Contacts of the strand formed by residues 303 - 311 (chain W) in PDB entry 5O9G
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 303 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295W ARG* 3.0 39.9 + - - -
296W ALA 3.4 9.4 - - - -
297W SER* 4.2 9.0 - - - -
301W GLY 5.1 1.1 - - - -
302W THR* 1.3 81.0 + - - +
304W GLN* 1.3 62.8 + - - +
1199W ARG* 4.3 4.3 + - - -
1207W THR* 4.3 5.7 - - - +
1208W ASP* 5.4 0.7 - - - +
1211W PHE* 4.0 20.2 - - - -
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Residues in contact with GLN 304 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295W ARG* 3.6 4.5 - - - +
296W ALA 3.0 29.9 + - - +
298W LEU* 3.7 36.3 - - + +
302W THR* 4.5 13.1 + - - +
303W SER* 1.3 76.2 - - - +
305W LEU* 1.3 62.4 + - - +
306W GLN* 3.5 10.8 + - + +
323W ASN* 2.5 42.2 + - - +
1207W THR* 4.4 11.4 - - + -
1208W ASP* 6.2 1.8 - - + -
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Residues in contact with LEU 305 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293W SER* 3.7 22.4 - - - +
294W GLN 3.6 6.1 - - - -
295W ARG* 3.5 47.5 - - + +
304W GLN* 1.3 70.4 - - - +
306W GLN* 1.3 60.9 + - - +
307W TYR* 3.7 26.9 - - + +
323W ASN* 3.0 15.7 + - - +
324W ALA* 3.2 19.3 + - + +
339W GLN* 6.0 1.1 - - - +
1200W ASP* 3.6 45.8 - - + +
1207W THR* 4.5 5.6 - - + +
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Residues in contact with GLN 306 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293W SER* 3.5 3.1 - - - -
294W GLN 3.3 36.1 + - - +
296W ALA* 4.5 12.3 - - + +
297W SER 5.6 1.2 + - - -
298W LEU* 4.9 14.6 - - - +
304W GLN* 4.1 12.5 + - + +
305W LEU* 1.3 76.0 - - - +
307W TYR* 1.3 63.8 + - - +
308W LEU 4.2 0.2 + - - -
321W TRP* 3.2 49.9 - - + +
322W GLU 3.4 6.5 - - - +
323W ASN* 4.1 19.9 - - + +
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Residues in contact with TYR 307 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290W ILE* 3.6 30.3 - - + -
292W ASP 3.6 2.5 - - - -
293W SER* 3.5 18.8 - - - -
305W LEU* 3.7 30.2 - - + +
306W GLN* 1.3 78.6 - - - +
308W LEU* 1.3 59.3 + - - +
309W VAL* 3.1 10.9 + - + +
321W TRP* 3.3 7.1 - - - -
322W GLU 2.8 32.3 + - - +
324W ALA* 3.6 25.0 - - + +
327W ILE* 4.2 24.5 - - + -
328W VAL* 5.1 1.1 - - + -
335W VAL* 4.4 22.6 - - + +
338W PHE* 5.0 8.7 - + - -
339W GLN* 4.8 3.1 + - - -
1200W ASP 4.4 0.3 + - - -
1202W PRO* 3.3 30.4 - - + +
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Residues in contact with LEU 308 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290W ILE* 3.7 1.9 - - - -
291W ILE* 2.8 65.4 + - + +
292W ASP* 2.9 34.7 + - + +
307W TYR* 1.3 68.1 - - - +
309W VAL* 1.3 63.3 + - - +
319W ALA* 3.4 35.2 - - + +
321W TRP* 3.5 27.9 - - + +
465W THR* 4.8 2.5 - - + -
468W GLU* 3.8 22.0 - - - +
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Residues in contact with VAL 309 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287W PRO* 3.7 28.0 - - + -
289W ARG 3.8 4.7 - - - +
290W ILE* 4.0 15.7 - - + -
307W TYR* 3.1 19.6 + - + +
308W LEU* 1.3 73.6 - - - +
310W LYS* 1.3 61.8 + - - +
311W TRP* 3.7 37.2 + - + -
319W ALA* 3.6 25.0 - - - +
320W THR 3.3 9.6 + - - +
322W GLU* 3.9 23.8 - - + -
327W ILE* 4.2 9.4 - - + -
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Residues in contact with LYS 310 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287W PRO* 3.5 2.6 - - - +
288W GLU* 2.7 44.9 + - - +
289W ARG* 2.8 35.7 + - + +
291W ILE* 4.3 15.9 - - + -
308W LEU 3.6 0.4 + - - -
309W VAL* 1.3 74.9 - - - +
311W TRP* 1.3 78.5 + - + +
314W LEU* 2.5 32.4 + - + +
315W ASN 3.3 21.3 - - - +
316W TYR* 3.7 35.0 - - + +
317W ASP 5.4 0.7 - - - +
319W ALA* 5.7 2.0 - - + +
457W MET* 5.8 2.3 - - - +
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Residues in contact with TRP 311 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221W SER* 3.1 33.7 + - - +
222W HIS* 5.3 4.9 - + - -
223W LEU* 3.7 10.3 - - + -
284W PHE* 3.3 24.2 - - - +
285W HIS 3.4 21.3 - - - -
286W VAL 3.6 3.4 - - - +
287W PRO* 3.6 31.2 - - + -
288W GLU* 2.8 7.2 - - - +
309W VAL* 3.7 36.6 + - + -
310W LYS* 1.3 108.7 + - + +
312W ARG* 1.3 64.6 + - - +
314W LEU* 4.1 25.0 + - + +
317W ASP 5.7 0.4 - - - -
318W GLU 3.9 22.4 + - - -
319W ALA* 5.2 0.2 - - - -
320W THR* 4.1 11.1 + - - -
322W GLU* 4.4 10.8 - - + -
327W ILE* 5.3 5.6 - - + -
330W LEU* 5.8 1.1 - - + -
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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