Contacts of the helix formed by residues 215 - 228 (chain C) in PDB entry 3NDR
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 GLN 215 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187C ILE* 3.4 9.1 - - - +
188C GLU* 3.3 35.2 + - - +
193C LYS* 5.7 2.0 - - - +
213C LYS* 3.1 18.9 - - - +
214C GLY* 1.3 72.7 - - - +
216C PRO* 1.3 72.9 - - + +
217C GLU* 3.5 20.2 - - + +
218C HIS* 2.7 53.0 + - + +
219C ILE 3.8 1.2 + - - -
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Residues in contact with PRO 216 (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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18C GLY* 4.2 8.3 - - - -
19C ILE* 4.0 17.0 - - + +
22C ALA* 3.5 24.0 - - + +
187C ILE* 3.6 19.5 - - + -
188C GLU 3.9 12.1 - - - +
189C SER* 4.3 9.9 - - - -
190C ASP* 5.7 0.7 - - - +
215C GLN* 1.3 101.7 - - + +
217C GLU* 1.3 69.0 + - - +
219C ILE* 3.0 7.4 + - + +
220C ALA* 3.0 20.3 + - - +
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Residues in contact with GLU 217 (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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232A ARG* 3.5 14.6 - - - +
22C ALA* 4.2 14.9 - - + +
215C GLN* 3.1 25.7 - - + +
216C PRO* 1.3 80.2 - - - +
218C HIS* 1.3 60.0 - - - +
220C ALA* 4.0 9.0 - - + -
221C ASP* 3.0 34.7 + - - +
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Residues in contact with HIS 218 (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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230A ASP 4.4 1.6 - - - +
232A ARG* 3.4 37.4 + - + +
233A TRP* 3.4 66.2 + + + +
213C LYS 4.3 4.9 - - - -
215C GLN* 2.7 47.7 + - + +
217C GLU* 1.3 80.1 - - - +
219C ILE* 1.3 58.8 + - + +
221C ASP* 4.1 2.1 + - - +
222C VAL* 3.2 24.4 + - - +
241C VAL* 4.0 3.9 - - - +
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Residues in contact with ILE 219 (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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233A TRP* 4.7 0.2 - - + -
19C ILE* 3.5 26.7 - - + -
23C ILE* 4.2 0.9 - - + -
139C ILE* 4.6 9.6 - - + -
182C VAL* 4.8 7.0 - - + -
184C PRO* 3.6 29.2 - - + -
187C ILE* 3.4 40.4 - - + -
215C GLN 4.3 1.1 - - - +
216C PRO 3.0 8.0 + - - +
218C HIS* 1.3 86.5 - - + +
220C ALA* 1.3 66.2 + - - +
221C ASP 3.2 0.4 - - - -
222C VAL* 3.0 8.7 + - - +
223C VAL* 2.9 34.4 + - + +
241C VAL* 4.3 18.8 - - + +
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Residues in contact with ALA 220 (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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22C ALA* 3.2 38.6 - - + +
23C ILE* 3.6 18.3 - - + +
26C ARG* 3.9 10.6 - - + +
27C LEU* 5.7 0.2 - - - +
216C PRO 3.0 14.1 + - - +
217C GLU* 3.4 7.8 + - + +
219C ILE* 1.3 77.7 - - - +
221C ASP* 1.3 58.7 + - - +
223C VAL* 3.2 3.5 + - - +
224C SER* 2.9 28.9 + - - -
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Residues in contact with ASP 221 (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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230A ASP* 3.4 32.6 - - - +
232A ARG* 2.5 38.4 + - - +
26C ARG* 3.0 34.6 + - - +
217C GLU* 3.0 22.0 + - - +
218C HIS 4.3 1.6 - - - +
220C ALA* 1.3 78.4 - - - +
222C VAL* 1.3 59.6 + - - +
224C SER* 3.7 4.8 - - - -
225C PHE* 3.6 12.6 + - - +
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Residues in contact with VAL 222 (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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225A PHE* 3.9 18.6 - - + -
230A ASP 3.4 17.3 - - - +
231A ALA 5.7 0.2 - - - -
233A TRP* 6.0 0.2 - - + -
234A ILE* 4.1 13.0 - - + -
182C VAL* 5.0 4.3 - - + -
218C HIS 3.2 21.1 - - - +
219C ILE* 3.0 6.0 + - - +
221C ASP* 1.3 76.0 - - - +
223C VAL* 1.3 66.9 + - - +
224C SER 3.1 1.3 - - - -
225C PHE* 3.1 5.8 + - + +
226C LEU* 3.1 25.4 + - + +
239C LEU* 4.3 17.9 - - + -
241C VAL* 4.0 30.7 - - + -
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Residues in contact with VAL 223 (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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23C ILE* 3.6 43.3 - - + -
27C LEU* 4.7 5.6 - - + -
86C VAL* 4.0 19.5 - - + -
137C ILE* 3.7 10.9 - - + +
139C ILE* 4.2 12.3 - - + -
182C VAL* 4.7 9.9 - - + -
219C ILE* 2.9 25.5 + - + +
220C ALA 3.5 6.7 - - - +
222C VAL* 1.3 77.6 - - - +
224C SER* 1.3 56.9 + - - +
226C LEU* 3.1 10.6 + - - +
227C ALA* 2.8 28.2 + - - +
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Residues in contact with SER 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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4C ARG* 2.9 17.5 + - - -
5C LEU* 5.1 0.3 - - - +
26C ARG* 3.1 35.5 + - - -
27C LEU* 4.0 10.1 - - - +
30C ASP* 2.8 28.3 + - - +
220C ALA 2.9 8.3 + - - -
221C ASP 3.7 7.6 - - - -
222C VAL 3.1 0.2 - - - -
223C VAL* 1.3 76.7 - - - +
225C PHE* 1.3 60.5 + - - +
227C ALA* 3.3 4.5 + - - +
228C SER* 3.3 20.8 + - - -
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Residues in contact with PHE 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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221A ASP 4.3 2.0 - - - -
222A VAL* 4.0 15.0 - - + -
225A PHE* 3.3 64.8 - + + -
230A ASP* 5.3 0.7 - - + +
239A LEU* 5.6 1.3 - - + -
4C ARG* 4.0 8.7 - - - +
221C ASP 3.6 4.4 + - - +
222C VAL* 3.1 10.6 + - + +
224C SER* 1.3 81.2 + - - +
226C LEU* 1.3 84.6 + - + +
228C SER* 2.6 31.4 + - - -
230C ASP* 3.7 32.5 - - + -
231C ALA* 3.5 17.2 - - + +
234C ILE* 3.9 16.2 - - + -
239C LEU* 5.0 5.2 - - + -
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Residues in contact with LEU 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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135C ARG* 3.1 23.6 + - - -
137C ILE* 3.7 24.3 - - + +
180C ASN* 4.2 30.4 + - + +
181C ALA 4.8 0.4 - - - +
182C VAL* 3.5 32.1 - - + -
222C VAL* 3.1 16.2 + - + +
223C VAL* 3.1 7.6 + - - +
225C PHE* 1.3 98.6 - - + +
227C ALA* 1.3 58.7 + - - +
228C SER 3.4 0.3 + - - -
231C ALA* 3.7 14.9 - - + +
234C ILE* 4.7 4.9 - - + -
239C LEU* 4.0 25.4 - - + -
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Residues in contact with ALA 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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5C LEU* 3.9 15.6 - - + +
27C LEU* 4.1 16.8 - - + -
84C ILE* 4.0 28.4 - - + +
135C ARG* 3.5 18.0 + - - +
137C ILE* 3.7 13.4 - - + +
223C VAL 2.8 15.6 + - - +
224C SER 3.6 6.3 - - - +
225C PHE 3.1 0.2 - - - -
226C LEU* 1.3 76.8 - - - +
228C SER* 1.3 58.8 + - - +
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Residues in contact with SER 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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4C ARG* 3.5 42.8 + - - +
5C LEU* 4.7 7.4 - - - -
135C ARG* 3.4 15.4 + - - -
224C SER 3.3 3.2 + - - -
225C PHE* 2.6 21.3 + - - +
227C ALA* 1.3 81.7 - - - +
229C ASP* 1.3 63.3 + - - +
230C ASP* 3.1 21.4 + - - +
231C ALA* 3.1 11.3 + - - +
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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