Contacts of the helix formed by residues 233 - 247 (chain A) in PDB entry 1LD7
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 ASN 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ALA* 3.1 43.0 + - - +
198A LYS* 3.7 21.7 - - - +
226A LEU* 5.2 1.5 + - - +
230A ASP* 3.1 26.3 + - + +
231A VAL 3.3 1.4 - - - -
232A ARG* 1.3 73.5 - - - +
234A ASN* 1.3 57.7 + - - +
235A SER* 2.9 25.1 + - - -
236A VAL* 2.9 40.2 + - + +
237A TRP* 3.3 14.2 + - - -
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Residues in contact with ASN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LYS* 4.8 3.2 - - + +
232A ARG 3.0 7.3 + - - -
233A ASN* 1.3 70.9 + - - +
235A SER* 1.3 61.3 + - - +
237A TRP* 3.4 4.6 + - - +
238A ASN* 3.0 21.0 + - - +
275A SER* 2.8 31.1 + - - +
278A ASN* 4.9 1.7 + - - -
735B TRP* 4.2 10.9 - - - -
736B GLU* 2.8 32.9 + - - +
746B GLU* 2.9 22.2 + - - +
792B CYS* 3.2 39.8 - - - +
793B ASN* 4.7 0.6 - - - +
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Residues in contact with SER 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ALA 4.2 1.1 - - - -
198A LYS* 3.8 10.1 + - - +
203A TRP* 3.5 34.6 - - - -
233A ASN* 2.9 13.4 + - - -
234A ASN* 1.3 77.9 - - - +
236A VAL* 1.3 56.8 + - - +
238A ASN* 3.4 7.6 + - - +
239A GLN* 3.1 25.5 + - - +
746B GLU* 2.7 28.1 + - - -
791B ARG* 3.3 13.5 + - - -
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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
----------------------------------------------------------
203A TRP* 4.0 15.0 - - + -
223A VAL* 3.5 25.7 - - + +
226A LEU* 3.7 24.0 - - + -
227A LEU* 3.4 30.7 - - + -
233A ASN* 2.9 37.1 + - + +
235A SER* 1.3 75.1 - - - +
237A TRP* 1.3 66.1 + - - +
238A ASN 3.1 1.3 - - - -
239A GLN* 3.1 7.8 + - + +
240A ARG* 2.9 22.0 + - - +
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Residues in contact with TRP 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.5 16.1 - - + +
231A VAL* 2.8 42.4 + - + -
233A ASN 3.3 19.7 + - - -
234A ASN* 3.4 7.4 + - - +
236A VAL* 1.3 77.4 - - - +
238A ASN* 1.3 62.6 + - - +
240A ARG* 3.2 15.1 + - - +
241A TYR* 3.2 20.6 + - - +
262A TYR* 3.7 30.3 - + - -
263A THR* 4.1 7.2 - - + -
266A MET* 4.0 10.1 - - + -
273A ASN* 4.2 0.4 - - - +
275A SER* 3.4 26.5 - - - +
276A ALA* 3.9 22.7 - - + -
279A TYR* 3.5 50.9 - + + -
735B TRP* 4.0 16.1 - - + -
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Residues in contact with ASN 238 (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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207A GLN* 3.5 10.5 - - - +
234A ASN 3.0 13.6 + - - +
235A SER 3.4 10.4 + - - +
236A VAL 3.1 0.2 - - - -
237A TRP* 1.3 75.8 - - - +
239A GLN* 1.3 60.0 + - - +
241A TYR* 3.2 4.0 + - - +
242A PHE* 2.9 25.6 + - - +
734B ASN* 3.1 14.6 + - - -
735B TRP* 2.8 36.2 + - + +
744B GLY 3.1 24.9 + - - +
745B MET* 3.7 3.2 - - - +
746B GLU* 3.1 31.2 - - + +
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Residues in contact with GLN 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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203A TRP* 3.4 35.5 - - + +
206A ARG* 4.2 3.1 - - - +
207A GLN* 3.0 35.6 - - - +
210A ILE* 4.0 7.4 - - - +
219A GLU* 2.8 29.8 - - + +
223A VAL* 3.7 14.8 - - + -
235A SER 3.1 14.3 + - - +
236A VAL* 3.1 9.6 + - - +
238A ASN* 1.3 73.7 - - - +
240A ARG* 1.3 59.9 + - - +
242A PHE* 3.1 17.1 + - - +
243A VAL* 2.8 35.0 + - - +
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Residues in contact with ARG 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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220A LEU* 3.7 22.2 - - + +
223A VAL* 3.8 22.4 - - + +
224A ASP* 2.9 29.1 + - - -
227A LEU* 4.0 4.5 - - - +
236A VAL 2.9 12.3 + - - +
237A TRP* 3.3 26.5 - - - +
238A ASN 3.2 0.2 - - - -
239A GLN* 1.3 77.6 - - - +
241A TYR* 1.3 61.2 + - - +
243A VAL* 3.3 2.8 + - - +
244A ILE* 3.1 30.5 + - + +
250A TYR* 4.4 0.2 - - - -
258A ARG* 4.7 4.4 - - - +
259A GLU* 2.7 41.0 + - - -
262A TYR* 3.8 31.8 - - - +
279A TYR* 3.6 17.5 - - + +
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Residues in contact with TYR 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 TRP 3.2 6.8 + - - +
238A ASN 3.6 7.4 - - - +
240A ARG* 1.3 78.3 - - - +
242A PHE* 1.3 63.1 + - - +
245A SER* 2.9 49.8 + - - -
250A TYR* 3.4 43.5 + + - -
279A TYR* 4.1 7.1 - + + -
282A GLY 4.3 4.4 + - - -
283A ILE* 4.0 17.7 - - + -
286A ASP* 4.7 1.2 + - - -
735B TRP* 3.6 42.0 - + + +
1C GLC 2.9 49.6 + - - -
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Residues in contact with PHE 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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207A GLN* 3.3 73.6 - - + +
210A ILE* 4.3 8.5 - - + -
211A GLN* 4.4 14.8 - - + -
216A TRP* 3.4 30.7 - + - -
238A ASN 2.9 10.4 + - - +
239A GLN* 3.2 23.8 - - - +
241A TYR* 1.3 79.5 - - - +
243A VAL* 1.3 65.6 + - + +
245A SER* 3.3 7.4 + - - -
246A ASN* 2.9 39.2 + - - +
743B PRO 5.5 1.6 - - - -
744B GLY* 4.4 16.4 - - - +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TRP* 4.2 15.7 - - + +
219A GLU* 3.3 36.8 - - + -
220A LEU* 4.2 29.4 - - + +
223A VAL* 4.5 5.2 - - + -
239A GLN* 2.8 25.5 + - + +
240A ARG* 3.8 4.9 - - - +
242A PHE* 1.3 81.6 - - + +
244A ILE* 1.3 59.9 + - + +
246A ASN* 3.3 3.1 + - - +
247A THR* 2.7 48.3 + - + +
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Residues in contact with ILE 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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220A LEU* 4.6 14.4 - - + -
240A ARG* 3.1 18.8 + - + +
243A VAL* 1.3 75.1 - - + +
245A SER* 1.3 58.9 + - - +
247A THR* 3.2 12.3 + - - +
248A THR* 3.3 15.4 + - - +
249A GLY 2.6 40.7 + - - +
250A TYR* 3.5 28.3 - - + +
255A VAL* 4.0 7.0 - - + -
258A ARG* 3.6 11.4 - - - +
259A GLU* 3.3 39.7 - - + +
279A TYR* 3.6 10.1 - - - +
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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 TYR* 2.9 48.4 + - - -
242A PHE* 3.3 7.8 + - - -
244A ILE* 1.3 77.7 - - - +
246A ASN* 1.3 67.7 + - - +
247A THR 3.8 0.3 + - - -
249A GLY* 4.1 14.2 - - - -
250A TYR* 3.8 11.8 - - - -
1C GLC 5.5 1.3 - - - -
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Residues in contact with ASN 246 (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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211A GLN* 3.1 26.3 - - - +
216A TRP* 3.3 37.2 + - + -
242A PHE* 2.9 30.8 + - - +
243A VAL 3.3 1.4 + - - -
244A ILE 3.1 0.8 - - - -
245A SER* 1.3 88.6 + - - +
247A THR* 1.3 62.8 + - - +
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Residues in contact with THR 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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216A TRP* 3.9 33.9 - - + +
243A VAL* 2.7 30.4 + - + +
244A ILE* 3.2 11.3 + - - +
245A SER 3.5 0.2 - - - -
246A ASN* 1.3 83.1 - - - +
248A THR* 1.3 77.0 + - - +
249A GLY 3.4 0.2 - - - -
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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