Contacts of the helix formed by residues 224 - 240 (chain B) in PDB entry 5ITY
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 ASP 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B ARG* 3.3 31.0 + - - -
186B LEU* 3.6 5.4 - - - -
200B ALA 5.3 3.8 - - - +
222B ASN 3.6 2.4 + - - -
223B PRO* 1.3 70.5 - - - +
225B LEU* 1.3 64.9 + - - +
226B LEU* 3.8 3.0 + - - +
227B GLU* 3.2 33.1 + - + +
228B LEU* 3.0 26.0 + - - +
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 3.9 27.8 - - + -
165B LEU* 4.8 7.6 - - + -
171B PHE* 5.9 0.4 - - + -
182B ILE* 3.6 24.9 - - + -
183B LEU* 4.7 10.8 - - + -
186B LEU* 3.5 20.2 - - + +
188B ILE* 4.8 8.5 - - + -
197B VAL* 4.6 10.8 - - + +
198B LEU* 3.8 29.6 - - + -
224B ASP* 1.3 74.8 + - - +
226B LEU* 1.3 63.3 + - + +
228B LEU* 3.0 5.2 + - - +
229B CYS* 2.9 32.0 + - - -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 3.3 14.1 - - - -
144B PHE* 3.5 25.1 - - + -
145B ARG* 3.5 40.6 - - + +
148B VAL* 4.1 19.1 - - + -
149B LEU* 3.9 28.7 - - + -
171B PHE* 3.8 19.7 - - + -
198B LEU* 4.4 16.4 - - + -
224B ASP* 3.5 2.8 + - + +
225B LEU* 1.3 77.8 - - + +
227B GLU* 1.3 63.0 + - - +
229B CYS* 3.4 16.1 + - - +
230B HIS 3.7 0.5 + - - -
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS* 5.3 6.2 + - - -
238A GLN* 5.9 1.2 + - - -
141B TYR* 3.4 24.9 - - + +
145B ARG* 3.8 0.6 - - - +
223B PRO* 3.6 27.0 - - + +
224B ASP* 3.2 30.6 - - + +
225B LEU 3.1 1.0 - - - -
226B LEU* 1.3 80.3 - - - +
228B LEU* 1.3 59.9 + - - +
230B HIS* 3.0 8.1 + - + +
231B SER* 2.9 31.0 + - - +
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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
----------------------------------------------------------
182B ILE* 4.0 17.9 - - + +
185B ARG* 3.8 28.5 - - + +
186B LEU* 3.4 39.7 - - + -
223B PRO* 3.9 24.7 - - + +
224B ASP 3.0 19.8 + - - +
225B LEU 3.0 5.8 + - - +
227B GLU* 1.3 73.1 - - - +
229B CYS* 1.3 63.3 + - - +
230B HIS 3.0 2.5 - - - -
231B SER* 3.6 15.5 - - - +
232B VAL* 2.9 42.1 + - + +
233B PRO* 3.4 0.3 - - - +
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Residues in contact with CYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 3.6 13.3 - - + +
144B PHE* 3.6 17.5 - - + -
165B LEU* 4.0 14.6 - - - -
171B PHE* 3.8 30.5 - - - -
174B ILE* 3.7 9.2 - - + +
182B ILE* 4.0 18.2 - - - -
225B LEU* 2.9 21.8 + - - -
226B LEU* 3.5 13.2 - - - +
227B GLU 3.2 0.6 - - - -
228B LEU* 1.3 76.0 - - - +
230B HIS* 1.3 57.1 + - - +
233B PRO* 2.9 21.1 - - - +
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Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLN* 5.0 4.5 + - - -
137B VAL* 2.6 25.6 + - + +
138B LEU* 3.0 26.8 + - + +
141B TYR* 3.4 40.7 - + + +
226B LEU 3.7 0.8 + - - -
227B GLU* 3.0 8.6 + - + +
228B LEU 3.0 0.4 - - - -
229B CYS* 1.3 82.0 - - - +
231B SER* 1.3 69.9 + - - +
232B VAL 3.5 0.4 - - - -
233B PRO* 3.8 4.0 - - - +
234B LYS* 3.1 55.9 + - + +
501B GOL 3.9 11.0 - - - -
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PRO* 5.5 1.2 - - - +
227B GLU* 2.9 22.3 + - - +
228B LEU* 3.6 19.6 - - - +
230B HIS* 1.3 85.0 - - - +
232B VAL* 1.3 68.9 + - - +
234B LYS* 3.2 8.4 + - - +
235B GLU* 3.0 30.2 + - - +
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.7 11.4 - - + -
181B GLU* 4.3 7.9 - - + -
182B ILE* 4.0 19.5 - - + -
185B ARG* 4.1 25.1 - - - +
228B LEU* 2.9 34.7 + - + +
231B SER* 1.3 77.1 + - - +
233B PRO* 1.3 72.0 - - + +
235B GLU* 2.9 26.8 + - - +
236B VAL* 3.4 5.4 + - - +
259B TRP* 3.6 28.0 - - + -
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Residues in contact with PRO 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLY* 5.8 0.2 - - - -
5B PRO* 3.7 23.7 - - + +
137B VAL* 4.5 7.0 - - + -
138B LEU* 3.8 14.4 - - + -
174B ILE* 4.3 4.7 - - + -
178B LEU* 4.0 21.1 - - + -
182B ILE* 4.7 2.2 - - + -
228B LEU 3.4 1.6 - - - +
229B CYS* 2.9 29.2 - - - +
230B HIS 3.8 4.9 - - - +
232B VAL* 1.3 99.2 - - + +
234B LYS* 1.3 62.6 + - - +
236B VAL* 3.1 15.7 + - + +
237B VAL* 3.1 15.6 + - - +
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU 5.6 1.2 + - - -
139A GLN* 3.6 24.0 + - - +
140A GLU* 5.1 1.0 - - - +
141A TYR* 5.0 9.5 - - - +
142A GLN* 6.1 2.2 - - - +
138B LEU* 3.6 12.3 - - + +
230B HIS* 3.1 46.5 + - + +
231B SER* 3.5 10.5 - - - +
232B VAL 3.1 0.6 - - - -
233B PRO* 1.3 76.4 - - - +
235B GLU* 1.3 61.9 + - - +
237B VAL* 3.2 7.8 + - + +
238B GLN* 3.1 48.5 + - - +
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 2.7 36.8 + - - -
231B SER* 3.0 20.7 + - - +
232B VAL* 2.9 12.3 + - - +
234B LYS* 1.3 73.6 - - - +
236B VAL* 1.3 67.8 + - - +
238B GLN* 2.9 17.1 + - - +
239B LEU* 3.3 16.1 + - - +
259B TRP* 2.7 36.9 + - + +
261B ARG* 4.5 2.6 + - - -
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 3.8 13.7 - - + -
6B GLU* 4.0 6.5 - - - +
9B LEU* 4.4 1.0 - - + +
177B TYR* 3.6 26.2 - - + +
178B LEU* 4.7 0.2 - - + -
232B VAL 3.7 6.5 - - - +
233B PRO* 3.1 11.6 + - + +
235B GLU* 1.3 76.3 - - - +
237B VAL* 1.3 63.1 + - - +
238B GLN 3.2 0.3 + - - -
239B LEU* 3.4 23.8 - - + +
240B GLY 3.9 5.9 + - - +
242B ARG* 4.4 8.0 - - - +
256B PHE* 4.0 18.4 - - + -
259B TRP* 3.4 41.5 - - + -
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 3.7 28.7 - - + +
8B HIS* 3.9 23.6 - - + +
9B LEU* 3.5 19.6 - - + +
12B GLN* 4.2 8.3 - - - +
138B LEU* 4.0 19.3 - - + -
233B PRO 3.1 12.8 + - - +
234B LYS* 3.4 12.1 - - + +
235B GLU 3.1 0.6 - - - -
236B VAL* 1.3 78.3 - - - +
238B GLN* 1.3 69.1 + - - +
240B GLY* 3.2 14.7 + - - -
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Residues in contact with GLN 238 (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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142A GLN* 3.4 43.8 - - + +
234B LYS* 3.1 48.2 + - - +
235B GLU* 2.9 9.9 + - - +
237B VAL* 1.3 85.9 - - - +
239B LEU* 1.3 66.5 + - - +
240B GLY* 3.2 1.4 + - - -
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Residues in contact with LEU 239 (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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235B GLU 3.3 13.5 + - - +
236B VAL* 3.4 19.7 - - + +
238B GLN* 1.3 78.5 - - - +
240B GLY* 1.3 58.2 + - - +
242B ARG* 5.3 7.4 - - + +
255B ALA* 4.3 19.1 - - + +
256B PHE* 4.3 24.5 - - + +
259B TRP* 4.1 33.7 - - + -
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Residues in contact with GLY 240 (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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9B LEU* 2.8 31.8 - - - +
236B VAL 4.1 0.7 - - - +
237B VAL 3.2 10.9 + - - +
238B GLN 4.4 0.7 - - - -
239B LEU* 1.3 80.5 - - - +
241B GLY* 1.3 57.2 + - - -
242B ARG* 3.0 12.6 + - - +
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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
------------------------------------------------------------
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