Contacts of the strand formed by residues 340 - 349 (chain A) in PDB entry 2FO1
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 TYR 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A ARG* 3.5 20.3 + - - +
339A LYS* 1.3 99.5 - - + +
341A PHE* 1.3 69.9 + - - +
362A ARG* 4.5 7.2 - - + -
363A ILE 3.3 13.7 - - - +
364A LYS* 3.3 48.3 - - + -
365A VAL* 4.8 0.7 - - - -
380A ASP* 4.6 8.8 + - - +
383A TYR* 3.1 44.8 - + - +
1272E ALA* 3.2 44.3 + - + +
1273E THR* 4.4 4.1 - - + -
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ALA* 4.1 8.3 - - + -
236A PHE* 3.3 29.6 - + - -
292A ILE* 3.7 32.8 - - + -
293A GLY 4.0 2.0 - - - +
332A ILE* 3.7 14.4 - - + -
338A ARG* 3.7 26.9 - - - +
340A TYR* 1.3 80.6 - - - +
342A ASP* 1.3 65.3 + - - +
343A LEU* 4.3 4.3 - - + -
362A ARG* 4.6 0.4 - - - -
363A ILE* 2.9 60.8 + - + +
365A VAL* 3.6 30.1 - - + -
1273E THR* 4.1 10.7 - - - +
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Residues in contact with ASP 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ILE 3.9 1.7 - - - +
293A GLY* 3.9 19.7 + - - +
338A ARG* 5.5 1.2 + - - -
341A PHE* 1.3 80.6 - - - +
343A LEU* 1.3 67.8 + - - +
344A ASN* 3.8 2.3 + - - +
359A VAL* 3.9 20.7 - - - +
360A SER 3.3 20.9 - - - +
361A GLN 3.7 11.9 - - - +
362A ARG* 4.3 14.9 + - - +
363A ILE* 5.1 0.2 - - - -
1273E THR* 3.8 18.9 - - + +
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE* 4.9 8.1 - - + -
221A HIS* 3.9 17.9 - - + -
236A PHE* 4.6 8.1 - - + -
240A PRO* 3.6 34.1 - - + -
290A ILE* 4.2 19.1 - - + -
291A GLY 3.4 13.5 - - - +
292A ILE* 4.0 20.6 - - + -
330A LEU* 4.9 2.5 - - + -
341A PHE* 4.3 7.8 - - + -
342A ASP* 1.3 75.5 - - - +
344A ASN* 1.3 59.5 + - - +
345A ALA 4.3 0.2 - - - -
359A VAL* 3.0 27.9 - - - +
360A SER* 3.2 24.1 + - - +
363A ILE* 4.2 8.0 - - + +
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Residues in contact with ASN 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A TYR 3.5 2.6 - - - +
290A ILE* 3.3 5.8 - - - +
291A GLY* 2.7 38.6 + - - +
292A ILE 4.6 6.4 + - - +
294A SER* 5.6 0.2 + - - -
299A ARG* 3.1 26.6 + - - +
342A ASP 4.7 2.1 + - - +
343A LEU* 1.3 74.5 + - - +
345A ALA* 1.3 59.4 + - - +
346A GLN* 3.1 27.6 + - - +
357A GLY 5.5 0.2 - - - -
358A PHE 3.4 8.9 - - - +
359A VAL* 4.6 11.0 - - - +
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE* 4.4 15.9 - - + -
242A ILE* 5.2 1.6 - - + -
289A TYR 3.6 5.4 - - - +
290A ILE* 3.3 20.2 - - + -
302A LEU* 5.6 0.7 - - + -
343A LEU 4.3 0.4 - - - -
344A ASN* 1.3 72.3 - - - +
346A GLN* 1.3 65.0 + - - +
347A PHE* 3.4 26.5 - - + -
357A GLY* 3.3 4.5 - - - -
358A PHE* 2.8 43.8 + - + +
359A VAL* 5.0 0.2 - - - +
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Residues in contact with GLN 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A VAL 3.6 1.2 - - - +
288A ALA* 3.1 25.1 - - - +
289A TYR* 3.0 17.0 + - + +
299A ARG* 3.7 25.0 - - - +
344A ASN* 3.1 26.7 + - - +
345A ALA* 1.3 75.1 - - - +
347A PHE* 1.3 63.7 + - - +
348A PHE* 4.9 8.1 - - + -
356A GLY 3.6 7.9 - - - +
357A GLY* 3.0 21.0 - - - -
92D GLN* 4.0 12.8 + - - +
95D VAL* 5.6 2.2 - - - +
96D THR* 4.3 23.1 - - - +
99D LEU* 5.1 13.5 - - + -
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Residues in contact with PHE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 4.4 10.8 - - + -
242A ILE* 3.5 35.9 - - + -
244A LEU* 4.7 9.2 - - + -
249A TRP* 6.2 2.5 - + + -
286A LEU* 5.3 10.5 - - + -
287A VAL 3.4 3.8 - - - +
288A ALA* 3.6 16.2 - - + -
302A LEU* 4.7 1.8 - - + -
304A PHE* 3.6 27.8 - + - -
345A ALA* 3.4 27.4 - - + -
346A GLN* 1.3 77.8 - - - +
348A PHE* 1.3 66.4 + - - +
355A ILE* 3.0 40.5 + - + +
356A GLY 3.1 11.7 + - - +
358A PHE* 3.4 28.5 - + - -
96D THR* 5.0 3.1 + - - -
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Residues in contact with PHE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLU 3.9 0.2 - - - +
286A LEU* 3.7 5.1 - - - +
287A VAL* 2.7 79.6 + - + +
289A TYR* 4.5 4.3 - + - -
346A GLN* 4.9 7.6 - - + -
347A PHE* 1.3 78.0 - - - +
349A TYR* 1.3 70.5 + - - +
352A GLY* 4.8 4.9 - - - -
353A MET 3.0 16.4 - - - +
354A GLU* 3.9 9.2 - - + -
355A ILE* 3.6 9.8 - - - +
96D THR* 3.8 19.5 - - - +
99D LEU* 3.8 27.8 - - + -
100D PHE* 3.6 30.5 - + + -
103D TYR* 4.1 8.3 - + + -
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Residues in contact with TYR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A TRP* 4.0 11.4 + - - -
252A LYS* 2.9 48.9 - - + +
253A LYS* 3.9 12.9 + - + -
256A VAL* 4.8 11.2 - - + -
283A ALA 4.7 0.9 - - - +
284A THR* 3.7 15.7 - - - -
285A GLU 3.2 15.0 - - - -
286A LEU* 3.7 26.5 - - + +
348A PHE* 1.3 87.7 - - - +
350A GLY* 1.3 66.4 + - - +
351A CYS* 3.1 8.1 - - - -
352A GLY 2.9 12.8 + - - -
353A MET* 2.5 39.9 + - + +
354A GLU 4.5 0.9 - - - -
355A ILE* 3.1 35.4 - - + -
554A GLN* 5.0 0.4 - - - -
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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