Contacts of the helix formed by residues 247 - 258 (chain D) in PDB entry 3UDB
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 SER 247 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114D GLU* 2.6 35.3 + - - -
246D ILE* 1.3 89.2 - - - +
248D PRO* 1.3 71.6 - - - +
249D GLU* 2.9 23.6 + - - -
250D CYS* 3.2 10.4 + - - +
251D ARG 3.0 4.2 + - - -
276D TRP* 3.6 2.3 - - - -
279D LYS* 4.7 2.7 - - - -
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Residues in contact with PRO 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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246D ILE 3.3 3.3 - - - +
247D SER* 1.3 83.6 - - - +
249D GLU* 1.3 74.5 + - + +
251D ARG* 3.1 13.6 + - + +
252D HIS* 2.8 29.5 + - - +
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Residues in contact with GLU 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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247D SER* 2.9 30.1 + - - -
248D PRO* 1.3 90.5 - - - +
250D CYS* 1.3 62.5 + - - +
252D HIS* 3.0 9.6 + - - +
253D LEU* 3.0 20.3 + - - +
274D HIS* 3.4 14.1 - - + -
275D GLU* 3.4 27.5 - - + +
276D TRP* 4.0 18.8 - - + +
279D LYS* 3.3 19.6 + - - +
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Residues in contact with CYS 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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114D GLU* 3.7 5.2 - - - +
207D LEU* 5.1 1.1 - - - -
211D LEU* 3.5 32.5 - - - -
246D ILE* 3.6 15.5 - - + -
247D SER* 3.1 23.5 + - - +
249D GLU* 1.3 79.3 - - - +
251D ARG* 1.3 62.8 + - - +
253D LEU* 3.5 2.6 + - - +
254D ILE* 3.2 25.5 + - - +
276D TRP* 3.3 39.6 - - - +
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Residues in contact with ARG 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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238D TYR* 5.4 0.2 + - - -
240D ILE* 4.3 35.6 + - + +
244D VAL 4.4 8.9 + - - -
245D HIS* 5.1 0.4 - - - +
246D ILE* 3.5 43.2 + - + +
247D SER 3.0 9.9 + - - +
248D PRO* 3.1 14.3 + - + +
250D CYS* 1.3 77.3 - - - +
252D HIS* 1.3 62.5 + - - +
254D ILE* 3.7 8.3 + - - +
255D SER* 3.3 21.1 + - - -
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Residues in contact with HIS 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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248D PRO 2.8 13.2 + - - +
249D GLU* 3.0 10.7 + - - +
251D ARG* 1.3 75.3 - - - +
253D LEU* 1.3 66.6 + - - +
255D SER* 2.7 29.9 + - - -
256D ARG* 3.0 37.2 + - + +
274D HIS* 3.0 26.9 + + + +
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Residues in contact with LEU 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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121D PHE* 3.9 20.9 - - + -
207D LEU* 4.3 7.0 - - + -
249D GLU 3.0 12.2 + - - +
250D CYS* 3.5 9.4 + - - +
252D HIS* 1.3 74.1 - - - +
254D ILE* 1.3 65.0 + - + +
256D ARG* 2.9 16.7 + - - +
257D ILE* 3.1 26.7 + - + +
266D ILE* 4.2 17.0 - - + -
271D ILE* 4.3 14.6 - - + -
274D HIS* 3.7 32.8 + - + +
276D TRP* 3.5 33.0 - - + -
277D PHE* 5.2 2.2 - - + -
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Residues in contact with ILE 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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204D GLY* 5.8 2.9 - - - +
207D LEU* 3.9 22.2 - - + -
208D TYR* 5.0 11.9 - - + +
211D LEU* 4.0 25.1 - - + -
238D TYR* 3.9 17.0 - - + +
240D ILE* 4.3 15.5 - - + -
246D ILE* 4.1 11.7 - - + -
250D CYS 3.2 16.8 + - - +
251D ARG* 4.0 5.8 - - - +
252D HIS 3.3 0.2 - - - -
253D LEU* 1.3 78.3 - - - +
255D SER* 1.3 60.2 + - - +
257D ILE* 3.2 9.1 + - - +
258D PHE* 3.1 51.9 + - + +
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Residues in contact with SER 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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238D TYR* 3.9 16.4 - - - -
251D ARG 3.3 9.9 + - - -
252D HIS* 2.7 32.7 + - - -
254D ILE* 1.3 79.4 - - - +
256D ARG* 1.3 62.1 + - - +
257D ILE 3.2 0.6 + - - -
258D PHE* 3.8 8.7 - - - +
259D VAL* 3.4 16.1 - - - +
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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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252D HIS* 3.0 46.4 + - + +
253D LEU* 2.9 10.2 + - - +
255D SER* 1.3 78.4 - - - +
257D ILE* 1.3 60.4 + - - +
259D VAL* 3.6 15.7 - - - +
264D LYS 3.1 24.9 + - - -
265D ARG* 3.9 0.2 - - - -
266D ILE* 3.1 67.3 + - + +
270D GLU* 4.3 12.5 + - - -
274D HIS* 5.4 0.2 - - - +
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Residues in contact with ILE 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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121D PHE* 4.3 17.0 - - + -
200D VAL* 3.5 30.1 - - + +
201D TRP* 3.8 9.8 - - - -
204D GLY* 3.6 28.7 - - - +
207D LEU* 4.8 2.9 - - + -
253D LEU* 3.1 33.2 + - + +
254D ILE* 3.2 10.0 + - + +
256D ARG* 1.3 78.0 - - - +
258D PHE* 1.3 63.5 + - + +
259D VAL 2.9 12.0 + - - -
265D ARG* 3.2 22.6 + - - +
266D ILE* 3.6 21.1 - - + -
271D ILE* 4.3 6.3 - - + -
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Residues in contact with PHE 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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201D TRP* 3.8 37.5 - + + -
204D GLY* 3.7 26.5 - - - -
205D VAL* 3.7 28.0 - - + -
208D TYR* 4.3 18.6 - + + -
216D PRO* 4.3 12.3 - - + -
217D PHE* 4.2 7.6 - + - -
236D VAL* 3.6 26.6 - - + +
238D TYR* 3.9 22.9 - + + +
254D ILE* 3.1 38.6 + - + +
255D SER* 3.8 5.3 - - - +
256D ARG 3.6 0.2 - - - -
257D ILE* 1.3 78.1 - - + +
259D VAL* 1.3 61.4 + - - +
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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