Contacts of the strand formed by residues 352 - 366 (chain A) in PDB entry 1PO3
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 HIS 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A PHE* 4.8 1.1 - - + -
347A GLN* 3.9 10.0 + - - +
348A PRO* 4.2 13.6 - - + +
349A ASP* 2.6 59.0 + - - +
350A SER 5.3 0.4 - - - -
351A GLN* 1.3 80.3 + - - +
353A LYS* 1.3 64.6 + - - +
391A TYR* 3.0 23.8 - + + +
392A SER 3.3 7.0 - - - -
393A GLN* 2.9 27.2 + - + -
394A ILE 6.1 0.2 - - - -
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Residues in contact with LYS 353 (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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345A GLN* 3.4 33.0 - - + +
346A PHE 3.6 5.8 - - - +
347A GLN* 3.6 24.0 - - + +
352A HIS* 1.3 78.2 - - - +
354A PHE* 1.3 61.6 + - - +
355A ASN* 3.2 20.5 + - - +
390A ARG* 3.9 9.8 - - - +
391A TYR* 3.4 5.7 - - - -
392A SER* 2.9 55.0 + - - -
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Residues in contact with PHE 354 (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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344A TYR* 4.7 13.9 - + - -
345A GLN* 3.1 4.0 - - - +
346A PHE* 2.5 70.2 + + + +
353A LYS* 1.3 73.4 - - - +
355A ASN* 1.3 83.2 + - - +
356A ILE* 3.7 33.9 - - + -
389A PRO* 4.2 7.0 - - + -
390A ARG 3.7 16.8 - - - -
391A TYR* 4.4 19.1 - + + +
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Residues in contact with ASN 355 (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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344A TYR 3.5 5.2 - - - +
345A GLN* 2.6 35.1 + - - +
353A LYS* 3.2 29.4 + - - +
354A PHE* 1.3 86.2 - - - +
356A ILE* 1.3 60.6 + - - +
388A GLU 4.6 0.4 - - - -
390A ARG* 2.9 71.2 + - - +
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Residues in contact with ILE 356 (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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342A LEU 4.0 1.0 - - - +
343A GLY* 3.4 2.1 - - - -
344A TYR* 2.8 48.7 + - + +
354A PHE* 3.7 21.3 - - + -
355A ASN* 1.3 76.8 - - - +
357A GLN* 1.3 62.9 + - - +
387A ILE* 4.2 24.2 - - + -
388A GLU 3.5 5.4 - - - +
389A PRO* 3.5 31.2 - - + -
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Residues in contact with GLN 357 (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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165A ASP* 3.9 21.8 + - - +
166A GLY* 4.2 13.3 - - - +
167A ILE* 4.0 9.5 - - - +
298A ASN* 4.5 15.8 - - - +
341A SER* 3.1 19.2 + - - +
342A LEU 3.4 6.0 + - - +
343A GLY* 4.6 2.9 - - - -
356A ILE* 1.3 75.1 - - - +
358A GLY* 1.3 69.6 + - - +
359A PHE* 4.9 8.1 - - + -
386A GLY 3.9 0.9 - - - +
387A ILE* 3.4 4.0 - - - -
388A GLU* 2.6 55.3 + - + +
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Residues in contact with GLY 358 (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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341A SER* 2.9 21.0 + - - -
342A LEU* 2.8 23.6 + - - -
357A GLN* 1.3 74.9 - - - +
359A PHE* 1.3 60.4 + - - -
386A GLY 3.1 9.4 - - - -
387A ILE* 3.8 15.3 - - - +
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Residues in contact with PHE 359 (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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166A GLY 5.6 1.3 - - - -
167A ILE* 3.9 23.3 - - + -
168A PRO* 3.5 35.0 - - + -
340A ALA 3.3 11.4 - - - +
341A SER* 3.8 11.7 - - - +
357A GLN* 4.9 9.4 - - + -
358A GLY* 1.3 77.3 - - - +
360A TYR* 1.3 65.3 + - - +
361A THR* 4.6 3.8 - - + -
384A VAL* 3.7 28.7 - - + -
385A ARG* 3.4 6.3 - - - +
386A GLY* 2.6 50.3 + - - -
388A GLU* 5.4 8.1 - - + -
409A ARG* 4.8 11.9 - - + -
411A LEU* 3.9 11.4 - - + -
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Residues in contact with TYR 360 (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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338A LYS* 5.2 3.4 - - + -
339A LEU* 3.6 0.5 - - - -
340A ALA* 2.8 45.1 + - + +
359A PHE* 1.3 76.2 - - - +
361A THR* 1.3 71.6 + - - +
362A GLN* 4.0 24.2 + - + -
383A TRP* 3.4 38.4 + + + -
384A VAL 3.4 12.1 - - - -
385A ARG* 4.7 8.7 - - + -
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Residues in contact with THR 361 (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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167A ILE* 4.6 10.8 - - + -
168A PRO 5.2 3.5 + - - +
170A PRO 5.0 3.3 + - - -
171A PHE* 5.7 0.5 - - - -
337A ARG* 3.9 21.6 + - - +
338A LYS 3.1 8.5 - - - -
339A LEU* 3.3 36.1 - - + -
359A PHE* 4.6 3.3 - - + -
360A TYR* 1.3 91.6 - - - +
362A GLN* 1.3 59.8 + - - +
363A THR* 4.1 2.4 + - - -
382A TYR 3.6 1.9 - - - +
383A TRP* 3.5 2.6 - - - -
384A VAL* 2.9 46.1 + - - +
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Residues in contact with GLN 362 (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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336A ARG 4.2 0.5 - - - +
337A ARG* 3.5 1.4 - - - -
338A LYS* 2.8 71.7 + - + +
360A TYR* 4.0 18.3 + - + +
361A THR* 1.3 71.4 - - - +
363A THR* 1.3 67.9 + - - +
364A LEU* 6.3 0.7 - - + -
381A ASN* 5.9 2.6 + - + +
382A TYR 3.3 4.5 - - - +
383A TRP* 2.5 45.8 - - + +
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Residues in contact with THR 363 (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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171A PHE* 3.8 27.8 - - + +
181A LEU* 3.5 29.6 - - + -
336A ARG 3.6 5.8 - - - +
337A ARG* 2.5 42.7 + - + +
361A THR* 4.5 3.3 + - - -
362A GLN* 1.3 76.7 + - - +
364A LEU* 1.3 65.7 + - - +
365A ARG* 5.3 0.9 - - + -
380A ARG 3.6 1.8 - - - +
381A ASN* 3.2 3.7 - - - +
382A TYR* 2.7 41.9 + - - +
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Residues in contact with LEU 364 (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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181A LEU* 3.6 2.3 - - - +
334A TRP* 4.3 22.0 - - + +
335A GLY* 3.2 2.3 - - - -
336A ARG* 2.8 40.4 + - - +
362A GLN* 6.3 0.7 - - + -
363A THR* 1.3 75.5 - - - +
365A ARG* 1.3 78.7 + - - +
366A SER* 4.6 1.6 - - - +
379A PRO* 4.6 7.2 - - + -
380A ARG 3.3 22.7 - - - +
381A ASN* 3.2 31.4 - - - +
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Residues in contact with ARG 365 (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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171A PHE* 4.0 25.1 - - + -
180A SER* 3.0 39.4 + - - -
181A LEU* 3.9 20.4 - - + -
333A PHE* 3.6 19.1 - - + -
334A TRP 3.6 7.6 - - - +
364A LEU* 1.3 79.8 - - - +
366A SER* 1.3 66.5 + - - +
378A SER 3.4 20.8 + - - -
380A ARG* 2.9 53.1 + - + +
382A TYR* 4.5 2.9 - - + -
742A FLC 3.2 30.3 + - - +
743A FLC 3.3 14.8 + - - -
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Residues in contact with SER 366 (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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333A PHE* 3.5 15.3 - - - -
334A TRP* 2.7 65.0 + - - +
364A LEU* 4.6 4.3 - - - +
365A ARG* 1.3 75.2 - - - +
367A GLY* 1.3 58.0 + - - +
377A LEU* 4.3 1.8 - - - +
378A SER 2.9 12.6 - - - -
379A PRO* 3.0 36.8 - - - +
380A ARG 4.2 0.2 - - - -
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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