Contacts of the strand formed by residues 219 - 223 (chain D) in PDB entry 2I6A
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 ILE 219 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192D ILE* 4.4 7.6 - - + -
193D PHE 3.2 3.4 + - - -
194D THR* 3.2 17.3 - - + -
195D LEU 3.1 25.1 + - - +
217D VAL* 3.1 5.5 - - - +
218D ASP* 1.3 85.9 - - + +
220D LEU* 1.3 64.9 + - - +
221D PHE* 3.8 27.7 - - + -
261D ILE* 3.2 36.6 - - + +
263D ILE* 5.0 3.1 - - + -
306D PHE* 4.0 27.8 - - + -
310D LEU* 4.4 21.8 - - + -
316D LEU* 5.1 0.2 - - + -
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Residues in contact with LEU 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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195D LEU* 3.4 36.6 - - + +
197D LEU* 3.8 38.1 - - + +
214D MET* 4.0 22.9 - - + -
217D VAL* 3.4 9.7 - - + +
219D ILE* 1.3 75.9 - - - +
221D PHE* 1.3 67.8 + - - +
230D PHE* 5.1 1.6 - - + -
248D THR* 3.7 27.8 - - + -
260D ARG* 4.9 1.8 - - - -
261D ILE 2.8 13.6 + - - +
262D VAL* 3.5 9.4 - - + +
263D ILE* 2.9 27.9 + - - +
264D PHE* 4.7 6.3 - - + -
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Residues in contact with PHE 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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166D TYR* 3.7 21.3 - + - -
194D THR* 3.6 27.1 - - + -
195D LEU 2.8 18.5 + - - +
196D ASN* 3.6 16.8 - - - +
197D LEU* 3.0 28.2 + - - +
219D ILE* 3.8 19.5 - - + -
220D LEU* 1.3 76.4 - - - +
222D GLY* 1.3 59.2 + - - +
263D ILE* 3.4 26.7 - - + -
264D PHE* 4.6 2.9 - - - -
302D PHE* 4.6 4.7 - + - -
303D VAL* 4.1 20.2 - - + -
306D PHE* 4.0 41.3 - + + -
307D LEU* 4.3 12.1 - - + -
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Residues in contact with GLY 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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196D ASN* 3.8 9.4 - - - +
197D LEU* 4.3 6.7 - - - -
221D PHE* 1.3 78.7 - - - +
223D ASN* 1.3 61.8 + - - -
226D GLU* 3.6 9.6 - - - -
263D ILE* 3.2 3.1 + - - +
264D PHE* 3.0 14.6 - - - -
265D THR* 2.8 27.5 + - - +
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Residues in contact with ASN 223 (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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38D GLN* 5.6 0.3 + - - -
222D GLY* 1.3 74.2 - - - -
224D GLU* 1.3 71.5 + - - +
225D THR* 3.5 11.2 + - - +
226D GLU* 2.7 58.0 + - - +
227D ALA* 2.9 25.0 + - - +
264D PHE* 4.9 1.3 - - - -
265D THR* 3.2 24.0 - - - +
267D GLY 6.1 0.2 - - - +
295D THR* 5.6 6.8 - - + +
296D ASN* 5.1 7.8 + - - -
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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