Contacts of the strand formed by residues 382 - 391 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362B TRP* 4.1 15.3 - - + -
378B LEU* 2.7 37.8 + - - +
379B SER 3.5 12.3 - - - +
380B PHE* 2.9 23.0 + - + +
381B ASN* 1.3 75.0 - - - +
383B ASP* 1.3 62.5 + - - +
384B TYR* 3.9 19.3 - - + -
461B SO4 3.6 7.4 - - - +
64D ARG* 3.5 22.4 - - - +
78D ILE* 5.0 0.4 - - - +
80D ASP* 3.6 37.3 + - - +
88D LEU* 4.1 15.0 + - - +
90D GLN* 3.0 35.7 + - - +
102D PRO* 3.7 24.0 - - - +
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Residues in contact with ASP 383 (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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328B SER* 3.7 1.6 - - - -
329B VAL* 3.7 32.4 + - + +
375B LEU* 4.0 12.7 - - + +
376B LEU 3.4 3.6 - - - +
377B HIS* 3.1 38.5 + - - +
381B ASN* 4.6 7.5 - - - +
382B ARG* 1.3 78.1 + - - +
384B TYR* 1.3 68.8 + - - +
461B SO4 2.9 28.4 + - - +
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Residues in contact with TYR 384 (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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326B ALA* 4.1 11.4 - - + -
327B GLN* 3.4 13.9 - - - +
328B SER* 3.4 22.0 - - - -
329B VAL* 4.7 0.4 - - - -
338B LEU* 3.2 32.9 - - - +
340B HIS* 3.6 27.1 - - + -
362B TRP* 4.0 10.8 - + - -
375B LEU* 3.7 5.9 - - - -
376B LEU* 2.7 43.8 + - + +
378B LEU* 3.6 24.5 - - + -
382B ARG* 3.9 20.8 - - + +
383B ASP* 1.3 85.0 - - - +
385B ASN* 1.3 59.5 + - - +
461B SO4 5.1 1.3 - - - -
90D GLN* 4.3 2.4 + - - -
99D THR* 3.7 24.5 - - - +
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Residues in contact with ASN 385 (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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326B ALA* 3.1 5.9 - - - -
327B GLN* 2.8 41.5 + - + +
328B SER 5.5 0.7 - - - +
329B VAL* 4.7 7.0 - - + +
374B SER* 2.4 38.2 + - - -
375B LEU* 4.4 10.6 - - + +
384B TYR* 1.3 72.3 - - - +
386B TRP* 1.3 64.9 + - - +
387B TYR* 3.3 20.1 + - - +
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Residues in contact with TRP 386 (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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305B GLY* 4.1 4.4 + - - -
306B VAL* 3.6 23.8 + - + +
307B PRO* 3.3 27.8 - - + +
324B ILE* 3.5 44.5 - - + +
325B LEU 3.7 3.8 - - - -
326B ALA* 4.1 3.8 - - - +
344B VAL* 3.9 14.1 - - + -
356B LEU* 3.8 35.2 - - + -
358B TYR* 5.7 1.6 - + + -
369B GLN* 4.6 10.1 - - + -
373B SER 5.1 1.1 - - - -
374B SER* 2.8 31.9 + - - +
376B LEU* 3.9 28.4 - - + +
384B TYR 3.8 1.2 + - - -
385B ASN* 1.3 70.5 - - - +
387B TYR* 1.3 60.0 + - - +
388B GLY 3.1 19.6 + - - -
389B SER* 3.0 21.6 + - - -
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Residues in contact with TYR 387 (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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302B TYR* 3.4 23.3 + + - -
304B GLU* 4.0 3.6 - - - +
305B GLY* 2.8 23.1 + - - -
325B LEU* 3.0 37.0 + - + +
326B ALA* 3.6 30.9 + - - -
327B GLN* 3.9 28.3 - - + +
385B ASN* 3.3 16.0 + - - +
386B TRP* 1.3 73.3 - - - +
388B GLY* 1.3 58.4 + - - +
97D ILE* 3.5 29.8 - - - +
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Residues in contact with GLY 388 (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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302B TYR* 3.3 16.8 - - - -
303B GLN 3.3 13.2 - - - -
305B GLY 3.5 6.1 - - - -
325B LEU* 2.9 24.2 + - - -
386B TRP* 3.1 12.3 + - - -
387B TYR* 1.3 82.2 - - - +
389B SER* 1.3 63.2 + - - -
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Residues in contact with SER 389 (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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301B HIS 3.7 0.3 - - - +
302B TYR* 3.3 9.0 - - - -
303B GLN* 2.8 36.0 + - - +
305B GLY 3.9 1.9 + - - -
307B PRO* 3.6 16.3 - - - +
322B ILE* 3.6 19.5 - - - -
323B MET 3.1 13.7 - - - -
325B LEU* 4.4 2.2 - - - +
386B TRP* 3.0 24.1 + - - -
388B GLY* 1.3 70.3 - - - -
390B MET* 1.3 62.2 + - - +
391B ILE* 3.9 10.4 + - - -
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Residues in contact with MET 390 (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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286B PRO* 3.9 35.7 - - + +
289B MET* 3.9 22.4 - - + -
290B ILE* 3.9 22.4 - - + -
300B ILE* 3.8 13.0 - - + -
301B HIS 3.7 0.4 - - - -
302B TYR* 3.8 40.2 - - + -
322B ILE* 3.6 1.6 - - - -
323B MET* 2.9 39.7 + - + -
325B LEU* 4.0 16.8 - - + +
389B SER* 1.3 71.4 - - - +
391B ILE* 1.3 60.8 + - - +
393B TYR* 3.6 17.2 - - + +
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Residues in contact with ILE 391 (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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299B ASP 3.5 1.9 - - - +
300B ILE* 3.3 6.3 - - - -
301B HIS* 2.9 41.3 + - + +
303B GLN* 3.6 41.1 - - + +
307B PRO* 5.3 3.1 - - + -
311B GLN* 4.0 10.8 - - - +
315B LEU* 3.8 28.3 - - + -
320B VAL* 4.1 10.8 - - + -
321B GLY 3.7 5.2 - - - +
322B ILE* 4.2 17.7 - - + -
389B SER* 4.2 10.1 - - - +
390B MET* 1.3 76.0 - - - +
392B GLY* 1.3 62.1 + - - +
393B TYR 4.0 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