Contacts of the strand formed by residues 227 - 235 (chain D) in PDB entry 2IH2
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 PHE 227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D GLU* 3.8 24.7 - - + -
27D VAL* 3.9 24.2 - - + -
29D ASP* 5.1 0.6 + - - -
30D PHE* 3.4 42.5 - - + +
33D SER* 5.3 0.3 + - - -
192D LEU* 3.8 20.4 - - + -
195D VAL* 4.0 24.0 - - + -
220D THR* 4.0 9.4 - - - -
221D GLN 3.4 9.2 - - - +
222D GLU* 4.1 15.5 - - + -
223D SER* 3.3 5.5 + - - -
226D GLY* 1.3 80.8 - - - -
228D THR* 1.3 64.1 + - - +
229D PRO* 4.0 1.9 - - - +
3005D GOL 3.9 30.1 - - - -
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Residues in contact with THR 228 (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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220D THR* 3.3 4.8 - - - -
221D GLN* 2.8 49.2 + - - +
223D SER* 3.5 19.6 + - - -
227D PHE* 1.3 71.7 + - - +
229D PRO* 1.3 80.3 - - + +
230D ILE* 3.8 15.0 + - + +
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Residues in contact with PRO 229 (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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30D PHE* 4.0 13.6 - - + -
34D LEU* 5.0 6.1 - - + -
190D TYR* 3.8 24.0 - - + -
218D TRP* 3.6 26.4 - - + -
219D ASP 3.5 7.2 - - - +
220D THR* 4.3 3.1 - - + -
227D PHE 4.0 5.8 - - - +
228D THR* 1.3 93.3 - - + +
230D ILE* 1.3 68.0 + - - +
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Residues in contact with ILE 230 (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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218D TRP* 3.4 3.2 - - - -
219D ASP* 2.8 54.5 + - + +
220D THR* 4.7 2.9 - - - -
221D GLN* 4.5 21.5 - - + +
228D THR* 3.9 22.9 - - + +
229D PRO* 1.3 83.0 - - - +
231D LEU* 1.3 69.3 + - - +
232D TRP* 6.1 2.9 - - + -
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216D SER* 4.4 1.6 - - - -
217D LEU 3.8 13.2 - - - +
218D TRP* 3.3 48.5 - - + +
230D ILE* 1.3 81.4 - - - +
232D TRP* 1.3 62.1 + - - +
233D ALA* 3.9 13.9 - - - +
234D GLU* 3.8 34.1 - - + +
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Residues in contact with TRP 232 (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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217D LEU* 2.8 27.4 + - + +
219D ASP* 4.0 18.8 - - + +
230D ILE* 3.3 4.1 + - + -
231D LEU* 1.3 76.6 - - - +
233D ALA* 1.3 73.5 + - + +
245D PHE* 3.3 39.6 - + + -
246D GLU 2.9 28.6 + - - +
247D THR* 3.8 25.4 - - + -
386D THR* 5.1 3.1 - - + -
389D ARG* 3.5 22.4 - - - -
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Residues in contact with ALA 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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216D SER* 3.6 0.2 - - - -
217D LEU* 2.8 35.9 + - + +
231D LEU* 3.9 3.7 - - - +
232D TRP* 1.3 95.0 - - + +
234D GLU* 1.3 68.4 + - - +
235D TYR* 3.8 30.5 - - + +
246D GLU* 5.7 0.7 - - + +
251D ARG* 5.3 8.7 - - - +
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Residues in contact with GLU 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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215D LEU 3.5 6.1 - - - +
216D SER* 3.2 19.5 + - - +
218D TRP* 5.4 1.7 - - - -
231D LEU* 3.8 31.1 - - + +
233D ALA* 1.3 81.1 - - - +
235D TYR* 1.3 70.6 + - - +
236D PRO* 3.6 13.2 - - + +
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Residues in contact with TYR 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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215D LEU* 2.8 55.7 + - + +
217D LEU* 4.8 7.2 - - + -
233D ALA* 3.8 28.1 - - + +
234D GLU* 1.3 80.3 - - - +
236D PRO* 1.3 67.1 - - - +
237D HIS 3.1 4.3 + - - +
238D TRP* 3.2 24.3 + + + +
243D ILE* 5.7 2.2 - - + -
244D ARG 3.8 15.0 + - - -
246D GLU* 2.7 41.2 + - - +
251D ARG* 5.0 2.3 + - - -
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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