Contacts of the helix formed by residues 231 - 238 (chain H) in PDB entry 1LWU
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 HIS 231 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230H MET* 1.3 83.1 + - + +
232H CYS* 1.3 76.9 + - - +
233H GLU* 2.9 25.4 - - + +
234H ASP* 3.5 10.8 - - + +
235H ILE* 3.5 19.9 + - - +
248H ILE* 3.7 10.2 - - - +
269H GLY 3.2 8.1 + - - -
271H THR* 3.1 14.4 + - - -
322H LEU* 4.2 15.1 - - + +
328H GLN* 2.9 29.7 + - - -
474H LEU* 2.8 32.3 + - + -
475H ARG* 3.1 11.6 - - - -
476H PRO* 3.4 10.9 - - + +
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Residues in contact with CYS 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H HIS* 1.3 76.1 - - - +
233H GLU* 1.3 55.9 + - - +
234H ASP 3.1 1.6 - - - -
235H ILE* 2.7 8.4 + - - +
236H TYR* 2.7 34.3 + - - +
248H ILE* 4.8 0.7 - - - -
259H VAL* 4.0 6.5 - - - -
261H CYS* 2.0 56.3 - - - -
263H MET* 3.7 14.1 - - + +
269H GLY* 3.7 8.9 - - - +
270H TRP 3.9 0.2 - - - -
271H THR* 3.2 36.3 + - - +
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Residues in contact with GLU 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H HIS* 2.9 22.8 - - + -
232H CYS* 1.3 76.5 - - - +
234H ASP* 1.3 63.5 + - - +
236H TYR* 3.0 14.6 + - - +
237H ARG* 2.9 56.0 + - - +
268H GLY 4.6 1.1 - - - +
269H GLY* 3.2 16.0 + - - +
475H ARG* 3.2 28.9 + - - +
476H PRO* 3.8 20.6 - - + +
477H LYS 4.4 11.7 - - - +
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Residues in contact with ASP 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229H GLY* 3.3 9.8 - - - -
230H MET* 3.2 37.1 + - + +
231H HIS* 3.5 20.2 + - + +
232H CYS 3.1 0.2 - - - -
233H GLU* 1.3 80.6 - - - +
235H ILE* 1.3 62.0 + - - +
237H ARG* 3.2 21.9 + - - +
238H ASN* 3.2 33.9 + - - +
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Residues in contact with ILE 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H VAL* 4.3 5.6 - - + -
228H SER* 3.6 6.7 - - - -
229H GLY 3.6 19.1 - - - +
231H HIS 3.6 7.6 - - - +
232H CYS* 2.7 11.9 + - - +
234H ASP* 1.3 74.8 - - - +
236H TYR* 1.3 56.1 + - - +
238H ASN* 2.7 26.3 + - - +
239H GLY 3.3 0.3 + - - -
240H GLY* 3.0 27.2 + - - +
246H TYR* 3.3 62.8 - - + -
247H TYR 3.8 7.6 - - - +
248H ILE* 3.7 19.3 - - + -
261H CYS* 4.0 6.1 - - - -
263H MET* 4.7 3.8 - - - -
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Residues in contact with TYR 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H CYS 2.7 15.1 + - - +
233H GLU* 3.2 20.2 - - - +
235H ILE* 1.3 72.4 - - - +
237H ARG* 1.3 61.3 + - + +
238H ASN 2.8 7.3 + - - -
239H GLY 2.8 12.1 + - - -
240H GLY 3.3 15.5 - - - -
241H ARG* 2.9 69.8 + - + -
263H MET* 3.9 34.9 + - + -
267H GLY 4.1 16.3 + - - -
268H GLY 5.5 0.2 - - - -
269H GLY* 4.2 12.6 - - - -
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Residues in contact with ARG 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233H GLU* 2.9 42.5 + - - +
234H ASP* 3.4 24.2 - - - +
235H ILE 3.2 0.2 - - - -
236H TYR* 1.3 78.9 - - + +
238H ASN* 1.3 66.7 + - - +
239H GLY 3.4 0.2 - - - -
241H ARG* 5.0 4.4 + - - +
477H LYS 6.3 1.4 - - - -
209I VAL* 3.5 16.8 - - - +
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Residues in contact with ASN 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H VAL* 3.3 25.9 - - + +
228H SER 3.1 18.6 - - - +
234H ASP* 3.2 22.0 + - - +
235H ILE 2.7 13.5 + - - +
237H ARG* 1.3 89.8 + - - +
239H GLY* 1.3 55.8 + - - +
240H GLY 3.4 0.7 - - - -
209I VAL* 4.2 6.5 - - - +
210I SER* 4.2 7.4 + - - -
212I ARG* 5.4 4.0 - - - +
213I GLU* 3.6 46.7 - - + +
214I GLY 4.4 2.1 - - - +
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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