Contacts of the strand formed by residues 225 - 232 (chain B) in PDB entry 1QQJ
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 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B TRP* 3.5 12.1 - - - -
204B PHE* 3.7 39.0 - - + -
205B PHE 3.9 2.5 - - - -
221B ALA 3.7 10.5 - - - +
222B HIS 3.5 7.1 + - - +
223B GLU 3.5 2.2 - - - -
224B HIS* 1.3 81.6 - - - +
226B PHE* 1.3 62.3 + - - +
227B GLY 4.4 0.2 - - - +
266B MET* 3.4 37.9 - - + +
293B TYR* 3.9 21.3 - - + +
326B MET* 3.8 36.3 - - + +
327B LEU* 4.0 12.8 - - + -
330B LEU* 4.3 5.4 - - + -
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Residues in contact with PHE 226 (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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19B TYR* 3.7 34.1 - + + -
67B LEU* 5.0 1.6 - - + -
70B PHE* 3.7 27.8 - + - -
71B MET* 3.8 34.8 - - + -
78B TRP* 3.5 49.7 - + + -
205B PHE* 2.9 21.1 + - + +
207B GLY 4.3 4.5 - - - +
224B HIS 3.8 1.4 + - - -
225B ILE* 1.3 74.6 - - - +
227B GLY* 1.3 61.6 + - - +
263B VAL* 3.6 29.2 - - + -
265B PRO* 3.5 10.5 - - + +
266B MET* 3.1 18.4 + - - +
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Residues in contact with GLY 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.2 4.7 - - - +
205B PHE* 2.9 26.9 + - - +
225B ILE* 3.7 1.4 - - - +
226B PHE* 1.3 83.4 - - - +
228B MET* 1.3 62.7 + - - -
263B VAL* 3.8 11.8 - - - +
264B VAL 3.0 15.5 - - - -
265B PRO* 4.0 1.6 - - - -
266B MET* 3.9 11.3 - - - +
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Residues in contact with MET 228 (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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202B MET* 3.7 25.6 - - + -
203B ALA 3.2 14.1 - - - +
204B PHE* 4.3 5.4 - - + -
205B PHE* 5.4 0.2 - - - -
227B GLY* 1.3 77.6 - - - +
229B VAL* 1.3 68.0 + - - +
262B TRP 3.6 0.7 - - - +
263B VAL* 3.5 1.6 - - - +
264B VAL 2.8 31.9 + - - -
266B MET* 3.8 14.4 - - - -
269B LEU* 3.7 21.5 - - + -
295B PHE* 5.2 0.4 - - - -
297B ILE* 4.2 9.4 - - - -
319B PHE* 3.5 35.9 - - + -
326B MET* 3.8 23.6 - - - -
405B PHE* 3.5 19.1 - - + -
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Residues in contact with VAL 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO* 4.9 0.9 - - + -
202B MET* 3.4 9.4 - - - +
203B ALA* 2.9 46.3 + - + +
205B PHE* 3.8 20.9 - - + -
228B MET* 1.3 80.5 - - - +
230B LEU* 1.3 68.9 + - - +
259B ILE* 4.0 18.6 - - + -
260B SER* 3.5 26.0 - - - +
262B TRP 3.8 11.4 - - - +
263B VAL* 3.9 10.1 - - + -
345B LEU* 4.2 9.9 - - + -
405B PHE* 4.2 7.6 - - - -
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Residues in contact with LEU 230 (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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201B GLU 3.9 3.1 - - - +
202B MET* 4.1 17.0 - - + -
229B VAL* 1.3 74.3 - - - +
231B MET* 1.3 61.4 - - - +
259B ILE* 3.2 7.8 - - - +
260B SER* 2.9 36.0 + - - +
299B LEU* 3.6 30.5 - - + -
392B ILE* 3.6 29.2 - - + +
393B THR* 3.8 7.9 - - - -
394B GLY* 3.9 5.4 - - - +
405B PHE* 3.6 22.0 - - + -
406B GLY 3.6 24.2 - - - +
408B CYS* 3.8 14.1 - - + -
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Residues in contact with MET 231 (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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124B TYR* 3.8 23.1 - - + -
166B ILE* 5.2 0.9 - - + -
199B GLU 3.3 0.9 - - - +
201B GLU* 2.9 55.2 + - + +
203B ALA* 4.0 9.0 - - + -
230B LEU* 1.3 77.3 - - - +
232B ASN* 1.3 65.2 + - - +
233B ASP* 4.1 2.2 - - - +
257B THR* 3.6 23.6 - - + -
258B THR 3.2 11.2 - - - +
259B ILE* 3.6 9.4 - - + -
345B LEU* 3.4 32.8 - - + -
347B ALA* 3.6 25.4 - - + -
392B ILE* 3.4 9.8 - - - +
408B CYS* 3.9 0.9 - - - -
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Residues in contact with ASN 232 (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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198B MET* 3.3 19.9 - - - +
199B GLU 3.0 25.2 + - - -
231B MET* 1.3 74.2 - - - +
233B ASP* 1.3 58.4 + - - +
234B TRP* 3.1 53.7 + - + +
257B THR* 3.6 0.2 - - - -
258B THR* 2.8 34.7 + - - +
390B VAL* 3.8 13.7 + - - +
392B ILE* 3.6 13.6 - - + +
408B CYS* 3.7 11.9 + - - +
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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