Contacts of the strand formed by residues 215 - 222 (chain D) in PDB entry 2IBS
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 LEU 215 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187D THR* 3.3 25.8 - - + +
189D VAL* 3.8 28.0 - - + -
214D GLY* 1.3 74.2 - - - -
216D SER* 1.3 70.8 + - - +
217D LEU* 5.3 2.0 - - + -
234D GLU* 3.5 3.1 - - - +
235D TYR* 2.7 61.9 + - + +
238D TRP* 3.7 32.5 - - + -
243D ILE* 3.7 39.9 - - + -
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Residues in contact with SER 216 (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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187D THR 2.8 9.3 + - - +
188D SER* 3.4 13.1 + - - -
189D VAL 2.8 27.7 + - - -
215D LEU* 1.3 79.8 + - - +
217D LEU* 1.3 60.6 + - - +
218D TRP* 3.4 25.2 - - - -
231D LEU* 4.7 1.1 - - - -
233D ALA 3.7 5.4 - - - -
234D GLU* 3.8 20.5 + - - +
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Residues in contact with LEU 217 (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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169D LEU* 5.3 1.8 - - + -
189D VAL* 3.7 23.3 - - + +
191D TYR 5.8 0.2 - - - +
215D LEU* 4.2 2.2 - - + +
216D SER* 1.3 71.8 - - - +
218D TRP* 1.3 65.0 + - - +
231D LEU* 3.8 4.2 - - - +
232D TRP* 2.9 31.0 + - + -
233D ALA* 2.8 29.2 + - + +
235D TYR* 4.8 8.9 - - + -
243D ILE* 3.8 25.1 - - + -
244D ARG 3.4 27.6 - - - +
245D PHE* 3.8 45.3 - - + -
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Residues in contact with TRP 218 (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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188D SER* 3.9 10.6 + - - -
189D VAL 2.7 20.8 + - - +
190D TYR* 3.5 39.4 - + + -
191D TYR* 3.0 28.8 + - - +
216D SER* 3.4 28.2 - - - -
217D LEU* 1.3 79.8 - - - +
219D ASP* 1.3 62.4 + - - +
229D PRO* 3.7 26.0 - - + -
230D ILE 3.4 4.3 - - - -
231D LEU* 3.5 49.4 - - + -
234D GLU* 5.7 1.3 - - - -
245D PHE* 4.0 8.7 - - - -
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Residues in contact with ASP 219 (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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191D TYR* 3.7 9.9 - - - +
218D TRP* 1.3 74.9 - - - +
220D THR* 1.3 75.8 + - - +
229D PRO* 3.4 4.9 - - - +
230D ILE* 2.7 47.7 + - + +
232D TRP* 4.4 21.5 - - + +
245D PHE* 4.5 2.7 - - + -
389D ARG* 2.9 41.1 + - - +
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Residues in contact with THR 220 (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* 3.9 27.6 - - + -
190D TYR* 4.3 11.2 - - + -
191D TYR* 2.5 27.7 + - - +
192D LEU* 3.6 24.5 + - + +
219D ASP* 1.3 93.7 + - - +
221D GLN* 1.3 63.7 + - - +
227D PHE* 4.1 11.9 - - + -
228D THR 3.3 10.1 - - - +
229D PRO* 4.3 2.9 - - + -
230D ILE* 4.6 2.5 - - - +
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Residues in contact with GLN 221 (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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50A HIS* 3.9 19.5 - - - +
55A ARG* 3.3 45.3 + - - +
220D THR* 1.3 75.2 - - - +
222D GLU* 1.3 61.9 + - - +
227D PHE* 3.4 7.5 - - - -
228D THR* 2.8 56.9 + - - +
230D ILE* 4.4 19.4 - - + +
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Residues in contact with GLU 222 (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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55A ARG* 2.8 34.6 + - - +
58A ARG* 5.3 1.7 + - - -
80A PRO* 3.6 16.7 - - + +
81A PRO* 3.4 24.1 - - - +
82A TRP* 4.0 21.9 + - - +
221D GLN* 1.3 74.4 + - - +
223D SER* 1.3 61.3 + - - +
226D GLY 3.9 6.3 - - - +
227D PHE* 3.9 23.0 - - + -
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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