Contacts of the helix formed by residues 252 - 261 (chain D) in PDB entry 5U03
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 ARG 252 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245D HIS* 6.1 1.3 - - - -
247D VAL* 3.8 26.0 - - + +
248D SER* 3.0 28.4 + - - +
249D SER 2.9 13.6 + - - +
250D ILE 2.9 0.4 + - - -
251D TYR* 1.3 111.9 + - + +
253D VAL* 1.3 57.5 + - - +
254D PRO 3.5 0.2 - - - -
255D LEU* 3.2 13.9 + - + +
256D LEU* 2.9 26.8 + - - +
289D ALA* 5.4 2.6 - - - +
292D TYR 5.6 0.2 - - - -
293D ASP* 2.7 33.5 + - - -
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Residues in contact with VAL 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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18D ILE* 4.4 9.4 - - + -
19D ILE* 3.9 23.6 - - + -
22D SER* 3.4 23.3 - - - +
244D VAL* 4.5 8.3 - - + -
247D VAL* 3.9 24.0 - - + -
250D ILE* 2.8 22.0 + - - +
252D ARG* 1.3 72.1 - - - +
254D PRO* 1.3 68.4 - - + +
255D LEU 3.0 1.3 - - - -
256D LEU* 2.9 7.9 + - - +
257D LEU* 2.8 28.0 + - + +
601D ATP 4.1 15.7 - - - +
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Residues in contact with PRO 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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22D SER* 3.8 20.4 - - - +
25D THR* 4.9 0.4 - - + -
26D ILE* 4.3 18.2 - - + -
77D PHE* 4.4 2.5 - - + -
250D ILE 3.3 9.4 - - - +
251D TYR 3.3 12.6 - - - +
253D VAL* 1.3 96.8 - - + +
255D LEU* 1.3 55.7 + - - +
257D LEU* 3.3 7.0 + - + +
258D GLU 3.0 20.6 + - - -
280D LYS* 3.3 22.0 + - - +
285D TRP* 4.2 39.3 - - + +
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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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251D TYR* 4.1 17.0 - - + +
252D ARG* 3.2 15.6 + - + +
253D VAL 3.0 0.6 - - - -
254D PRO* 1.3 74.3 - - - +
256D LEU* 1.3 66.1 + - - +
258D GLU* 3.0 23.0 + - - +
259D GLU* 2.9 30.9 + - + +
280D LYS* 4.9 2.0 - - - +
282D LEU* 4.4 13.0 - - + -
285D TRP* 3.9 28.0 - - + +
286D LYS* 4.5 8.1 - - + +
289D ALA* 3.8 28.5 - - + -
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Residues in contact with LEU 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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243D CYS 3.7 13.0 - - - +
244D VAL* 3.8 39.3 - - + -
245D HIS* 3.8 38.6 - - + +
247D VAL* 4.6 5.6 - - + -
252D ARG 2.9 13.5 + - - +
253D VAL* 2.9 10.5 + - - +
255D LEU* 1.3 75.7 - - - +
257D LEU* 1.3 68.5 + - + +
259D GLU* 2.9 29.8 + - - +
260D GLN* 2.9 31.6 + - + +
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Residues in contact with LEU 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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19D ILE* 4.8 11.4 - - + +
22D SER* 3.7 24.7 - - - -
23D VAL* 3.9 17.3 - - + -
26D ILE* 3.7 23.6 - - + -
215D VAL* 6.0 2.5 - - + -
242D ILE* 4.6 5.6 - - + -
244D VAL* 4.5 13.7 - - + -
253D VAL* 2.8 24.1 + - + +
254D PRO 3.6 5.6 - - - +
256D LEU* 1.3 83.7 - - + +
258D GLU* 1.3 51.9 + - - +
260D GLN* 3.1 5.9 + - - +
261D GLY 2.7 29.8 + - - -
262D VAL* 3.4 36.1 + - + +
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Residues in contact with GLU 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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254D PRO 3.0 6.5 + - - +
255D LEU* 3.0 15.8 + - - +
257D LEU* 1.3 74.9 - - - +
259D GLU* 1.3 66.8 + - + +
261D GLY* 2.9 15.4 + - - +
263D VAL* 5.5 3.4 - - - -
278D PRO* 5.9 1.2 - - - +
279D ARG* 3.7 28.6 + - - +
280D LYS* 3.0 43.4 + - - +
282D LEU* 3.4 34.3 - - - +
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Residues in contact with GLU 259 (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 HIS* 5.8 1.9 + - - -
255D LEU* 2.9 20.8 + - + +
256D LEU* 2.9 22.6 + - - +
258D GLU* 1.3 77.8 - - + +
260D GLN* 1.3 69.1 + - - +
261D GLY* 3.5 0.5 + - - -
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Residues in contact with GLN 260 (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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227D LYS* 5.3 10.9 + - - +
239D GLU* 5.0 13.3 - - - +
241D VAL 4.5 4.0 - - - +
242D ILE* 4.0 23.8 - - + +
243D CYS* 4.1 17.9 + - - +
256D LEU* 2.9 33.8 + - + +
257D LEU* 3.3 8.1 - - - +
259D GLU* 1.3 85.0 + - - +
261D GLY* 1.3 62.0 + - - +
262D VAL* 3.3 18.1 + - + +
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Residues in contact with GLY 261 (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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239D GLU* 4.4 5.8 - - - +
257D LEU 2.7 10.1 + - - -
258D GLU* 2.9 13.2 + - - -
259D GLU 4.4 0.7 - - - -
260D GLN* 1.3 75.8 - - - +
262D VAL* 1.3 65.4 + - - +
263D VAL* 3.0 5.1 + - - -
264D ASP* 3.2 24.9 + - - +
265D TYR* 3.3 9.4 + - - +
279D ARG* 5.1 7.6 - - - -
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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