Contacts of the helix formed by residues 244 - 258 (chain D) in PDB entry 4UC5
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 ASP 244 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242D ASN 3.6 0.6 - - - -
243D TYR* 1.3 96.4 - - + +
245D ALA* 1.3 63.8 + - - +
246D GLU* 3.3 9.4 + - - +
247D HIS* 3.0 37.9 + - - +
248D VAL* 3.0 20.2 + - - +
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Residues in contact with ALA 245 (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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244D ASP* 1.3 74.2 - - - +
246D GLU* 1.3 64.0 + - - +
248D VAL* 3.2 8.7 + - - +
249D SER* 2.9 24.8 + - - -
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Residues in contact with GLU 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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244D ASP* 3.3 10.1 + - - +
245D ALA* 1.3 78.1 - - - +
247D HIS* 1.3 61.3 + - + +
249D SER* 3.3 7.8 + - - -
250D GLU* 3.0 29.3 + - - +
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Residues in contact with HIS 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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235D LEU* 4.9 2.0 - - + +
240D GLU* 5.7 3.9 - - + +
241D PRO 3.8 17.6 + - - -
242D ASN* 3.4 41.0 - - + +
244D ASP* 3.0 35.5 + - - +
246D GLU* 1.3 77.7 - - + +
248D VAL* 1.3 58.4 + - - +
250D GLU* 3.4 7.2 + - + +
251D ALA* 2.9 30.1 + - - +
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Residues in contact with VAL 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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235D LEU* 4.1 14.4 - - + -
243D TYR 3.6 15.3 - - - +
244D ASP 3.0 19.1 + - - +
245D ALA* 3.5 10.3 - - - +
247D HIS* 1.3 73.8 - - - +
249D SER* 1.3 61.2 + - - +
251D ALA* 3.5 6.3 + - - +
252D ALA* 3.0 29.7 + - + +
264D LEU* 4.2 15.8 - - + +
266D ILE* 4.0 18.2 - - + -
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Residues in contact with SER 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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245D ALA 2.9 13.7 + - - -
246D GLU* 3.5 11.2 - - - -
248D VAL* 1.3 76.4 - - - +
250D GLU* 1.3 63.2 + - - +
252D ALA* 3.3 7.6 + - - +
253D GLU* 3.1 23.4 + - - +
256D ARG* 4.8 1.6 + - - -
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Residues in contact with GLU 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 GLU 3.0 16.7 + - - +
247D HIS* 3.4 8.7 + - + +
249D SER* 1.3 74.9 - - - +
251D ALA* 1.3 63.6 + - - +
253D GLU* 3.4 6.9 + - - +
254D GLN* 3.1 37.4 + - - +
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Residues in contact with ALA 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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195D LEU* 3.5 31.4 - - + +
233D VAL* 5.6 0.2 - - + -
235D LEU* 4.4 9.0 - - + -
247D HIS 2.9 17.2 + - - +
248D VAL* 3.7 5.2 - - - +
250D GLU* 1.3 76.2 - - - +
252D ALA* 1.3 57.7 + - - +
254D GLN* 3.2 5.4 + - - +
255D LEU* 2.9 35.2 + - + +
264D LEU* 3.8 20.2 - - + -
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Residues in contact with ALA 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 VAL* 3.0 19.8 + - + +
249D SER* 3.3 8.0 + - - +
251D ALA* 1.3 74.2 - - - +
253D GLU* 1.3 58.2 + - - +
255D LEU* 3.2 12.4 + - - +
256D ARG* 3.0 52.9 + - - +
262D ASP* 3.7 16.1 - - + +
264D LEU* 4.7 2.0 - - + +
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Residues in contact with GLU 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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249D SER 3.1 14.3 + - - +
250D GLU* 3.9 6.7 - - - +
252D ALA* 1.3 76.0 - - - +
254D GLN* 1.3 59.6 + - + +
256D ARG* 3.4 22.4 + - - +
257D ALA* 2.9 31.3 + - - +
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Residues in contact with GLN 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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195D LEU* 3.7 18.1 - - - +
196D LYS* 5.0 4.7 + - - +
199D ILE* 3.5 28.5 - - + +
250D GLU* 3.1 24.3 + - - +
251D ALA 3.2 8.7 + - - +
253D GLU* 1.3 77.7 - - + +
255D LEU* 1.3 61.4 + - - +
257D ALA* 3.3 9.0 + - - +
258D ALA* 3.2 22.0 + - - +
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Residues in contact with LEU 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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195D LEU* 6.0 0.4 - - + -
199D ILE* 3.7 22.4 - - + -
202D ILE* 4.3 3.1 - - + -
233D VAL* 4.0 26.5 - - + -
251D ALA* 2.9 28.6 + - + +
252D ALA* 3.2 6.7 + - - +
254D GLN* 1.3 72.1 - - - +
256D ARG* 1.3 66.8 + - - +
258D ALA* 3.2 6.9 + - - -
260D VAL* 3.0 46.2 + - + +
261D THR 3.5 26.5 - - - +
262D ASP* 3.7 16.8 - - - -
263D LYS 5.2 0.2 - - - +
264D LEU* 4.2 15.5 - - + -
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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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249D SER 4.8 1.6 + - - -
252D ALA* 3.0 31.7 + - - +
253D GLU* 3.5 28.4 - - - +
255D LEU* 1.3 75.1 - - - +
257D ALA* 1.3 58.6 + - - +
259D GLY* 3.0 19.0 + - - +
260D VAL 3.9 4.9 + - - +
262D ASP* 3.0 35.0 + - + +
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Residues in contact with ALA 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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253D GLU 2.9 18.6 + - - +
254D GLN* 3.4 9.2 - - - +
255D LEU 3.2 0.2 - - - -
256D ARG* 1.3 75.8 - - - +
258D ALA* 1.3 58.4 + - - +
259D GLY 3.6 0.5 + - - -
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Residues in contact with ALA 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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199D ILE* 3.7 31.0 - - + -
254D GLN 3.2 9.3 + - - +
255D LEU 3.2 4.2 + - - +
257D ALA* 1.3 75.6 - - - +
259D GLY* 1.3 60.9 + - - +
260D VAL* 3.4 11.7 + - + +
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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