3.7 29.8 - - + +
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Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU 3.0 13.3 + - - -
189B ALA* 3.2 5.8 + - - -
190B TRP 3.0 0.8 - - - -
191B ALA* 1.3 75.8 - - - +
193B HIS* 1.3 63.4 + - - +
195B VAL* 3.4 9.8 - - - +
196B HIS* 3.3 28.5 + - - +
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Residues in contact with HIS 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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127B ILE* 3.2 32.0 + - + -
189B ALA 3.0 10.6 + - - +
190B TRP* 3.0 48.5 + + + +
192B GLY* 1.3 75.7 - - - +
194B LEU* 1.3 58.9 + - - +
196B HIS* 4.7 2.7 - - - -
197B VAL* 2.9 61.3 + - + +
198B ALA* 3.4 3.2 + - - +
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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
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127B ILE* 5.5 2.0 - - + -
190B TRP* 2.9 53.0 + - + +
191B ALA* 3.8 4.0 - - - +
192B GLY 3.3 0.2 - - - -
193B HIS* 1.3 77.4 - - - +
195B VAL* 1.3 59.6 + - - +
198B ALA* 3.5 22.3 + - + -
199B ILE* 2.8 36.5 + - + +
270B LEU* 5.0 11.4 - - + +
273B ILE* 3.7 22.0 - - + +
274B ALA* 3.4 43.1 - - + +
277B HIS* 4.3 0.9 - - - +
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Residues in contact with VAL 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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191B ALA 3.4 13.0 + - - +
192B GLY* 3.4 15.9 - - - +
194B LEU* 1.3 76.5 - - - +
196B HIS* 1.3 64.7 + - - +
199B ILE* 4.2 7.2 - - + -
200B PRO* 3.4 16.2 - - - +
217B PRO* 3.7 40.4 - - + +
254B ILE* 4.1 23.7 - - + +
255B LEU* 4.0 17.7 - - + -
274B ALA* 4.0 18.4 - - + -
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Residues in contact with HIS 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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192B GLY* 3.3 19.5 + - - +
193B HIS* 4.1 0.9 - - - +
195B VAL* 1.3 86.0 - - + +
197B VAL* 1.3 68.5 + - + +
200B PRO* 3.2 7.4 - - - +
207B VAL* 3.1 30.0 - - - +
212B PHE* 3.4 43.5 + + + -
215B THR* 4.4 10.3 + - - +
217B PRO* 3.4 34.0 - - + +
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Residues in contact with VAL 197 (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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127B ILE 4.3 4.5 - - - +
128B GLY* 4.6 8.7 - - - +
193B HIS* 2.9 44.2 + - + +
195B VAL 3.5 0.6 - - - -
196B HIS* 1.3 92.7 - - + +
198B ALA* 1.3 66.0 + - - +
199B ILE 3.3 1.6 - - - -
200B PRO* 3.3 2.6 - - - +
201B GLU* 3.0 35.8 + - - +
207B VAL* 3.6 27.8 - - + +
208B GLY* 5.8 1.1 - - - -
212B PHE* 5.6 4.7 - - + -
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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