Contacts of the strand formed by residues 369 - 376 (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 TYR 369 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B LEU* 3.2 3.8 - - - -
357B VAL* 2.8 33.0 + - - +
366B SER* 4.1 8.5 - - - -
367B ARG* 3.5 47.4 + - + +
368B GLN* 1.3 74.7 - - - +
370B GLU* 1.4 62.6 + - - +
371B ILE* 3.8 4.6 + - - +
386B PHE* 3.6 56.8 - + + -
387B ASP 3.9 11.7 + - - -
388B SER* 3.3 9.0 + - - -
389B ASP* 3.2 27.7 + - - -
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Residues in contact with GLU 370 (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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80A LYS* 4.3 7.3 + - - -
354B HIS* 2.8 33.2 + - + +
355B VAL 3.3 12.8 - - - +
356B LEU* 3.6 18.2 - - + +
369B TYR* 1.4 73.3 - - - +
371B ILE* 1.3 65.1 + - - +
372B PHE* 4.1 9.3 - - - +
373B GLN* 3.4 32.0 + - - +
384B ASN* 3.9 13.3 + - - -
386B PHE* 5.4 2.4 - - - +
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Residues in contact with ILE 371 (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* 4.0 25.1 - - + +
344B VAL* 4.1 13.0 - - + -
355B VAL* 2.8 20.2 + - + +
357B VAL* 4.0 27.1 - - + -
369B TYR 4.0 8.1 - - - +
370B GLU* 1.3 80.5 - - - +
372B PHE* 1.3 62.1 + - - +
382B TYR* 4.1 32.1 - - + +
383B SER 4.4 3.3 - - - +
384B ASN* 3.5 35.9 + - + +
386B PHE* 4.2 18.4 - - + -
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Residues in contact with PHE 372 (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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353B GLY 4.1 0.2 - - - +
354B HIS* 3.4 1.2 - - - -
355B VAL* 3.0 37.3 + - + +
370B GLU* 3.7 5.5 - - - +
371B ILE* 1.3 83.5 - - - +
373B GLN* 1.3 78.8 + - - +
374B GLY* 3.8 12.3 - - - -
375B THR 3.5 23.6 - - - -
376B LEU* 3.9 16.4 - - + -
382B TYR* 3.7 39.7 - + + -
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Residues in contact with GLN 373 (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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80A LYS* 3.5 23.7 - - - +
353B GLY 3.2 5.6 - - - -
354B HIS* 2.6 44.9 + - + -
370B GLU* 3.4 19.8 + - - +
372B PHE* 1.3 88.9 - - - +
374B GLY* 1.3 56.1 + - - +
406B ASN* 4.7 1.7 + - - +
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Residues in contact with GLY 374 (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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352B THR* 3.2 6.2 - - - -
353B GLY 2.8 35.0 + - - +
372B PHE* 3.8 9.1 - - - -
373B GLN* 1.3 74.0 - - - +
375B THR* 1.3 64.5 + - - -
376B LEU* 3.3 1.4 + - - +
406B ASN* 5.5 0.6 + - - -
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Residues in contact with THR 375 (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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350B LYS* 3.3 37.2 - - - +
351B VAL 3.6 3.4 - - - -
352B THR* 3.6 15.1 - - + +
372B PHE* 3.5 11.9 - - - -
374B GLY* 1.3 67.8 - - - -
376B LEU* 1.3 63.4 + - - +
377B LYS* 3.3 31.9 + - + +
382B TYR* 3.1 17.8 + - - -
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Residues in contact with LEU 376 (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* 3.7 20.9 - - + -
349B LYS 4.4 0.8 - - - +
350B LYS* 3.2 9.4 - - - +
351B VAL* 2.7 56.4 + - + +
353B GLY* 3.9 34.5 - - - +
354B HIS 4.1 7.2 - - - +
355B VAL* 3.9 20.9 - - + -
372B PHE* 3.9 23.6 - - + -
374B GLY 3.7 5.6 - - - +
375B THR* 1.3 72.5 - - - +
377B LYS* 1.3 59.5 + - - +
382B TYR* 4.2 0.9 - - - -
402B TRP* 4.2 17.7 - - + -
415B VAL* 5.0 8.5 - - + -
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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