Contacts of the strand formed by residues 382 - 391 (chain A) in PDB entry 1PXV
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 ARG 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A TRP* 4.0 17.9 - - + -
378A LEU* 2.8 33.9 + - + +
379A SER 3.5 11.9 - - - +
380A PHE* 2.8 20.7 + - + +
381A ASN* 1.3 79.5 - - - +
383A ASP* 1.3 62.6 + - - +
384A TYR* 4.0 19.3 - - + -
462A SO4 3.1 6.7 - - - +
64C ARG* 3.5 22.8 - - - +
78C ILE* 4.8 1.6 + - - +
80C ASP* 3.2 40.5 + - - +
88C LEU* 3.7 23.8 + - - +
90C GLN* 3.3 33.5 + - - +
102C PRO* 3.7 13.8 - - - +
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Residues in contact with ASP 383 (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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328A SER* 3.9 14.2 - - - -
329A VAL* 4.7 2.4 + - - +
375A LEU* 4.1 15.4 - - + +
376A LEU 3.4 4.3 - - - +
377A HIS* 2.9 40.9 + - - +
378A LEU 5.3 0.2 - - - +
381A ASN* 4.6 10.6 + - - +
382A ARG* 1.3 80.5 + - - +
384A TYR* 1.3 70.1 + - - +
462A SO4 2.8 31.7 + - - +
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Residues in contact with TYR 384 (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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326A ALA* 3.7 14.8 - - + -
327A GLN 3.6 10.8 - - - -
328A SER* 3.5 21.1 - - - +
329A VAL* 5.9 0.9 - - - -
338A LEU* 3.5 32.7 - - + +
340A HIS* 3.6 26.5 - - + -
362A TRP* 4.2 8.0 - + - -
375A LEU* 3.7 3.6 - - - +
376A LEU* 2.7 37.3 + - + +
378A LEU* 3.5 30.3 - - + -
382A ARG* 4.0 19.0 - - + +
383A ASP* 1.3 83.2 - - - +
385A ASN* 1.3 62.8 + - - +
462A SO4 5.2 1.1 - - - -
90C GLN* 4.4 2.6 + - - -
99C THR* 3.5 26.9 + - - +
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Residues in contact with ASN 385 (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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326A ALA* 3.2 3.7 - - - -
327A GLN* 2.8 38.7 + - + +
328A SER 5.3 0.2 - - - -
329A VAL* 4.9 16.4 - - + +
374A SER* 2.4 35.8 + - - -
375A LEU* 3.6 27.1 - - - +
384A TYR* 1.3 73.8 - - - +
386A TRP* 1.3 60.4 - - - +
387A TYR* 3.2 10.9 + - + +
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Residues in contact with TRP 386 (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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305A GLY* 3.9 9.3 + - - -
306A VAL* 3.9 24.3 - - + +
307A PRO* 3.3 23.3 - - + -
324A ILE* 3.6 42.5 - - + +
325A LEU 3.8 4.0 - - - -
326A ALA* 4.3 0.2 - - - +
344A VAL* 3.9 14.8 - - + -
356A LEU* 3.7 34.8 - - + -
358A TYR* 5.6 2.0 - + + -
369A GLN* 4.5 15.0 - - + -
373A SER 4.9 1.8 - - - -
374A SER* 2.8 29.4 + - - +
376A LEU* 4.0 27.0 - - + +
384A TYR 4.0 0.8 + - - -
385A ASN* 1.3 69.8 - - - +
387A TYR* 1.3 58.0 + - - +
388A GLY 3.1 22.4 + - - -
389A SER* 3.0 21.6 + - - -
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Residues in contact with TYR 387 (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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286A PRO* 5.2 2.1 - - - +
302A TYR* 3.5 22.0 + + - -
304A GLU* 3.9 5.6 - - + +
305A GLY* 2.7 21.7 + - - -
325A LEU* 3.0 38.7 + - + +
326A ALA 3.7 15.9 - - - -
327A GLN* 3.7 36.3 + - + -
339A GLY* 5.9 0.9 - - - -
385A ASN* 3.2 7.1 + - + +
386A TRP* 1.3 72.9 - - - +
388A GLY* 1.3 58.3 + - - +
97C ILE* 3.5 29.2 - - + +
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Residues in contact with GLY 388 (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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302A TYR* 3.7 11.2 - - - -
303A GLN 3.3 12.6 - - - -
305A GLY 3.4 7.9 - - - -
325A LEU* 2.8 32.2 + - - -
386A TRP* 3.1 12.5 + - - -
387A TYR* 1.3 81.2 - - - +
389A SER* 1.3 63.0 + - - -
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Residues in contact with SER 389 (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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301A HIS 3.7 0.2 - - - +
302A TYR* 3.3 9.4 - - - -
303A GLN* 2.9 35.9 + - - +
305A GLY 3.8 1.7 + - - -
307A PRO* 3.5 16.1 - - - +
322A ILE* 3.6 17.3 - - - -
323A MET 3.1 12.6 - - - -
325A LEU* 4.5 2.0 - - - +
386A TRP* 3.0 24.8 + - - -
388A GLY* 1.3 71.6 - - - -
390A MET* 1.3 63.3 + - - +
391A ILE* 3.9 10.9 + - - -
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Residues in contact with MET 390 (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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286A PRO* 3.7 39.3 - - + +
289A MET* 4.0 12.3 - - + -
290A ILE* 3.7 31.6 - - + -
300A ILE* 3.9 4.7 - - + -
301A HIS 3.6 1.1 - - - -
302A TYR* 3.8 35.2 - - + -
322A ILE* 3.6 0.7 - - - -
323A MET* 2.9 36.9 + - + +
325A LEU* 4.0 21.1 - - + -
389A SER* 1.3 72.1 - - - +
391A ILE* 1.3 59.7 + - - +
393A TYR* 3.4 27.1 - - + +
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Residues in contact with ILE 391 (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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299A ASP 3.9 1.4 - - - +
300A ILE* 3.4 4.3 - - - +
301A HIS* 2.9 40.6 + - + +
303A GLN* 3.8 40.8 - - + +
307A PRO* 5.3 2.7 - - + -
311A GLN* 4.1 11.7 - - - +
315A LEU* 3.9 34.8 - - + -
320A VAL* 4.3 3.8 - - + -
321A GLY 3.8 3.1 - - - -
322A ILE* 4.0 18.8 - - + +
389A SER* 4.1 9.4 - - - +
390A MET* 1.3 77.0 - - - +
392A GLY* 1.3 63.4 + - - +
393A TYR 4.0 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