Contacts of the helix formed by residues 232 - 241 (chain D) in PDB entry 4RYD
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 THR 232 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453C ASP* 4.1 16.0 + - - +
565C LYS* 6.0 5.6 - - + -
230D GLU* 3.2 41.3 + - + +
231D VAL* 1.3 74.7 - - - +
233D ASP* 1.3 66.3 + - - +
234D ALA* 3.4 8.9 + - - +
235D VAL* 2.9 27.8 + - + +
236D GLU* 3.0 23.2 + - - +
1K 2UE 3.5 9.6 - - - -
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Residues in contact with ASP 233 (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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490C ARG* 5.4 0.2 + - - -
530C ASP* 4.5 6.9 - - - +
565C LYS* 5.7 12.7 + - + +
232D THR* 1.3 73.1 - - - +
234D ALA* 1.3 57.5 + - - +
236D GLU* 3.2 4.4 + - - +
237D ALA* 2.8 28.5 + - - +
267D ALA* 3.1 33.6 + - + +
268D ARG* 3.6 1.4 + - - -
269D LEU* 2.9 33.4 + - + +
270D ALA* 2.9 28.6 + - - +
1K 2UE 3.7 14.3 + - - +
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Residues in contact with ALA 234 (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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451C ILE* 4.0 18.2 - - + -
453C ASP* 3.9 30.5 - - + +
565C LYS* 6.5 0.2 - - + -
567C THR* 4.5 3.6 - - + +
232D THR* 3.2 8.1 + - - +
233D ASP* 1.3 77.3 - - - +
235D VAL* 1.3 64.7 + - + +
237D ALA* 3.8 1.9 - - - +
238D ARG* 3.0 34.7 + - - +
269D LEU* 4.3 15.8 - - + +
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Residues in contact with VAL 235 (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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175D VAL* 3.8 28.2 - - + +
176D ASN* 4.5 4.9 - - - +
178D GLN* 6.2 0.9 - - - +
226D MET* 3.6 42.2 - - + +
230D GLU 3.6 15.5 - - - +
231D VAL* 4.5 5.6 - - + -
232D THR* 2.9 29.7 + - + +
234D ALA* 1.3 76.9 - - + +
236D GLU* 1.3 58.8 + - - +
238D ARG* 3.5 0.4 + - - +
239D SER* 2.7 32.4 + - - -
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Residues in contact with GLU 236 (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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226D MET* 4.4 5.4 - - + -
231D VAL* 3.9 13.2 - - + +
232D THR 3.0 11.9 + - - +
233D ASP* 3.2 7.2 + - - +
235D VAL* 1.3 77.5 - - - +
237D ALA* 1.3 57.7 + - - +
239D SER* 3.0 6.1 + - - -
240D LEU* 2.9 38.4 + - + +
254D TRP* 4.0 18.4 - - + -
270D ALA* 3.7 16.1 - - + +
308D TYR* 2.6 30.9 + - - -
1K 2UE 2.8 29.5 + - - -
2K ARG* 3.0 22.3 + - - +
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Residues in contact with ALA 237 (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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451C ILE* 3.7 18.2 - - + +
233D ASP 2.8 17.0 + - - +
234D ALA 3.8 2.9 - - - +
236D GLU* 1.3 76.1 - - - +
238D ARG* 1.3 58.9 + - - +
241D GLY* 2.9 27.2 + - - -
269D LEU* 3.5 36.8 - - + +
270D ALA* 4.2 3.3 - - - +
273D ALA* 3.7 15.6 - - + +
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Residues in contact with ARG 238 (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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451C ILE* 3.6 43.0 + - + +
452C ILE* 5.7 0.4 - - - +
453C ASP 5.9 1.1 - - - +
474C CYS* 6.2 2.0 - - - -
477C GLU* 6.3 0.4 - - - +
173D PHE* 3.5 30.7 - - - -
175D VAL* 3.8 22.8 - - + +
178D GLN* 2.6 41.0 + - - +
234D ALA* 3.0 23.2 + - - +
235D VAL 4.0 3.4 - - - +
237D ALA* 1.3 77.8 - - - +
239D SER* 1.3 60.7 + - - +
241D GLY* 3.8 1.7 - - - -
242D LEU* 3.2 24.1 + - - +
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Residues in contact with SER 239 (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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152D LEU* 3.7 24.5 - - - +
175D VAL* 3.8 4.0 - - - +
224D VAL* 3.6 16.8 - - - +
226D MET* 3.3 38.1 - - - +
235D VAL 2.7 18.3 + - - -
236D GLU 3.0 8.6 + - - -
238D ARG* 1.3 74.7 - - - +
240D LEU* 1.3 64.9 + - - +
241D GLY 3.1 1.1 - - - -
242D LEU* 3.2 18.2 + - - +
250D TYR* 3.8 3.6 - - - -
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Residues in contact with LEU 240 (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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152D LEU* 3.7 22.7 - - + -
236D GLU* 2.9 24.5 + - + +
239D SER* 1.3 77.5 - - - +
241D GLY* 1.3 57.9 + - - +
244D PRO* 5.5 0.3 - - - +
250D TYR* 3.5 20.5 + - - -
254D TRP* 5.3 3.6 - - + -
270D ALA* 4.1 25.4 - - + +
273D ALA* 3.9 13.5 - - + +
274D PHE* 3.8 42.6 - - + -
277D GLY* 5.9 0.7 - - - -
287D SER* 5.4 0.5 + - - -
289D PHE* 3.7 27.0 - - + -
291D TRP* 3.9 19.5 - - + -
308D TYR* 5.4 1.3 - - + -
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Residues in contact with GLY 241 (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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237D ALA 2.9 17.7 + - - -
238D ARG* 3.8 4.3 - - - -
239D SER 3.1 0.2 - - - -
240D LEU* 1.3 78.7 - - - +
242D LEU* 1.3 62.6 + - - +
243D ASN 3.3 0.5 + - - -
244D PRO* 3.3 24.4 - - - +
273D ALA* 4.3 8.5 - - - +
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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