Contacts of the strand formed by residues 338 - 348 (chain A) in PDB entry 1HPL
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 TRP 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A ASN* 4.5 11.4 - - + -
278A ASP* 2.8 45.5 + - - -
279A GLY* 3.9 12.3 - - - -
334A ASN* 4.8 4.7 - - - -
336A ALA* 3.7 27.4 - - + -
337A ARG* 1.3 79.1 - - - +
339A ARG* 1.3 60.9 + - - +
340A TYR* 3.4 25.7 - - + -
387A ASP* 4.4 1.1 - - - -
388A SER* 2.9 39.9 + - - +
389A ASP 3.7 22.7 - - - -
390A VAL* 4.0 6.7 - - - +
391A GLU* 3.5 37.6 - - + +
425A ASN* 5.3 10.3 - - - +
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Residues in contact with ARG 339 (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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283A PHE* 4.4 13.4 - - + -
291A PHE* 3.5 42.1 + - - -
292A THR* 5.3 3.4 - - - +
294A ASN* 3.8 9.3 + - - -
297A PHE* 3.4 41.8 - - + -
328A ASN* 3.2 14.8 + - - -
337A ARG 4.2 1.4 + - - -
338A TRP* 1.3 72.7 - - - +
340A TYR* 1.3 74.3 + - - +
385A GLU* 2.8 46.0 + - + +
386A PHE 3.3 10.8 - - - +
387A ASP* 3.0 40.7 + - - +
425A ASN* 4.1 17.2 + - - +
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Residues in contact with TYR 340 (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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297A PHE* 3.9 5.2 - - - -
338A TRP* 3.4 33.9 - - + -
339A ARG* 1.3 78.3 - - - +
341A ARG* 1.3 61.0 + - - +
342A VAL* 4.2 0.7 - - - -
359A LEU* 3.8 24.0 - - + -
384A ASN 4.1 0.2 - - - +
385A GLU* 3.1 7.3 - - - +
386A PHE* 3.0 47.4 + + + -
388A SER* 3.8 20.4 - - - -
390A VAL 4.1 6.3 - - - -
391A GLU* 3.8 12.5 + - + +
392A VAL* 3.1 41.4 + - + +
393A GLY 4.4 1.0 + - - -
395A LEU* 4.7 2.2 - - + -
422A VAL* 4.1 9.4 - - + -
423A GLU 3.5 12.6 - - - -
424A ARG* 3.9 25.8 - - + -
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Residues in contact with ARG 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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294A ASN* 3.6 25.9 + - - +
297A PHE* 3.6 24.4 - - + -
340A TYR* 1.3 72.3 - - - +
342A VAL* 1.3 65.9 + - - +
343A ASP* 4.0 11.3 + - - +
383A SER* 3.2 31.9 + - - +
384A ASN* 3.4 17.4 - - - +
385A GLU* 3.2 34.3 + - + +
421A THR 3.7 0.9 - - - +
422A VAL* 3.4 4.9 - - - +
423A GLU* 2.9 47.6 + - + +
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Residues in contact with VAL 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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340A TYR* 4.9 0.4 - - + -
341A ARG* 1.3 80.9 - - - +
343A ASP* 1.3 66.8 + - - +
344A VAL* 4.2 2.5 - - + +
357A VAL* 4.3 11.4 - - + -
359A LEU* 4.2 19.3 - - + -
371A ILE* 4.0 27.4 - - + +
382A TYR 3.9 0.5 - - - +
383A SER* 3.2 3.8 + - - -
384A ASN 2.9 35.1 + - - +
386A PHE* 3.7 23.1 - - + -
420A ILE* 4.1 19.7 - - + -
421A THR 3.4 3.4 - - - -
422A VAL* 4.3 10.8 - - + -
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Residues in contact with ASP 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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341A ARG* 4.0 13.9 + - - +
342A VAL* 1.3 74.4 - - - +
344A VAL* 1.3 60.5 + - - +
345A THR* 5.3 0.4 - - - -
381A THR* 4.1 17.5 - - + +
382A TYR 3.4 4.5 - - - -
383A SER* 2.8 29.5 + - - -
419A LYS 3.7 1.2 - - - +
420A ILE* 3.1 7.1 - - - +
421A THR* 3.0 48.1 + - - +
423A GLU* 6.1 0.5 - - - +
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Residues in contact with VAL 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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342A VAL* 5.1 2.0 - - + -
343A ASP* 1.3 75.1 - - - +
345A THR* 1.3 64.3 + - - +
346A LEU* 3.6 23.6 - - + -
355A VAL* 4.2 11.4 - - + -
357A VAL* 5.0 4.5 - - + -
371A ILE* 3.6 25.1 - - + -
380A ASN 3.6 1.6 - - - +
381A THR* 3.1 2.8 - - - -
382A TYR* 2.8 59.4 + - + +
400A PHE* 4.2 9.2 - - + -
417A ALA* 3.8 18.6 - - + -
419A LYS 3.6 2.9 - - - -
420A ILE* 3.9 13.5 - - + -
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Residues in contact with THR 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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343A ASP 5.3 0.7 + - - -
344A VAL* 1.3 71.8 - - - +
346A LEU* 1.3 62.1 + - - +
379A ASP* 3.3 29.6 - - - +
380A ASN 3.1 4.0 - - - +
381A THR* 2.8 20.8 + - - +
417A ALA* 3.2 4.2 - - - -
418A SER* 2.8 48.9 + - - +
419A LYS* 2.9 22.6 + - + +
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Residues in contact with LEU 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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344A VAL* 3.6 24.0 - - + -
345A THR* 1.3 73.4 - - - +
347A SER* 1.3 59.4 + - - +
355A VAL* 4.4 6.1 - - + -
376A LEU* 3.6 49.8 - - + -
377A LYS 4.0 11.0 - - - +
378A PRO* 3.3 2.6 - - + +
379A ASP* 2.8 34.8 + - - -
380A ASN 3.1 6.3 + - - -
382A TYR* 3.7 22.9 - - + -
400A PHE* 3.8 17.9 - - + -
415A VAL* 4.3 4.9 - - + -
416A GLY 3.4 14.1 - - - +
418A SER* 4.7 0.4 + - - -
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Residues in contact with SER 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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345A THR 3.8 0.4 + - - -
346A LEU* 1.3 76.8 - - - +
348A GLY* 1.3 61.8 + - - +
349A LYS 4.7 0.5 - - - +
378A PRO* 4.3 6.1 - - - -
379A ASP* 4.8 1.8 - - - +
415A VAL* 3.4 9.0 - - - +
416A GLY* 2.9 42.7 + - - +
417A ALA 3.9 1.6 + - - -
418A SER* 4.2 20.0 + - - -
434A SER 5.6 0.5 + - - -
435A GLU 6.0 0.2 - - - -
436A GLU 4.0 8.0 + - - -
437A THR* 4.8 3.3 - - - -
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Residues in contact with GLY 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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347A SER* 1.3 77.3 + - - +
349A LYS* 1.3 66.3 + - - -
378A PRO* 3.3 21.6 - - - +
414A LYS 3.5 9.4 - - - -
437A THR* 3.8 11.9 - - - -
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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