Contacts of the strand formed by residues 221 - 229 (chain B) in PDB entry 1G9Y
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 GLY 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B PHE 3.7 1.4 + - - -
217B VAL* 2.8 35.1 + - - -
219B GLY 3.5 0.4 - - - -
220B ASP* 1.3 76.7 - - - +
222B SER* 1.3 63.2 + - - -
244B GLN 3.2 11.9 - - - -
245B VAL* 4.1 5.6 - - - +
298B LYS* 2.9 21.5 + - - -
415C G 3.5 8.5 - - - +
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Residues in contact with SER 222 (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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217B VAL* 4.8 2.4 - - - +
221B GLY* 1.3 76.5 - - - -
223B ILE* 1.3 63.5 + - - +
224B ILE* 3.2 21.9 - - - +
242B THR 3.7 1.2 - - - +
243B PHE* 3.6 3.2 - - - -
244B GLN* 2.8 54.0 + - - +
298B LYS* 4.1 2.6 - - - +
336B ASN* 4.8 0.3 + - - -
415C G 3.6 13.6 - - - +
416C A 2.9 26.9 + - - -
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Residues in contact with ILE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B VAL* 4.9 5.4 - - + -
222B SER* 1.3 74.0 + - - +
224B ILE* 1.3 60.0 + - - +
242B THR 3.7 5.2 - - - +
243B PHE* 4.4 16.4 - - + +
288B LEU* 4.1 15.0 - - + -
291B LEU* 5.6 0.2 - - + -
295B LEU* 4.0 11.9 - - + -
298B LYS* 3.6 26.0 - - + +
301B GLN* 3.7 21.7 - - + +
302B ALA* 3.5 28.5 - - + +
305B VAL* 3.5 30.3 - - + -
332B ILE* 3.7 7.3 - - - +
336B ASN* 3.2 23.2 + - - +
416C A 4.5 1.8 + - - -
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Residues in contact with ILE 224 (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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222B SER* 3.2 29.2 - - - +
223B ILE* 1.3 74.4 - - - +
225B ALA* 1.3 65.6 + - - +
226B GLN* 3.7 17.9 - - + +
240B SER 4.6 0.4 - - - -
241B LEU* 3.4 5.2 - - - +
242B THR* 2.8 48.9 + - - +
244B GLN* 3.8 22.9 - - + +
305B VAL* 4.5 6.1 - - - +
332B ILE* 4.7 0.9 - - - -
336B ASN* 4.6 2.7 - - - +
416C A 3.7 28.0 - - + -
417C C 3.3 39.0 - - + +
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Residues in contact with ALA 225 (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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224B ILE* 1.3 76.0 - - - +
226B GLN* 1.3 68.6 + - - +
240B SER 3.5 6.3 - - - +
241B LEU* 4.6 3.8 - - + +
305B VAL* 5.0 1.8 - - + -
308B ILE* 4.3 7.2 - - + -
329B VAL* 3.3 28.7 - - + +
332B ILE* 3.3 39.3 - - + +
333B ALA* 5.5 1.0 - - - +
341B ARG* 3.9 6.9 + - - -
417C C 4.1 6.0 + - - +
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Residues in contact with GLN 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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224B ILE* 3.7 13.7 - - + +
225B ALA* 1.3 80.9 - - - +
227B ILE* 1.3 65.7 + - - +
228B LYS* 3.2 34.3 + - + +
238B GLN 3.4 1.0 - - - +
239B LEU* 3.7 4.3 - - - +
240B SER* 2.7 39.4 + - - +
242B THR* 4.5 9.7 + - - -
329B VAL* 3.9 4.0 - - - +
341B ARG* 4.8 1.1 - - - +
417C C 3.6 35.1 - - - +
418C G 2.8 49.3 + - - +
419C T 4.6 1.0 - - - +
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Residues in contact with ILE 227 (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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226B GLN* 1.3 76.6 - - - +
228B LYS* 1.3 59.0 + - - +
229B PRO* 3.5 0.9 - - - +
237B HIS* 3.6 21.1 - - + -
238B GLN 3.4 4.9 - - - +
239B LEU* 4.3 6.5 - - + -
326B CYS* 3.6 22.7 - - + -
329B VAL* 3.4 33.2 - - + -
341B ARG* 4.4 0.9 - - - +
343B THR* 3.0 42.5 + - + +
344B THR* 3.6 29.4 - - - -
348B VAL* 3.5 22.0 - - + -
418C G 4.4 5.8 + - - -
419C T 5.7 0.2 - - - +
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Residues in contact with LYS 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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226B GLN* 3.2 30.9 - - + +
227B ILE* 1.3 74.3 - - - +
229B PRO* 1.3 71.1 - - + +
230B ASN* 3.1 3.9 + - + +
237B HIS* 3.3 1.7 - - - -
238B GLN* 2.8 60.3 + - + +
240B SER* 2.7 36.5 + - - -
242B THR* 5.2 0.6 + - - -
418C G 4.7 0.9 - - - +
419C T 2.6 47.1 - - + +
420C T 4.1 11.2 - - + +
505D A 4.2 4.9 - - - +
506D A 4.1 10.5 - - - +
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Residues in contact with PRO 229 (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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227B ILE 3.5 9.4 - - - +
228B LYS* 1.3 80.4 - - + +
230B ASN* 1.3 60.3 + - - +
231B GLN* 5.6 2.2 - - - +
236B LYS 3.6 1.1 - - - +
237B HIS* 3.6 23.1 - - + +
343B THR* 3.7 16.4 - - + +
419C T 3.8 26.7 - - + +
420C T 4.1 15.8 - - + +
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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