Contacts of the helix formed by residues 232 - 245 (chain M) in PDB entry 5LN3
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 GLY 232 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191M LEU* 4.6 6.2 - - - +
194M GLN* 6.0 1.1 - - - -
230M GLY* 3.4 3.4 - - - -
231M THR* 1.4 64.2 - - - +
233M LYS* 1.4 66.5 + - - +
234M THR 3.4 2.2 - - - -
235M LEU* 3.5 37.7 - - - +
236M LEU* 3.6 15.3 - - - +
394M ALA* 5.9 0.2 - - - +
397M LYS* 5.3 6.7 - - - -
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Residues in contact with LYS 233 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H ASP* 3.2 27.3 + - - -
194M GLN* 5.7 2.7 - - - +
225M MET* 4.2 32.3 - - + +
228M PRO 5.5 0.4 - - - +
229M PRO* 4.3 10.2 - - + +
230M GLY* 3.6 30.1 - - - +
231M THR* 3.3 18.0 - - - +
232M GLY* 1.4 76.5 - - - +
234M THR* 1.4 81.1 + - - +
236M LEU* 3.4 27.9 - - - +
237M ALA* 3.7 5.0 + - - +
331M ALA* 5.9 8.1 - - + -
332M THR 5.3 8.7 - - - +
333M ASN* 5.9 4.9 - - - +
354M PHE* 5.9 0.2 - - + -
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Residues in contact with THR 234 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H ASP* 5.1 2.9 + - - -
232M GLY 3.4 0.2 - - - -
233M LYS* 1.4 99.8 + - - +
235M LEU* 1.3 68.7 + - + +
237M ALA* 3.1 9.8 + - - +
238M ARG* 3.0 58.4 + - + +
284M PHE* 4.1 32.6 - - + -
286M ASP* 4.9 3.7 + - - +
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Residues in contact with LEU 235 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307H ASP* 6.1 2.7 - - - +
183M GLU* 3.5 40.3 - - + +
191M LEU* 5.6 4.0 - - + -
232M GLY* 3.5 26.7 - - - +
233M LYS 3.3 0.2 - - - -
234M THR* 1.3 82.8 - - - +
236M LEU* 1.3 59.8 + - + +
238M ARG* 3.3 28.7 + - - +
239M ALA* 2.9 27.4 + - - +
397M LYS* 6.2 1.8 - - - +
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Residues in contact with LEU 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185M TYR* 5.2 6.6 - - + +
188M ILE* 5.1 7.0 - - + -
191M LEU* 3.8 26.5 - - + -
194M GLN* 4.0 41.1 - - + +
195M ILE* 4.2 20.9 - - + -
198M LEU* 3.5 26.8 - - + +
232M GLY 3.6 13.0 - - - +
233M LYS* 3.4 16.2 - - - +
235M LEU* 1.3 77.4 - - + +
237M ALA* 1.4 56.1 + - - +
239M ALA* 3.2 7.6 + - + +
240M CYS 3.0 23.7 + - - -
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Residues in contact with ALA 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198M LEU* 4.5 5.1 - - - +
233M LYS 3.7 4.2 + - - +
234M THR* 3.1 17.7 + - - +
236M LEU* 1.4 75.0 - - - +
238M ARG* 1.4 57.2 + - - +
240M CYS* 3.5 6.4 + - - +
241M ALA* 3.2 25.8 + - - +
248M PHE* 4.2 16.4 - - + -
282M ILE* 5.4 1.2 - - - +
284M PHE* 5.1 11.7 - - + -
329M ILE* 4.2 26.7 - - + -
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Residues in contact with ARG 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H ASP 4.3 3.8 + - - -
308H GLY* 3.4 37.4 + - - -
309H PHE* 3.2 48.1 - - + +
181M PRO* 3.5 19.1 - - + +
183M GLU* 3.8 22.6 - - + +
234M THR* 3.0 39.0 + - + +
235M LEU* 3.4 29.9 - - - +
237M ALA* 1.4 72.1 - - - +
239M ALA* 1.4 64.6 + - - +
241M ALA* 3.4 3.7 + - - +
242M ALA* 3.2 17.3 + - - +
248M PHE* 4.2 21.5 - - + -
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Residues in contact with ALA 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183M GLU* 3.6 15.2 - - + +
184M GLN* 3.7 10.2 - - - +
185M TYR* 3.8 37.9 - - + +
188M ILE* 6.3 0.2 - - + -
235M LEU 2.9 14.3 + - - +
236M LEU* 3.2 13.2 + - + +
238M ARG* 1.4 76.9 - - - +
240M CYS* 1.4 61.0 + - - +
242M ALA* 3.2 5.5 + - - +
243M GLN* 3.2 22.3 + - - +
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Residues in contact with CYS 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M TYR* 4.8 4.6 - - - -
198M LEU* 4.2 18.1 - - + +
199M VAL* 6.2 2.9 - - + -
202M ILE* 3.9 26.5 - - - -
203M VAL* 3.8 28.7 - - - -
236M LEU 3.0 15.8 + - - +
237M ALA* 3.7 6.3 - - - +
239M ALA* 1.4 70.8 - - - +
241M ALA* 1.3 66.6 + - - +
243M GLN* 3.3 8.6 + - - +
244M THR* 3.1 25.7 + - - +
282M ILE* 4.9 4.5 - - - -
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Residues in contact with ALA 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180M ARG* 3.4 13.7 + - - -
181M PRO* 3.9 8.1 - - + -
237M ALA 3.2 8.1 + - - +
238M ARG 3.6 8.1 - - - +
239M ALA 3.3 0.2 - - - -
240M CYS* 1.3 79.5 - - - +
242M ALA* 1.4 61.0 + - - +
243M GLN 3.4 0.3 + - - -
244M THR* 3.6 12.2 + - - +
245M LYS 3.7 0.2 + - - -
246M ALA 4.0 4.3 - - - +
248M PHE* 3.3 42.6 - - + +
282M ILE* 3.7 19.0 - - + +
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Residues in contact with ALA 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180M ARG* 3.2 31.7 + - - +
181M PRO* 3.7 28.5 - - + +
183M GLU 3.2 26.2 - - - +
184M GLN* 5.0 4.0 - - + +
238M ARG 3.2 10.3 + - - +
239M ALA 3.2 3.8 + - - +
241M ALA* 1.4 74.4 - - - +
243M GLN* 1.4 61.0 + - - +
245M LYS* 4.1 2.1 + - - +
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Residues in contact with GLN 243 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M GLN* 3.0 34.5 + - - +
185M TYR* 3.1 33.0 + - + +
203M VAL* 5.9 8.5 - - + -
239M ALA 3.2 4.7 + - - +
240M CYS* 3.5 10.1 - - - +
241M ALA 3.2 0.2 - - - -
242M ALA* 1.4 80.8 - - - +
244M THR* 1.4 62.3 + - - +
245M LYS* 3.8 10.6 + - - +
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Residues in contact with THR 244 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202M ILE* 5.5 0.4 - - + -
203M VAL* 4.6 19.5 - - - +
206M MET* 3.1 31.0 - - + +
207M ASN* 5.6 0.9 + - - -
240M CYS* 3.1 18.8 + - - +
241M ALA* 3.6 12.6 - - - +
242M ALA 3.5 0.2 - - - -
243M GLN* 1.4 80.2 - - - +
245M LYS* 1.4 78.7 + - - +
246M ALA* 3.8 20.9 - - + +
282M ILE* 4.1 7.9 - - + -
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Residues in contact with LYS 245 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180M ARG* 3.7 27.4 - - - +
207M ASN* 5.9 0.8 + - - -
241M ALA 3.7 4.4 + - - -
242M ALA 5.0 0.9 - - - +
243M GLN 3.6 12.0 + - - +
244M THR* 1.4 89.4 + - - +
246M ALA* 1.4 60.3 + - - +
280M PRO* 3.5 16.5 - - - +
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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