Contacts of the strand formed by residues 188 - 196 (chain B) in PDB entry 4Y2H
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 SER 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B PRO* 3.7 2.2 - - - +
187B ALA* 1.3 81.2 - - - +
189B ALA* 1.3 62.6 + - - +
190B GLU* 5.2 2.4 + - - -
255B GLN* 3.6 14.5 + - - -
256B LEU 3.2 13.7 - - - -
257B GLU* 3.6 15.0 - - - -
258B LEU* 4.3 7.1 - - - +
294B VAL* 3.2 9.0 - - - +
295B THR* 3.1 42.4 + - - +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B TRP* 4.4 11.0 - - + -
161B LEU* 4.0 27.1 - - + -
188B SER* 1.3 77.3 - - - +
190B GLU* 1.3 63.4 + - - +
254B ALA 4.3 0.2 - - - +
255B GLN* 3.2 5.4 + - - -
256B LEU* 2.7 46.0 + - + +
258B LEU* 5.0 0.4 - - + -
293B GLN 3.2 11.7 - - - +
294B VAL* 4.0 12.1 - - + -
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B SER* 5.2 2.6 + - - -
189B ALA* 1.3 80.1 - - - +
191B LEU* 1.3 63.7 + - - +
192B PHE* 3.7 20.7 - - + -
252B ARG* 2.6 40.8 + - - -
254B ALA 3.4 3.6 - - - -
255B GLN* 3.9 16.6 + - + +
292B PHE* 3.0 10.2 - - - +
293B GLN* 2.7 63.2 + - + +
295B THR* 4.3 10.0 + - - -
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B GLY 3.9 11.0 - - - +
161B LEU* 3.9 38.6 - - + -
162B LEU* 4.9 0.7 - - + -
190B GLU* 1.3 76.3 - - - +
192B PHE* 1.3 60.5 - - - +
252B ARG* 3.3 8.8 - - - +
253B PHE* 2.9 50.0 + - + -
254B ALA* 2.9 16.5 + - + +
256B LEU* 5.2 2.2 - - + -
271B VAL* 3.7 30.3 - - + -
290B ILE* 5.0 4.5 - - + -
291B TRP 3.5 14.4 - - - +
292B PHE* 4.1 3.1 - - + -
343B LEU* 3.8 19.5 - - + -
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B GLU* 3.7 40.4 - - + -
191B LEU* 1.3 73.4 - - - +
193B ILE* 1.3 60.3 + - - +
250B PRO* 4.9 10.3 - - + -
251B GLN 3.3 7.9 - - - +
252B ARG* 3.6 33.9 - - + -
253B PHE* 3.4 8.7 - - - -
289B ALA 4.5 0.2 - - - -
290B ILE* 3.2 24.4 - - - -
291B TRP* 2.9 52.7 + + + +
292B PHE* 4.5 0.4 - - - -
293B GLN* 3.8 30.7 - - + -
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B PHE* 1.3 75.8 - - - +
194B ALA* 1.3 64.1 + - - +
250B PRO* 3.5 1.1 - - - +
251B GLN* 2.8 44.5 + - + +
253B PHE* 3.8 16.8 - - + -
275B PHE* 3.8 48.2 - - + -
288B PHE* 3.7 36.6 - - + -
289B ALA 3.3 12.6 - - - +
290B ILE* 3.9 3.6 - - + -
291B TRP* 4.8 1.6 - - - -
323B LEU* 5.0 0.4 - - + -
341B ILE* 4.2 20.9 - - + -
357B LEU* 4.4 4.7 - - + -
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ILE* 1.3 77.7 - - - +
195B PRO* 1.3 75.0 - - + +
196B ILE* 3.8 2.5 - - + +
246B VAL* 3.8 28.5 - - + -
248B ALA 4.1 1.1 - - - +
249B ARG 5.2 0.4 - - - -
250B PRO* 3.9 13.9 - - + -
288B PHE* 3.3 8.7 - - - -
289B ALA 3.0 28.5 + - - -
291B TRP* 3.9 13.9 - - + -
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Residues in contact with PRO 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ALA* 1.3 87.6 - - + +
196B ILE* 1.3 62.2 + - - +
246B VAL* 3.8 1.2 - - - -
247B LEU* 2.9 33.8 + - + -
248B ALA* 3.8 24.9 - - + +
275B PHE* 6.1 0.7 - - + -
277B CYS* 3.7 24.9 - - - -
279B CYS* 4.5 8.1 - - - -
285B MET* 3.8 28.7 - - + -
287B GLY 3.4 8.1 - - - +
288B PHE* 3.9 11.9 - - + -
337B VAL* 4.5 4.7 - - + -
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Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ALA* 3.8 4.7 - - + +
195B PRO* 1.3 79.5 - - - +
197B SER* 1.3 63.0 + - - +
198B ASP* 4.0 20.6 - - + +
241B LEU* 3.7 23.8 - - + -
245B ASP 3.1 12.1 - - - +
246B VAL* 4.2 15.7 - - + -
247B LEU* 3.4 11.4 - - - +
285B MET* 3.6 0.3 - - - -
286B HIS* 3.0 27.5 + - + -
287B GLY 2.9 25.0 + - - +
288B PHE 3.7 3.1 - - - +
289B ALA* 3.6 38.6 - - + +
322B LEU* 4.5 9.9 - - + -
324B TYR* 4.9 3.4 - - + -
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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