Contacts of the strand formed by residues 338 - 348 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B ASN* 4.5 12.3 - - + -
278B ASP* 2.9 42.1 + - - -
279B GLY* 3.8 14.4 - - - -
334B ASN* 4.9 4.7 - - - -
336B ALA* 3.6 27.8 - - + -
337B ARG* 1.3 75.9 - - - +
339B ARG* 1.3 61.8 + - - +
340B TYR* 3.6 17.4 - - + +
387B ASP* 4.4 1.1 - - - -
388B SER* 2.8 44.1 + - - +
389B ASP 3.5 19.1 - - - -
390B VAL* 3.9 4.0 - - - +
391B GLU* 3.6 43.2 - - + +
425B ASN* 5.3 9.4 - - - +
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Residues in contact with ARG 339 (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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283B PHE* 4.1 16.8 - - + -
291B PHE* 3.5 42.1 + - - -
292B THR* 5.1 4.8 - - - +
294B ASN* 3.6 9.5 + - - -
297B PHE* 3.5 30.4 - - + -
328B ASN* 2.9 27.1 + - - -
337B ARG 4.3 1.2 + - - -
338B TRP* 1.3 71.6 - - - +
340B TYR* 1.3 71.5 + - - +
385B GLU* 3.0 52.7 + - + +
386B PHE* 3.3 11.6 - - - +
387B ASP* 3.1 26.6 + - - +
425B ASN* 3.9 19.3 + - - +
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Residues in contact with TYR 340 (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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297B PHE* 4.0 4.5 - - - -
338B TRP* 3.6 26.0 - - + -
339B ARG* 1.3 76.2 - - - +
341B ARG* 1.3 65.1 + - - +
342B VAL* 5.0 0.7 - - - -
359B LEU* 3.9 16.6 - - + -
384B ASN 4.2 0.2 - - - +
385B GLU* 3.1 6.3 - - - +
386B PHE* 2.9 48.2 + + + -
388B SER* 3.8 19.5 - - - -
390B VAL 4.2 2.5 - - - -
391B GLU* 3.6 14.6 + - + +
392B VAL* 3.1 42.3 + - + +
393B GLY 4.5 2.0 + - - -
395B LEU* 4.6 2.9 - - + -
422B VAL* 4.1 19.3 - - + -
423B GLU 3.5 6.7 - - - +
424B ARG* 3.9 27.4 - - + -
425B ASN 5.9 0.4 - - - -
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Residues in contact with ARG 341 (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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294B ASN* 3.3 25.7 + - - +
297B PHE* 3.5 43.4 + - + +
340B TYR* 1.3 71.8 - - - +
342B VAL* 1.3 65.6 + - - +
343B ASP* 3.8 22.0 + - - +
383B SER* 4.5 12.7 - - - -
384B ASN 3.7 9.8 - - - +
385B GLU* 2.7 35.5 + - + +
421B THR 3.7 0.6 - - - +
422B VAL* 3.2 5.5 - - - +
423B GLU* 2.8 53.2 + - + +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B TYR* 4.9 0.4 - - + -
341B ARG* 1.3 80.3 - - - +
343B ASP* 1.3 65.2 + - - +
344B VAL* 3.8 17.0 - - + -
357B VAL* 4.1 7.6 - - + -
359B LEU* 4.3 13.7 - - + -
371B ILE* 4.0 20.9 - - + +
382B TYR 3.7 1.4 - - - +
383B SER* 3.2 22.9 - - - -
384B ASN 3.1 12.5 + - - +
386B PHE* 3.6 28.5 - - + -
420B ILE* 3.7 23.8 - - + -
421B THR 3.4 2.7 - - - -
422B VAL* 4.4 11.0 - - + -
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Residues in contact with ASP 343 (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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341B ARG* 3.8 21.1 + - - +
342B VAL* 1.3 76.4 - - - +
344B VAL* 1.3 61.3 + - - +
345B THR* 4.2 0.6 + - - -
381B THR* 4.3 13.9 - - + +
382B TYR 3.3 4.0 - - - +
383B SER* 2.8 28.3 + - - +
419B LYS 3.9 0.9 - - - +
420B ILE* 3.0 5.7 - - - +
421B THR* 2.8 50.1 + - - +
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Residues in contact with VAL 344 (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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342B VAL* 3.8 22.0 - - + -
343B ASP* 1.3 74.5 - - - +
345B THR* 1.3 61.6 + - - +
346B LEU* 3.8 20.2 + - + -
355B VAL* 4.5 4.3 - - + -
357B VAL* 4.1 7.0 - - + -
371B ILE* 4.1 24.9 - - + -
380B ASN 3.7 0.9 - - - +
381B THR* 3.2 1.9 - - - +
382B TYR* 2.7 44.0 + - + +
400B PHE* 4.4 8.5 - - + -
417B ALA* 3.8 24.5 - - + -
419B LYS 3.7 3.1 - - - -
420B ILE* 4.0 11.9 - - + -
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Residues in contact with THR 345 (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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343B ASP 4.2 0.9 + - - -
344B VAL* 1.3 71.6 - - - +
346B LEU* 1.3 62.1 + - - +
379B ASP* 3.1 29.2 - - - +
380B ASN 3.3 2.7 - - - -
381B THR* 2.8 23.0 + - - +
417B ALA* 3.0 5.8 - - - -
418B SER* 2.8 45.8 + - - +
419B LYS* 2.8 24.0 + - - +
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Residues in contact with LEU 346 (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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344B VAL* 3.8 21.3 - - + -
345B THR* 1.3 78.3 - - - +
347B SER* 1.3 63.4 + - - +
355B VAL* 4.8 7.4 - - + -
376B LEU* 3.7 34.5 - - + -
377B LYS 3.9 17.5 - - - +
378B PRO* 4.2 2.7 - - + -
379B ASP* 3.3 20.7 + - - -
380B ASN 2.9 9.0 + - - +
382B TYR* 3.5 34.8 - - + -
400B PHE* 4.1 15.3 - - + -
415B VAL* 4.3 7.6 - - + -
416B GLY 3.4 15.0 - - - +
418B SER* 3.8 6.2 + - - -
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Residues in contact with SER 347 (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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346B LEU* 1.3 75.5 - - - +
348B GLY* 1.3 66.7 + - - +
349B LYS 3.7 1.0 + - - +
378B PRO* 3.9 10.3 - - - +
379B ASP 4.7 0.2 - - - +
415B VAL* 3.4 11.8 - - - +
416B GLY* 3.0 43.4 + - - -
417B ALA 3.3 6.8 + - - -
418B SER* 3.8 11.2 + - - -
434B SER 5.4 0.9 + - - -
435B GLU 5.4 2.3 + - - -
436B GLU 4.3 3.8 + - - -
437B THR* 4.1 5.7 - - - +
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Residues in contact with GLY 348 (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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347B SER* 1.3 78.1 + - - +
349B LYS* 1.3 68.7 - - - +
378B PRO* 3.1 22.4 - - - +
414B LYS 3.6 2.5 - - - -
437B THR* 3.5 22.5 - - - +
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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