Contacts of the helix formed by residues 233 - 248 (chain U) in PDB entry 5IYB
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 LEU 233 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202U LYS* 4.4 26.9 - - + +
203U ASN* 6.5 0.4 - - + -
231U ASP 5.1 0.4 - - - +
232U GLU* 1.3 83.2 - - + +
234U LYS* 1.3 60.7 + - + +
235U GLU 3.5 0.2 - - - -
236U MET* 3.5 11.6 + - - +
237U ARG* 3.0 61.3 + - + +
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Residues in contact with LYS 234 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1218A ARG* 3.3 33.2 - - - +
1250A ASP* 3.8 6.5 + - - -
1251A ASN* 3.5 60.0 - - + +
1252A ALA 5.0 2.7 - - - -
200U ASP* 5.9 1.1 - - - +
202U LYS* 5.7 4.0 - - - -
226U GLU 4.7 0.4 + - - -
227U GLU* 4.1 2.4 - - - +
229U ALA* 3.5 18.0 - - + +
232U GLU 2.9 4.8 + - - -
233U LEU* 1.3 78.5 - - + +
235U GLU* 1.3 53.6 + - - +
237U ARG* 3.5 14.0 - - + +
238U LYS* 2.6 47.8 + - + +
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Residues in contact with GLU 235 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225U ALA* 4.0 19.6 - - - +
229U ALA* 3.4 20.4 + - - +
230U SER* 2.4 42.5 + - - -
231U ASP 4.7 2.5 - - - +
232U GLU* 3.5 6.5 + - - +
233U LEU 3.5 0.4 - - - -
234U LYS* 1.3 73.4 - - - +
236U MET* 1.3 58.6 + - + +
238U LYS* 3.6 11.6 - - - +
239U ASN* 2.7 40.3 + - + +
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Residues in contact with MET 236 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232U GLU* 4.5 8.9 - - + -
233U LEU* 3.5 20.7 + - - +
234U LYS 3.3 0.4 - - - -
235U GLU* 1.3 76.4 - - + +
237U ARG* 1.3 55.1 + - + +
239U ASN* 3.1 12.2 + - - +
240U LEU* 2.7 43.6 + - + +
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Residues in contact with ARG 237 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253A GLU* 3.5 33.9 + - - +
202U LYS* 5.5 1.8 - - - +
233U LEU* 3.0 46.7 + - + +
234U LYS* 3.5 12.7 - - + +
236U MET* 1.3 77.6 - - + +
238U LYS* 1.3 53.3 + - - +
240U LEU* 3.4 17.5 - - + +
241U THR* 2.4 38.5 + - - +
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Residues in contact with LYS 238 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1218A ARG* 3.5 35.8 - - + +
1222A THR* 3.7 31.0 - - + +
226U GLU* 3.3 37.4 + - + +
229U ALA* 6.0 0.7 - - + -
234U LYS* 2.6 30.6 + - + +
235U GLU* 3.7 13.5 - - - +
237U ARG* 1.3 72.6 - - - +
239U ASN* 1.3 54.0 + - - +
241U THR* 3.3 6.6 + - + -
242U LYS* 2.8 49.8 + - + +
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Residues in contact with ASN 239 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235U GLU* 2.7 26.2 + - + +
236U MET* 3.5 13.4 - - - +
238U LYS* 1.3 70.8 - - - +
240U LEU* 1.3 56.0 + - - +
242U LYS* 2.9 25.6 + - - +
243U GLU* 2.7 46.3 + - - +
246U ARG* 5.2 2.4 + - - -
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Residues in contact with LEU 240 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236U MET* 2.7 25.0 + - + +
237U ARG* 3.4 25.8 - - + +
239U ASN* 1.3 73.1 - - - +
241U THR* 1.3 66.3 + - - +
243U GLU* 3.1 16.4 + - + +
244U ALA* 2.9 29.3 + - + +
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Residues in contact with THR 241 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1218A ARG* 5.3 3.8 - - + +
1219A LYS* 4.1 39.1 - - + +
1222A THR* 4.1 19.7 - - + +
237U ARG* 2.4 28.0 + - - +
238U LYS* 3.4 10.0 - - - -
240U LEU* 1.3 84.0 - - - +
242U LYS* 1.3 57.8 + - - +
244U ALA* 3.3 6.0 + - + +
245U ILE* 3.0 35.1 + - + +
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Residues in contact with LYS 242 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152A GLU* 3.9 24.7 + - - -
1222A THR* 5.0 5.2 - - + -
226U GLU* 6.5 0.4 - - + -
238U LYS* 2.8 38.0 + - + +
239U ASN* 3.1 27.4 + - - +
241U THR* 1.3 74.2 - - - +
243U GLU* 1.3 62.0 + - - +
245U ILE* 3.6 13.2 - - + +
246U ARG* 3.2 39.6 + - - +
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Residues in contact with GLU 243 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239U ASN* 2.7 31.8 + - - +
240U LEU* 3.1 16.4 + - + +
242U LYS* 1.3 73.8 - - - +
244U ALA* 1.3 52.5 + - - +
246U ARG* 2.8 44.0 + - - +
247U GLU* 2.7 41.2 + - - +
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Residues in contact with ALA 244 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240U LEU* 2.9 17.0 + - + +
241U THR* 3.3 7.2 + - + +
243U GLU* 1.3 78.5 - - - +
245U ILE* 1.3 60.6 + - + +
247U GLU* 3.1 10.6 + - - +
248U HIS* 3.0 24.6 + - - +
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Residues in contact with ILE 245 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155A LYS* 4.5 22.3 + - + -
1219A LYS* 4.0 15.0 - - + +
1222A THR* 4.7 12.1 - - + +
1223A ASP* 3.9 40.1 - - + +
241U THR* 3.0 27.0 + - + +
242U LYS* 3.6 17.0 - - + +
244U ALA* 1.3 76.8 - - + +
246U ARG* 1.3 68.9 + - + +
248U HIS* 3.6 17.6 - - - +
249U GLN* 4.0 10.4 + - - +
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Residues in contact with ARG 246 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151A ALA* 5.0 18.4 - - + -
1152A GLU* 4.6 28.7 + - + +
1155A LYS* 6.1 0.9 - - + -
239U ASN* 5.2 3.4 + - - -
242U LYS* 3.2 36.1 + - - +
243U GLU* 2.8 36.9 + - - +
245U ILE* 1.3 84.2 - - + +
247U GLU* 1.3 63.5 + - - +
248U HIS 3.2 0.7 - - - -
249U GLN* 3.2 25.3 + - + +
250U MET* 3.5 37.9 + - + +
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Residues in contact with GLU 247 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729A PRO* 3.4 18.8 - - + +
243U GLU* 2.7 23.4 + - - +
244U ALA* 3.1 17.8 + - - +
246U ARG* 1.3 70.1 - - - +
248U HIS* 1.3 54.1 + - - +
249U GLN 3.0 10.7 + - - -
250U MET* 3.1 42.0 + - + +
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Residues in contact with HIS 248 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729A PRO* 3.2 29.2 + - + +
730A GLY* 5.5 1.0 - - - -
731A ASN 5.8 2.4 + - - -
1223A ASP* 4.8 9.4 + - - +
1308A TYR* 3.2 29.4 + + - -
244U ALA 3.0 11.7 + - - +
245U ILE* 3.6 15.9 - - - +
246U ARG 3.2 0.4 - - - -
247U GLU* 1.3 74.5 - - - +
249U GLN* 1.3 60.4 + - + +
252U LYS* 3.0 21.6 + - - -
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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