Contacts of the helix formed by residues 223 - 234 (chain C) in PDB entry 1NDD
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 VAL 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C ASP 3.8 0.8 + - - -
222C LYS* 1.3 71.4 - - - +
224C GLU* 1.3 63.0 + - - +
226C ILE* 3.0 21.4 + - + +
227C LYS* 3.0 21.2 + - - +
243C LEU* 4.2 4.7 - - + -
250C MET* 3.6 49.6 - - + +
251C ASN 3.2 26.0 - - - +
252C ASP* 3.5 14.8 + - - +
254C LYS 2.8 16.5 + - - +
255C THR 4.5 4.7 - - - -
256C ALA 4.8 0.4 - - - +
259C TYR* 4.0 11.4 - - + -
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Residues in contact with GLU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C LYS* 3.1 6.9 - - + -
223C VAL* 1.3 76.9 - - - +
225C ARG* 1.3 58.5 + - - +
227C LYS* 3.2 7.1 + - - +
228C GLU* 2.9 51.6 + - - +
238C PRO* 3.4 29.4 - - - +
252C ASP* 3.0 47.2 + - + +
253C GLU* 4.9 6.5 - - - +
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Residues in contact with ARG 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C ILE* 6.2 0.2 - - - -
220C THR 3.8 6.3 + - - -
221C ASP* 3.6 27.8 + - + +
222C LYS* 2.9 72.0 + - - +
224C GLU* 1.3 78.2 - - - +
226C ILE* 1.3 64.6 + - - +
228C GLU* 3.3 20.2 + - + +
229C ARG* 3.1 21.5 + - - +
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Residues in contact with ILE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C ILE* 4.2 17.3 - - + -
205C VAL* 4.8 4.3 - - + -
215C ILE* 4.8 3.8 - - + -
217C ILE* 3.7 41.7 - - + -
221C ASP* 5.0 4.5 - - + +
222C LYS 3.8 9.9 - - - +
223C VAL* 3.0 18.3 + - + +
225C ARG* 1.3 75.6 - - - +
227C LYS* 1.3 57.1 + - - +
229C ARG* 3.1 9.0 + - - +
230C VAL* 3.0 32.0 + - + +
243C LEU* 4.0 16.6 - - + -
250C MET* 4.3 16.4 - - + -
256C ALA* 4.3 12.3 - - + -
261C ILE* 5.0 0.2 - - + -
267C LEU* 4.3 8.1 - - + -
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Residues in contact with LYS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C VAL* 3.0 20.5 + - - +
224C GLU* 3.2 10.7 + - - +
226C ILE* 1.3 78.1 - - - +
228C GLU* 1.3 55.9 + - - +
230C VAL* 3.2 1.2 + - - -
231C GLU* 2.9 16.1 + - - +
238C PRO* 3.6 29.3 + - + +
241C GLN* 2.8 68.4 + - + +
242C ARG* 4.5 0.6 - - - +
243C LEU* 3.7 27.1 - - + +
250C MET 4.1 5.0 + - - -
252C ASP* 2.7 34.7 + - - +
3003C SO4 3.0 18.4 + - - -
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Residues in contact with GLU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLU* 2.9 41.3 + - - +
225C ARG* 3.6 27.6 - - + +
226C ILE 3.2 0.2 - - - -
227C LYS* 1.3 72.6 - - - +
229C ARG* 1.3 61.2 + - - +
231C GLU* 3.3 14.7 + - - +
232C GLU* 3.0 39.4 + - - +
238C PRO* 4.2 8.3 - - + -
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Residues in contact with ARG 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C ILE* 3.5 30.8 - - + +
216C ASP* 2.8 39.8 + - - +
217C ILE* 4.4 4.8 - - + +
221C ASP* 5.8 0.2 + - - -
225C ARG 3.1 12.6 + - - +
226C ILE* 3.3 11.0 - - - +
228C GLU* 1.3 74.2 - - - +
230C VAL* 1.3 65.5 + - - +
232C GLU* 3.3 20.5 + - - +
233C LYS* 3.2 47.1 + - - +
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Residues in contact with VAL 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C VAL* 4.2 19.5 - - + -
213C ILE* 4.8 7.6 - - + -
215C ILE* 3.7 20.2 - - + -
226C ILE* 3.0 22.0 + - + +
227C LYS 3.2 7.6 + - - +
229C ARG* 1.3 77.6 - - - +
231C GLU* 1.3 52.6 + - - +
233C LYS 3.3 0.5 + - - -
234C GLU* 2.8 47.5 + - + +
236C ILE* 4.7 3.6 - - + -
241C GLN* 3.4 25.6 - - - +
243C LEU* 5.1 3.6 - - + -
269C LEU* 4.1 20.4 - - + -
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Residues in contact with GLU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C LYS 2.9 12.6 + - - +
228C GLU* 3.5 16.6 - - - +
229C ARG 3.2 0.2 - - - -
230C VAL* 1.3 78.3 - - - +
232C GLU* 1.3 61.6 + - + +
235C GLY* 2.8 29.8 + - - +
236C ILE 3.3 29.2 - - - +
237C PRO* 4.0 6.9 - - - +
238C PRO* 3.6 27.6 - - + +
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Residues in contact with GLU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C GLU* 3.0 27.3 + - + +
229C ARG* 3.3 23.9 + - - +
231C GLU* 1.3 82.4 - - + +
233C LYS* 1.3 60.9 + - + +
235C GLY 4.9 0.2 + - - -
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Residues in contact with LYS 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLN* 5.2 0.3 + - - -
213C ILE* 3.9 24.0 - - + -
214C GLU 4.0 11.4 + - - +
215C ILE* 3.9 22.0 - - + +
229C ARG* 3.2 40.7 + - + +
230C VAL 4.1 1.6 - - - +
232C GLU* 1.3 81.2 - - + +
234C GLU* 1.3 75.3 + - - +
235C GLY 3.9 0.2 - - - -
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO* 3.3 6.8 - - - +
140B GLN* 2.8 50.9 + - + +
173B LEU* 3.4 29.4 - - + +
174B ARG 4.3 6.9 + - - +
213C ILE* 3.2 41.2 - - + +
230C VAL* 2.8 26.4 + - + +
233C LYS* 1.3 85.4 - - - +
235C GLY* 1.3 60.2 + - - +
236C ILE* 3.4 19.4 + - + -
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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