Contacts of the helix formed by residues 224 - 240 (chain A) in PDB entry 5ITX
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ARG* 2.8 33.6 + - - -
186A LEU* 3.9 7.2 - - - -
201A LEU* 3.7 21.3 - - + +
222A ASN 3.6 2.6 + - - +
223A PRO* 1.3 75.2 - - - +
225A LEU* 1.3 66.3 + - - +
226A LEU* 3.0 5.2 + - - +
227A GLU* 2.9 39.4 + - - +
228A LEU* 3.0 12.3 + - - +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ILE* 4.0 25.8 - - + -
165A LEU* 4.9 6.7 - - + -
171A PHE* 6.0 0.2 - - + -
182A ILE* 3.3 30.7 - - + +
183A LEU* 4.6 5.4 - - + -
186A LEU* 3.6 16.3 - - + +
188A ILE* 4.2 17.0 - - + -
197A VAL* 3.7 25.6 - - + -
198A LEU* 4.4 10.5 - - + -
201A LEU* 4.2 13.0 - - + +
224A ASP* 1.3 77.0 - - - +
226A LEU* 1.3 65.5 + - + +
228A LEU* 3.4 3.0 + - - +
229A CYS* 3.2 25.7 + - - -
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A TYR* 3.4 13.6 - - + -
144A PHE* 3.6 13.4 - - + -
145A ARG* 3.5 42.4 - - + +
148A VAL* 4.2 11.9 - - + -
149A LEU* 3.9 21.1 - - + -
171A PHE* 4.0 24.5 - - + -
198A LEU* 3.9 18.8 - - + -
201A LEU* 3.3 25.3 - - + +
224A ASP* 3.0 2.6 + - - +
225A LEU* 1.3 77.2 - - + +
227A GLU* 1.3 65.4 + - - +
229A CYS* 3.2 18.4 + - - +
230A HIS 3.6 0.7 + - - -
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A TYR* 3.3 24.5 + - + +
145A ARG* 4.9 1.2 + - - -
222A ASN 4.5 1.2 - - - +
223A PRO* 3.4 19.5 - - + +
224A ASP* 2.9 39.8 + - - +
226A LEU* 1.3 78.5 - - - +
228A LEU* 1.3 57.1 + - - +
230A HIS* 3.3 7.9 + - + +
231A SER* 3.1 28.0 + - - +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ILE* 4.2 15.7 - - + +
185A ARG* 4.1 26.2 - - + +
186A LEU* 3.5 40.2 - - + -
223A PRO* 4.0 22.4 - - + +
224A ASP 3.0 10.4 + - - +
225A LEU* 3.8 7.6 - - - +
226A LEU 3.2 0.2 - - - -
227A GLU* 1.3 73.7 - - - +
229A CYS* 1.3 60.7 + - - +
230A HIS 3.0 2.7 - - - -
231A SER* 3.4 15.3 - - - +
232A VAL* 2.7 52.9 + - + +
235A GLU* 6.0 0.2 - - - +
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Residues in contact with CYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 3.5 17.5 - - + +
144A PHE* 3.6 18.2 - - + -
165A LEU* 4.0 26.9 - - - -
171A PHE* 4.0 15.7 - - - -
174A ILE* 4.0 5.0 - - + +
182A ILE* 4.1 22.0 - - + -
225A LEU* 3.2 22.4 + - - -
226A LEU* 3.2 9.8 + - - +
228A LEU* 1.3 77.4 - - - +
230A HIS* 1.3 56.4 + - - +
233A PRO* 3.0 21.1 - - - +
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Residues in contact with HIS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 2.9 26.4 + - + +
138A LEU* 3.3 23.7 + - - +
141A TYR* 3.5 40.4 - + + +
144A PHE* 4.9 0.2 - - - -
226A LEU 3.6 1.6 + - - -
227A GLU* 3.3 7.4 + - + +
228A LEU 3.0 0.4 - - - -
229A CYS* 1.3 80.0 - - - +
231A SER* 1.3 70.3 + - - +
232A VAL 3.4 0.4 - - - -
233A PRO* 3.5 3.6 - - - +
234A LYS* 3.1 56.2 + - + +
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A PRO* 5.5 1.4 - - - +
227A GLU* 3.1 19.8 + - - +
228A LEU* 3.4 21.1 - - - +
230A HIS* 1.3 84.6 - - - +
232A VAL* 1.3 69.0 + - - +
234A LYS* 3.5 6.5 + - - +
235A GLU* 3.1 30.4 + - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 3.9 11.2 - - + -
181A GLU* 4.3 12.3 - - + -
182A ILE* 4.1 16.4 - - + -
185A ARG* 4.3 21.1 - - - +
228A LEU* 2.7 49.0 + - + +
231A SER* 1.3 72.3 + - - +
233A PRO* 1.3 67.0 - - + +
235A GLU* 2.9 26.1 + - - +
236A VAL* 3.5 4.9 + - - +
259A TRP* 3.6 28.0 - - + -
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Residues in contact with PRO 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLY* 6.0 0.2 - - - -
5A PRO* 3.7 24.1 - - + +
137A VAL* 4.3 11.4 - - + -
138A LEU* 3.7 12.8 - - + -
173A GLY 5.8 0.4 - - - +
174A ILE* 4.4 3.1 - - + -
178A LEU* 3.9 21.8 - - + -
182A ILE* 4.9 0.9 - - + -
228A LEU 3.5 1.8 - - - +
229A CYS* 3.0 30.3 - - - +
230A HIS* 3.5 7.0 - - - +
232A VAL* 1.3 92.0 - - + +
234A LYS* 1.3 63.9 + - - -
236A VAL* 3.0 15.2 + - + +
237A VAL* 3.1 14.2 + - - +
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Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 3.3 19.3 + - + +
230A HIS* 3.1 46.0 + - - +
231A SER* 3.7 7.4 - - - +
232A VAL 3.2 0.2 - - - -
233A PRO* 1.3 78.5 - - - +
235A GLU* 1.3 62.1 + - - +
237A VAL* 3.2 8.8 + - + +
238A GLN* 3.0 44.9 + - + +
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ARG* 2.8 34.3 + - - -
228A LEU* 6.0 0.3 - - - +
231A SER* 3.1 21.1 + - - +
232A VAL* 2.9 14.1 + - - +
234A LYS* 1.3 75.2 - - - +
236A VAL* 1.3 58.3 + - - +
238A GLN* 3.3 13.9 + - - +
239A LEU* 3.1 32.0 + - - +
259A TRP* 2.7 34.9 + - + +
261A ARG* 4.6 3.0 + - - -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 3.6 13.2 - - + -
6A GLU* 3.9 5.8 - - - +
9A LEU* 4.7 2.2 - - + +
177A TYR* 3.3 25.6 - - + +
178A LEU* 4.4 0.9 - - + -
232A VAL 3.7 6.3 - - - +
233A PRO* 3.0 11.4 + - + +
235A GLU* 1.3 73.5 - - - +
237A VAL* 1.3 66.4 + - - +
239A LEU* 3.1 24.7 + - + +
240A GLY 3.5 7.3 + - - +
242A LYS* 4.5 7.8 - - + +
256A PHE* 4.1 14.6 - - + -
259A TRP* 3.3 41.7 - - + -
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PRO* 3.6 35.2 - - + +
8A HIS* 3.7 27.4 - - + +
9A LEU* 3.9 11.0 - - + +
12A GLN* 3.9 10.3 - - - +
138A LEU* 3.9 19.3 - - + -
233A PRO 3.1 7.3 + - - +
234A LYS* 3.6 11.9 - - + +
236A VAL* 1.3 77.5 - - - +
238A GLN* 1.3 60.5 + - + +
240A GLY* 2.9 22.3 + - - -
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Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A LYS* 3.0 42.7 + - + +
235A GLU* 3.7 13.9 - - - +
236A VAL 3.2 0.4 - - - -
237A VAL* 1.3 80.6 - - + +
239A LEU* 1.3 62.1 + - - +
240A GLY* 3.3 0.3 + - - -
222B ASN* 5.4 5.5 + - - -
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLU 3.1 22.1 + - - +
236A VAL* 3.1 13.8 + - - +
238A GLN* 1.3 77.6 - - - +
240A GLY* 1.3 64.9 + - - +
241A GLY 4.0 0.5 + - - -
252A ASP* 4.8 6.8 - - - +
255A ALA* 4.0 26.1 - - + +
256A PHE* 4.0 18.8 - - + -
259A TRP* 3.6 41.1 - - + -
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Residues in contact with GLY 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.9 16.2 - - - +
236A VAL 3.5 2.2 + - - +
237A VAL 2.9 17.5 + - - -
238A GLN 3.1 1.9 - - - -
239A LEU* 1.3 87.9 - - - +
241A GLY* 1.3 66.9 + - - +
242A LYS* 3.6 11.6 - - - +
252A ASP* 5.1 2.0 - - - +
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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