Contacts of the helix formed by residues 245 - 258 (chain D) in PDB entry 3UYS
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 PRO 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D LEU* 4.0 29.8 - - + -
241D CYS* 5.3 1.6 - - - +
244D TYR* 1.3 95.9 - - + +
246D SER* 1.3 66.1 + - - +
247D GLU* 2.8 16.3 + - - +
248D PHE* 3.1 30.0 + - + +
249D ALA* 4.2 1.2 + - - +
276D LEU* 3.5 22.2 - - + -
280D GLN* 5.6 2.0 - - - +
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Residues in contact with SER 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ARG* 4.0 23.8 - - - -
244D TYR 3.5 3.2 + - - -
245D PRO* 1.3 70.1 - - - +
247D GLU* 1.3 80.6 + - - +
249D ALA* 2.9 13.2 + - - +
250D THR* 2.9 28.2 + - - -
279D ARG* 5.5 0.2 + - - -
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Residues in contact with GLU 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D PRO* 2.8 12.8 + - - +
246D SER* 1.3 92.9 + - - +
248D PHE* 1.3 57.6 + - + +
250D THR* 3.5 7.8 + - - -
251D TYR* 2.9 29.6 + - - +
272D LEU* 3.4 39.5 - - + +
273D PHE* 3.9 17.8 - - + -
276D LEU* 3.6 25.0 - - + +
279D ARG* 3.3 32.4 + - - -
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Residues in contact with PHE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LEU* 3.8 25.8 - - + -
105D VAL* 3.8 25.1 - - + -
106D LEU* 4.0 12.3 - - + -
109D ALA* 5.7 0.4 - - + -
200D GLY 5.8 0.7 - - - -
203D LEU* 4.3 17.0 - - + -
204D MET* 3.8 21.1 - - + -
207D ASN* 3.6 29.6 - - - -
241D CYS* 4.1 4.9 - - + -
244D TYR* 4.7 2.0 - - + -
245D PRO* 3.1 33.7 + - + +
247D GLU* 1.3 73.7 - - - +
249D ALA* 1.3 66.3 + - - +
251D TYR* 3.8 4.8 - - + +
252D LEU* 3.2 28.8 + - - +
273D PHE* 3.7 22.2 - + - -
276D LEU* 4.3 5.2 - - + -
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Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ARG* 5.7 9.4 - - + +
237D ILE* 3.7 24.1 - - + +
238D GLU* 5.4 4.0 - - - -
241D CYS* 3.9 15.1 - - + +
245D PRO 4.2 0.6 + - - -
246D SER* 2.9 15.3 + - - +
248D PHE* 1.3 78.5 - - - +
250D THR* 1.3 63.8 + - - +
252D LEU 3.5 0.7 + - - -
253D ASN* 3.0 35.1 + - - +
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Residues in contact with THR 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D SER* 2.9 21.3 + - - -
247D GLU* 3.7 8.5 - - - -
249D ALA* 1.3 75.4 - - - +
251D TYR* 1.3 65.4 + - - +
253D ASN* 3.4 5.9 + - - +
254D PHE* 3.0 23.2 + - + +
268D TYR* 3.6 24.5 - - + +
272D LEU* 3.7 20.1 - - + +
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Residues in contact with TYR 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ILE* 4.2 12.3 - - + -
196D LEU* 2.5 42.2 + - - +
199D LEU* 3.5 19.1 - - + +
200D GLY* 3.3 26.5 - - - -
203D LEU* 4.8 2.5 - - + -
247D GLU 2.9 18.6 + - - +
248D PHE* 3.8 5.4 - - - +
249D ALA 3.3 0.2 - - - -
250D THR* 1.3 76.7 - - - +
252D LEU* 1.3 68.6 + - + +
254D PHE* 3.1 7.7 + - - +
255D CYS* 3.1 33.7 + - - -
269D LEU* 3.9 29.2 - - + -
272D LEU* 4.3 10.3 - - + +
273D PHE* 3.5 33.9 - + + -
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Residues in contact with LEU 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D GLU* 4.1 13.9 - - + +
200D GLY* 3.5 41.1 - - - +
201D TYR* 4.0 14.8 - - + +
204D MET* 4.5 1.8 - - + -
237D ILE* 3.2 22.0 - - + -
240D LEU* 3.5 32.1 - - + -
241D CYS* 3.8 18.2 - - - -
248D PHE 3.2 11.4 + - - +
249D ALA 3.9 2.2 - - - +
251D TYR* 1.3 84.8 - - + +
253D ASN* 1.3 62.6 + - - +
255D CYS* 3.3 4.6 + - - +
256D ARG* 3.0 28.3 + - + +
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Residues in contact with ASN 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ARG 4.4 4.0 - - - +
257A SER* 3.2 46.6 + - - +
259A ARG* 6.0 2.2 - - - +
237D ILE* 3.6 25.5 - - - +
238D GLU 5.9 0.4 - - - +
249D ALA* 3.0 28.7 + - - +
250D THR* 3.9 6.0 - - - +
252D LEU* 1.3 76.7 - - - +
254D PHE* 1.3 61.0 + - - +
256D ARG* 3.3 7.1 + - - +
257D SER* 2.9 29.4 + - - -
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Residues in contact with PHE 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D THR* 3.0 14.7 + - + +
251D TYR 3.3 9.0 - - - +
253D ASN* 1.3 76.3 - - - +
255D CYS* 1.3 60.1 + - - +
257D SER* 2.9 23.6 + - - -
258D LEU* 3.3 39.2 + - + +
265D ASP* 4.1 33.2 - - + -
268D TYR* 3.7 26.5 - + + -
269D LEU* 3.7 31.6 - - + -
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Residues in contact with CYS 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D ARG* 4.3 13.4 - - - +
196D LEU* 3.6 26.0 - - - -
197D GLU* 4.1 25.3 - - + +
251D TYR* 3.1 40.8 + - - -
252D LEU* 3.3 8.7 + - - +
254D PHE* 1.3 81.0 - - - +
256D ARG* 1.3 60.9 + - - +
257D SER 3.3 0.5 + - - -
258D LEU* 3.6 25.7 + - - +
269D LEU* 4.7 9.0 - - - -
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Residues in contact with ARG 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ASN* 4.3 6.6 - - - +
256A ARG* 4.7 15.0 - - - +
182D ILE* 3.4 29.3 - - - +
183D ASN* 5.9 0.7 + - - +
197D GLU* 3.5 26.9 - - + +
201D TYR* 2.5 34.2 + - - -
232D LYS 4.6 5.9 + - - -
235D THR 4.9 3.6 + - - -
236D PRO* 5.2 1.2 - - - +
237D ILE* 3.2 40.5 - - + +
252D LEU* 3.0 23.0 + - + +
253D ASN* 3.7 9.6 + - - +
254D PHE 3.1 0.2 - - - -
255D CYS* 1.3 75.8 - - - +
257D SER* 1.3 59.9 + - - +
258D LEU 4.6 3.2 - - - +
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Residues in contact with SER 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU* 6.1 0.3 - - - +
253A ASN* 3.6 41.8 + - - +
257A SER* 4.0 10.7 + - - -
253D ASN 2.9 15.8 + - - -
254D PHE* 2.9 13.6 + - - -
256D ARG* 1.3 77.6 - - - +
258D LEU* 1.3 67.8 + - - +
259D ARG* 3.7 5.2 + - - +
262D ASP* 4.9 0.3 - - - +
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Residues in contact with LEU 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU* 4.5 1.9 - - - +
193D ARG* 3.2 50.3 + - + -
196D LEU* 4.9 4.0 - - + -
254D PHE* 3.3 35.0 + - + +
255D CYS* 3.6 20.8 + - + +
256D ARG 4.6 3.3 - - - +
257D SER* 1.3 81.7 - - - +
259D ARG* 1.3 61.3 + - - +
262D ASP* 3.9 24.2 - - + +
263D LYS 4.4 1.8 - - - +
264D PRO* 3.9 35.0 - - + -
265D ASP 5.2 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