Contacts of the helix formed by residues 215 - 233 (chain B) in PDB entry 4LT6
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 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B VAL* 3.4 4.5 - - - +
214B PRO* 1.3 82.4 - - + +
216B LYS* 1.3 63.2 + - - +
217B GLU* 2.9 25.1 + - - +
218B THR* 3.3 33.5 + - - +
219B PHE* 3.2 21.7 + - - +
256B CYS* 5.4 1.8 - - - +
260B PRO 4.5 13.8 + - - +
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Residues in contact with LYS 216 (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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210B LEU* 3.9 40.8 - - + +
211B HIS* 6.1 3.8 - - - -
213B VAL* 3.9 12.8 - - + +
214B PRO 4.2 0.4 - - - -
215B ASN* 1.3 74.5 + - - +
217B GLU* 1.3 61.7 + - - +
219B PHE* 3.3 3.6 + - - +
220B ARG* 3.1 57.4 + - - +
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Residues in contact with GLU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASN* 2.9 13.5 + - - +
216B LYS* 1.3 80.4 - - - +
218B THR* 1.3 67.3 + - - +
219B PHE 3.3 0.7 + - - -
220B ARG* 3.4 12.5 + - - +
221B LEU* 3.3 20.6 + - - +
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Residues in contact with THR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASN* 3.3 36.3 + - - +
217B GLU* 1.3 79.9 - - - +
219B PHE* 1.3 66.4 + - - +
221B LEU* 4.1 5.5 - - - +
222B THR* 2.9 31.1 + - - -
256B CYS* 5.0 1.6 - - - +
260B PRO 5.3 1.9 + - - -
262B ALA 3.6 18.2 + - - +
263B ALA* 4.7 2.2 - - - -
264B ALA* 4.3 13.6 - - + +
267B LEU* 3.7 21.8 - - - +
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Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.1 12.6 - - + -
106B VAL* 5.6 0.2 - - + -
209B ILE* 4.0 19.5 - - + -
210B LEU* 3.6 31.9 - - + -
213B VAL* 3.8 24.2 - - + -
215B ASN 3.2 21.0 + - - +
216B LYS* 3.3 6.5 - - - +
217B GLU 3.1 0.2 - - - -
218B THR* 1.3 80.4 + - - +
220B ARG* 1.3 66.9 + - + +
222B THR* 3.6 1.9 - - - -
223B LEU* 2.8 42.6 + - + +
249B ALA* 3.7 25.6 - - + -
252B VAL* 4.0 15.9 - - + -
253B ALA* 3.9 10.3 - - + -
256B CYS* 3.9 13.9 - - - -
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Residues in contact with ARG 220 (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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103B ARG* 5.2 2.4 + - - +
104B LEU 2.8 30.1 + - - +
105B GLY* 3.8 15.7 - - - +
106B VAL* 3.4 16.1 - - + +
210B LEU* 4.8 11.7 - - - +
216B LYS* 3.1 56.3 + - - +
217B GLU* 3.4 10.4 + - - +
219B PHE* 1.3 86.2 - - + +
221B LEU* 1.3 63.6 + - - +
223B LEU* 3.3 1.0 + - - -
224B ARG* 2.9 34.2 + - - +
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Residues in contact with LEU 221 (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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38B THR* 3.7 20.0 - - + -
41B LEU* 5.2 3.8 - - + -
42B ILE* 4.0 19.5 - - + -
45B MET* 3.7 29.8 - - + +
51B PHE* 4.1 20.9 - - + -
217B GLU 3.3 12.6 + - - +
218B THR* 4.1 0.9 - - - +
219B PHE 3.2 0.8 - - - -
220B ARG* 1.3 80.0 - - - +
222B THR* 1.3 63.1 + - - +
224B ARG* 3.2 9.2 + - - +
225B ALA* 3.0 20.1 + - - +
264B ALA* 3.6 27.1 - - + -
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Residues in contact with THR 222 (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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218B THR 2.9 22.6 + - - -
219B PHE* 3.6 3.1 - - - -
221B LEU* 1.3 76.2 - - - +
223B LEU* 1.3 58.0 + - - +
225B ALA* 3.0 8.1 + - - +
226B VAL* 2.9 34.7 + - + +
252B VAL* 3.6 21.3 - - + -
255B THR* 5.8 1.3 - - + -
264B ALA* 3.7 9.1 + - - +
267B LEU* 3.2 29.0 - - + +
268B VAL* 3.9 28.5 - - + +
271B PHE* 5.2 2.7 - - + -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.5 6.1 - - + -
106B VAL* 3.4 37.9 - - + -
219B PHE* 2.8 27.6 + - + +
220B ARG* 3.5 5.4 - - - +
221B LEU 3.1 0.2 - - - -
222B THR* 1.3 77.3 - - - +
224B ARG* 1.3 63.6 + - - +
226B VAL* 3.0 12.2 + - + -
227B LYS* 3.0 35.3 + - + +
245B GLY 5.6 0.4 - - - +
248B TRP* 4.1 2.7 - - + +
249B ALA* 3.9 37.7 - - + +
252B VAL* 3.8 23.3 - - + +
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Residues in contact with ARG 224 (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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45B MET* 4.2 6.4 - - - +
50B VAL* 3.4 36.4 + - + +
51B PHE* 3.3 45.2 - - - +
52B GLU* 4.6 3.4 - - - +
105B GLY 2.8 26.4 + - - -
106B VAL* 3.7 23.6 + - + +
107B HIS* 3.5 16.2 + - - -
108B THR* 6.4 0.4 - - + -
220B ARG* 2.9 24.3 + - - +
221B LEU* 3.6 10.3 - - - +
223B LEU* 1.3 75.8 - - - +
225B ALA* 1.3 63.1 + - - +
227B LYS* 3.6 5.8 + - - +
228B LEU* 3.1 24.9 + - - +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.2 12.1 - - + -
45B MET* 3.6 22.4 - - - -
221B LEU 3.0 12.2 + - - +
222B THR 3.0 8.9 + - - +
224B ARG* 1.3 78.8 - - - +
226B VAL* 1.3 57.2 + - - +
228B LEU* 3.4 3.1 + - - +
229B TRP* 2.9 30.9 + - - +
268B VAL* 3.6 28.0 - - + -
360B LEU* 5.8 3.4 - - + +
361B LEU* 5.3 0.9 - - - +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B THR* 2.9 30.2 + - + +
223B LEU* 3.0 2.6 + - + +
225B ALA* 1.3 78.9 - - + +
227B LYS* 1.3 57.2 + - - +
229B TRP* 3.3 12.2 - - + -
230B ALA* 2.9 24.8 + - - +
248B TRP* 3.7 21.5 - - + -
252B VAL* 3.6 25.8 - - + -
268B VAL* 5.0 7.2 - - + -
271B PHE* 3.5 44.9 - - + -
272B PHE* 5.8 1.3 - - + -
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Residues in contact with LYS 227 (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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101B SER* 2.9 29.5 + - - -
104B LEU* 6.0 0.8 - - - +
106B VAL* 4.3 16.0 + - + +
107B HIS* 5.6 0.8 - - - +
108B THR* 6.2 3.8 - - + -
223B LEU* 3.0 45.2 + - + +
224B ARG* 4.2 5.2 - - - +
226B VAL* 1.3 73.7 - - - +
228B LEU* 1.3 58.3 + - - +
230B ALA* 3.2 5.7 + - - +
231B LYS* 2.7 51.5 + - - +
236B TYR* 3.4 35.2 + - + -
245B GLY* 4.3 7.4 + - - +
248B TRP* 4.5 7.2 - - + -
601B 3AT 3.4 13.3 + - - -
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Residues in contact with LEU 228 (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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45B MET* 4.0 17.0 - - + -
48B PHE* 4.0 32.5 - - + +
50B VAL* 3.6 23.6 - - + -
224B ARG 3.1 19.1 + - - +
225B ALA* 3.5 4.3 - - - +
227B LYS* 1.3 80.1 - - - +
229B TRP* 1.3 55.4 + - - +
231B LYS* 3.8 10.1 - - + +
232B ARG* 2.9 37.7 + - + +
361B LEU* 3.5 40.4 - - + -
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Residues in contact with TRP 229 (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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225B ALA 2.9 17.7 + - - +
226B VAL* 3.3 18.2 - - + +
228B LEU* 1.3 75.1 - - - +
230B ALA* 1.3 73.7 + - + +
232B ARG* 3.1 4.5 + - - +
233B ARG* 2.8 57.0 + - + +
235B ILE* 3.8 14.8 - - + -
248B TRP* 3.9 28.5 - + - -
271B PHE* 4.3 2.9 - + - -
272B PHE* 3.3 36.5 - + + -
339B GLU* 3.5 27.0 + - + -
340B PHE* 3.7 20.6 - + - -
343B GLY* 4.8 0.8 - - - -
360B LEU* 3.3 44.8 - - + +
361B LEU* 4.3 14.4 - - + -
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Residues in contact with ALA 230 (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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226B VAL 2.9 18.7 + - - +
227B LYS* 3.2 4.0 + - - +
229B TRP* 1.3 81.5 - - + +
231B LYS* 1.3 65.7 + - - +
233B ARG 3.2 1.6 + - - +
234B GLY 3.0 4.3 + - - -
235B ILE* 3.0 33.8 + - + -
236B TYR* 3.8 8.5 - - + -
248B TRP* 3.7 40.2 - - + +
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Residues in contact with LYS 231 (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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108B THR* 5.1 17.0 + - + +
227B LYS* 2.7 37.3 + - - +
228B LEU* 3.8 10.1 - - + +
230B ALA* 1.3 72.2 - - - +
232B ARG* 1.3 69.0 + - - +
234B GLY* 3.0 13.9 + - - -
236B TYR* 3.5 54.7 + - + +
418B GLN* 5.8 2.3 + - - -
601B 3AT 4.4 5.5 + - - -
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Residues in contact with ARG 232 (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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48B PHE* 3.6 32.0 - - + -
228B LEU* 2.9 36.0 + - + +
229B TRP* 3.6 6.5 - - - +
231B LYS* 1.3 81.6 - - - +
233B ARG* 1.3 60.9 + - - +
234B GLY 3.6 0.5 + - - -
361B LEU* 2.4 56.6 + - + +
362B GLU* 4.1 0.2 - - - +
363B PRO* 3.6 33.9 - - - +
364B PRO* 3.4 15.9 - - - +
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Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B TRP* 2.8 50.5 + - + +
230B ALA 3.2 2.8 + - - +
232B ARG* 1.3 74.9 - - - +
234B GLY* 1.3 63.6 + - - +
235B ILE* 3.3 16.6 + - + +
339B GLU* 3.1 41.0 + - + +
342B GLN* 4.8 18.4 - - - +
343B GLY* 5.2 2.6 - - - +
346B VAL* 6.2 1.6 - - - +
360B LEU* 3.9 16.6 + - - +
362B GLU 3.1 26.1 + - - -
363B PRO 4.7 0.4 + - - -
364B PRO* 3.5 45.0 - - + +
369B LYS* 5.8 0.8 - - - +
414B HIS* 5.9 1.2 + - - -
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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
------------------------------------------------------------
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