Contacts of the helix formed by residues 235 - 250 (chain A) in PDB entry 5NDD
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 LEU 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A VAL* 3.6 33.9 - - + -
230A LEU* 4.6 4.9 - - + -
232A GLU* 3.2 34.1 + - + +
234A LEU* 1.3 82.5 - - + +
236A VAL* 1.3 58.4 + - - +
237A GLY 3.2 2.7 - - - -
238A ASP* 3.1 26.2 + - + +
239A MET* 2.9 38.8 + - + +
1131A VAL* 6.0 4.0 - - + -
1134A ALA* 5.5 9.2 - - + +
1135A LYS* 6.4 3.6 - - + -
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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
----------------------------------------------------------
230A LEU* 3.6 20.4 - - + -
233A GLN* 3.2 23.1 - - - +
234A LEU 3.3 1.6 - - - -
235A LEU* 1.3 78.1 - - - +
237A GLY* 1.3 57.1 + - - +
239A MET* 3.6 6.9 - - - +
240A PHE* 2.8 30.0 + - - +
311A TYR* 3.4 32.5 - - + +
314A ILE* 3.6 26.5 - - + +
315A LYS* 3.5 23.6 - - + +
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Residues in contact with GLY 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU 4.4 3.6 + - - -
235A LEU* 3.2 1.2 - - - +
236A VAL* 1.3 80.6 - - - +
238A ASP* 1.3 55.4 + - - +
240A PHE* 3.6 1.7 + - - +
241A ASN* 2.4 37.9 + - - -
315A LYS* 4.4 23.3 + - - +
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Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU 6.0 0.2 - - - -
235A LEU* 3.1 29.8 + - + +
237A GLY* 1.3 75.1 - - - +
239A MET* 1.3 66.9 + - + +
241A ASN* 3.6 6.0 + - - +
242A TYR* 3.1 25.2 + - - +
1131A VAL* 5.5 5.2 - - - +
1135A LYS* 4.7 15.5 + - - +
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Residues in contact with MET 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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208A PRO* 4.1 16.6 - - - +
209A LEU* 4.4 7.9 - - + -
212A VAL* 5.1 10.5 - - + -
214A GLN* 4.1 23.1 - - - +
230A LEU* 4.2 23.6 - - + -
235A LEU* 2.9 25.1 + - + +
236A VAL* 3.2 5.8 + - - +
238A ASP* 1.3 79.8 - - + +
240A PHE* 1.3 61.1 + - - +
242A TYR* 3.4 7.5 + - - +
243A PHE* 3.1 50.9 + - - -
311A TYR* 3.8 30.1 - - + +
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Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL 2.8 16.6 + - - +
237A GLY 3.9 3.8 - - - +
239A MET* 1.3 77.2 - - - +
241A ASN* 1.3 74.4 + - - +
243A PHE* 3.3 2.3 + - - +
244A LEU* 3.0 48.9 + - + +
308A VAL* 3.8 27.6 - - + +
311A TYR* 4.0 13.4 - - + +
312A PHE* 3.6 51.6 - + + -
315A LYS* 3.8 33.2 - - + -
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Residues in contact with ASN 241 (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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237A GLY 2.4 30.1 + - - +
238A ASP* 4.1 7.7 + - - +
239A MET 3.5 0.2 - - - -
240A PHE* 1.3 90.4 - - - +
242A TYR* 1.3 57.4 + - - +
244A LEU* 3.2 7.8 + - - +
245A SER* 2.8 36.5 + - - +
315A LYS* 4.4 10.7 + - - +
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Residues in contact with TYR 242 (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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160A TYR* 5.5 0.2 - - - -
205A VAL* 2.9 34.4 + - + -
206A THR* 3.8 4.5 - - - +
208A PRO* 3.5 26.0 - - + -
209A LEU* 3.4 28.7 - - + +
238A ASP 3.1 19.4 + - - +
239A MET* 3.5 9.2 - - - +
240A PHE 3.2 0.2 - - - -
241A ASN* 1.3 77.0 - - - +
243A PHE* 1.3 103.4 + + - +
245A SER* 3.2 8.2 + - - -
246A LEU* 3.2 51.3 + - + +
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Residues in contact with PHE 243 (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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156A TYR* 3.4 45.5 - + - -
160A TYR* 4.1 12.2 + - - -
209A LEU* 4.0 9.2 - - + -
239A MET* 3.1 34.3 + - - +
240A PHE* 4.2 2.0 - - - +
242A TYR* 1.3 105.6 - + - +
244A LEU* 1.3 60.1 + - - +
246A LEU* 4.0 5.0 - - + +
247A ALA* 3.2 26.9 + - - +
304A ASN* 4.9 1.0 - - - +
307A LEU* 3.6 37.9 - - + +
308A VAL* 3.7 6.3 - - + +
311A TYR* 3.5 34.1 - + + -
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Residues in contact with LEU 244 (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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240A PHE* 3.0 41.6 + - + +
241A ASN* 3.6 8.7 - - - +
242A TYR 3.2 0.2 - - - -
243A PHE* 1.3 77.8 - - - +
245A SER* 1.3 64.3 + - - +
247A ALA* 3.6 2.4 + - + +
248A ILE* 3.3 44.6 + - + +
308A VAL* 3.8 29.6 - - + +
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Residues in contact with SER 245 (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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241A ASN* 2.8 23.6 + - - +
242A TYR* 3.2 10.8 + - - -
244A LEU* 1.3 76.7 - - - +
246A LEU* 1.3 62.8 + - - +
248A ILE* 3.3 5.9 + - - +
249A GLY* 2.9 27.7 + - - -
250A VAL* 4.8 0.3 - - - +
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 3.4 44.9 - - + +
205A VAL* 3.9 28.7 - - + -
242A TYR* 3.2 51.5 + - + +
243A PHE* 4.2 7.2 - - + +
245A SER* 1.3 81.0 - - - +
247A ALA* 1.3 59.0 + - - +
250A VAL* 2.9 47.5 + - + +
251A PHE* 3.1 7.4 + - - +
304A ASN* 4.6 2.2 - - - -
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Residues in contact with ALA 247 (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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243A PHE 3.2 20.0 + - - +
244A LEU* 3.9 5.4 - - + +
245A SER 3.3 0.2 - - - -
246A LEU* 1.3 76.2 - - - +
248A ILE* 1.3 60.6 + - + +
251A PHE* 3.1 32.3 - - + +
252A LEU* 3.2 12.5 + - - +
304A ASN* 4.0 21.5 + - + +
308A VAL* 3.9 19.5 - - + -
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Residues in contact with ILE 248 (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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244A LEU* 3.3 37.7 + - + +
245A SER* 3.3 5.1 + - - +
246A LEU 3.1 0.2 - - - -
247A ALA* 1.3 80.0 - - + +
249A GLY* 1.3 63.4 + - - +
250A VAL 3.4 0.2 - - - -
252A LEU* 3.3 22.5 + - + +
253A PHE* 3.0 30.4 + - + +
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Residues in contact with GLY 249 (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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164A LEU* 5.5 0.7 - - - +
245A SER 2.9 13.1 + - - -
248A ILE* 1.3 80.0 - - - +
250A VAL* 1.3 64.4 + - - +
251A PHE 3.6 0.2 - - - -
253A PHE* 3.8 17.7 - - - +
254A PRO* 3.5 13.0 - - - +
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 3.8 26.5 - - + +
163A ILE* 3.6 19.4 - - - +
164A LEU* 3.8 32.3 - - + -
202A ILE* 5.7 1.1 - - + -
205A VAL* 5.9 2.0 - - + -
245A SER 4.8 0.4 - - - +
246A LEU* 2.9 41.0 + - + +
249A GLY* 1.3 80.8 - - - +
251A PHE* 1.3 56.9 + - - +
254A PRO* 3.5 15.3 - - - +
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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