Contacts of the helix formed by residues 228 - 237 (chain B) in PDB entry 5D9I
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 LYS 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ASN* 2.6 30.7 + - - +
228A LYS* 4.8 9.2 - - + +
229A GLU* 2.7 28.8 + - - +
144B SER 4.1 11.2 - - - +
145B PHE* 3.1 39.2 + - + +
226B VAL* 3.5 1.9 - - - +
227B ASN* 1.3 85.9 - - + +
229B GLU* 1.4 65.3 + - - +
230B TYR 3.4 2.2 - - - -
231B LEU* 4.0 18.4 - - + -
232B MET* 3.0 23.6 + - - +
23Y A 5.2 11.1 + - - -
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Residues in contact with GLU 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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228A LYS* 2.6 40.2 + - - +
231A LEU* 5.8 2.1 - - - +
158B CYS* 3.5 34.8 - - + +
196B PHE* 3.5 11.7 - - + -
198B LEU* 4.7 5.7 - - + +
226B VAL* 3.7 16.5 - - - +
227B ASN 3.8 2.7 - - - -
228B LYS* 1.4 71.7 - - - +
230B TYR* 1.3 63.2 + - - +
233B TYR* 3.1 18.5 + - - +
257B PHE* 3.8 22.3 - - + -
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Residues in contact with TYR 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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230A TYR* 3.6 15.0 - + - -
231A LEU* 3.9 28.1 - - + +
254A GLU* 2.6 38.2 + - - -
229B GLU* 1.3 77.1 + - - +
231B LEU* 1.3 76.3 + - + +
232B MET 3.3 0.2 + - - -
233B TYR* 3.3 5.0 + + - -
234B SER* 2.8 41.9 + - - -
252B LEU 5.7 0.4 - - - -
253B LYS* 4.1 3.4 - - - -
254B GLU* 3.5 36.5 + - + +
257B PHE* 3.6 47.3 - + + -
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Residues in contact with LEU 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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229A GLU* 5.7 2.7 - - - +
230A TYR* 4.0 30.1 - - + +
231A LEU* 6.2 1.1 - - + -
254A GLU* 3.7 34.8 - - + +
257A PHE* 4.1 20.0 - - + +
258A ASN* 4.4 8.1 + - - +
145B PHE* 3.7 32.9 - - + -
228B LYS* 3.5 23.5 + - + -
229B GLU 3.4 0.2 - - - -
230B TYR* 1.3 82.8 - - + +
232B MET* 1.3 59.1 + - - +
234B SER* 3.9 2.4 - - - -
235B ALA* 3.0 31.0 + - - +
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Residues in contact with MET 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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138B PHE* 4.1 8.7 - - + -
142B LEU* 3.9 32.5 - - + -
145B PHE* 3.8 23.5 - - + -
146B LEU* 3.8 21.1 - - + -
160B ALA* 3.7 26.7 - - + -
194B ILE* 4.6 1.3 - - + -
196B PHE* 3.9 16.8 - - + -
226B VAL* 3.7 15.0 - - + -
228B LYS 3.0 19.9 + - - +
229B GLU 3.6 3.8 - - - +
231B LEU* 1.3 75.1 - - - +
233B TYR* 1.3 65.0 + - - +
235B ALA* 3.3 1.9 + - - +
236B LEU* 3.1 37.6 + - + +
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Residues in contact with TYR 233 (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* 3.7 9.6 - + - -
185B SER* 3.6 24.0 - - - -
187B HIS* 4.1 10.3 - + - -
196B PHE* 3.7 34.7 - + + -
229B GLU 3.1 8.3 + - - +
230B TYR* 4.0 4.7 - + - +
232B MET* 1.3 78.3 - - - +
234B SER* 1.3 68.1 + - - +
236B LEU* 3.1 16.0 + - - +
237B THR* 3.3 31.9 + - + +
243B VAL* 4.6 0.7 - - - +
246B GLU* 2.6 32.1 + - - -
250B GLY 4.8 0.3 + - - -
251B GLY* 3.4 2.6 - - - -
252B LEU* 3.2 51.5 + - + -
257B PHE* 4.5 8.7 - + + -
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Residues in contact with SER 234 (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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254A GLU* 2.5 28.5 + - - -
230B TYR* 2.8 41.9 + - - -
231B LEU 3.9 1.3 - - - -
233B TYR* 1.3 82.4 - - - +
235B ALA* 1.3 61.7 + - - +
237B THR* 2.6 27.6 + - - -
238B ARG* 2.6 29.0 + - - -
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Residues in contact with ALA 235 (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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258A ASN* 4.0 19.1 - - - +
141B GLU 5.7 0.4 - - - +
142B LEU* 4.0 11.7 - - + -
145B PHE* 4.0 11.2 - - + -
231B LEU 3.0 18.8 + - - +
232B MET 3.8 3.6 - - - +
233B TYR 3.3 0.2 - - - -
234B SER* 1.3 76.7 - - - +
236B LEU* 1.3 56.1 + - - +
237B THR 3.2 0.4 - - - -
238B ARG* 3.1 39.3 + - - +
241B PHE* 3.3 11.0 - - + -
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Residues in contact with LEU 236 (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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142B LEU* 3.9 14.1 - - + -
187B HIS* 2.8 53.0 + - + +
194B ILE* 3.8 43.1 - - + -
196B PHE* 4.0 17.0 - - + -
232B MET* 3.1 34.9 + - + +
233B TYR* 3.1 10.6 + - - +
235B ALA* 1.3 76.5 - - - +
237B THR* 1.3 54.9 + - - +
238B ARG 3.5 0.4 - - - -
241B PHE* 3.3 30.4 - - + +
242B SER 3.4 7.3 + - - -
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Residues in contact with THR 237 (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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233B TYR* 3.3 39.0 - - + +
234B SER* 2.6 19.2 + - - -
236B LEU* 1.3 79.6 - - - +
238B ARG* 1.3 65.0 + - - +
241B PHE 3.9 6.5 - - - +
242B SER* 4.5 4.9 - - - +
243B VAL* 3.8 26.5 + - + +
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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