Contacts of the strand formed by residues 348 - 358 (chain B) in PDB entry 1Z5A
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 HIS 348 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG 5.6 0.4 + - - -
101B ASN* 3.4 16.8 + - - -
240B GLU* 4.7 9.2 + - - -
344B ALA* 3.3 5.0 - - - -
345B TYR* 2.7 56.5 + + + +
346B GLN* 3.4 25.5 + - + -
347B GLY* 1.3 74.0 - - - +
349B PRO* 1.3 67.2 - - - +
350B PHE 3.6 0.5 + - - -
417B SER* 3.8 12.1 - - - +
418B THR* 3.1 22.3 + - - +
419B LYS* 3.6 39.7 + - + +
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Residues in contact with PRO 349 (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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101B ASN* 4.7 5.4 - - - +
229B VAL* 4.6 4.5 - - + -
230B LYS 4.9 0.7 - - - +
232B HIS* 5.0 3.1 - - + +
263B GLN* 3.9 25.1 - - - +
309B PRO* 3.8 21.5 - - + -
310B SER 5.0 4.3 - - - +
314B LEU* 4.0 17.9 - - + +
342B PRO* 5.7 1.1 - - + -
343B LYS 3.4 7.9 - - - +
344B ALA* 4.9 0.2 - - - -
347B GLY 3.8 7.0 - - - +
348B HIS* 1.3 83.6 - - - +
350B PHE* 1.3 54.1 + - - +
417B SER* 2.8 29.1 + - - -
418B THR* 3.4 24.6 + - + +
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Residues in contact with PHE 350 (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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314B LEU* 3.7 3.6 - - - +
342B PRO* 3.4 2.6 - - - +
343B LYS* 2.7 71.8 + - + +
344B ALA 3.6 19.3 - - - -
345B TYR* 3.8 27.4 - + + -
349B PRO* 1.3 74.3 - - - +
351B ILE* 1.3 63.4 + - - +
352B VAL* 4.0 8.3 - - + -
415B LEU* 3.6 21.5 - - + -
416B CYS 3.2 14.4 - - - +
417B SER* 3.7 11.7 - - - +
435B ASP* 3.8 21.3 - - + -
436B ILE* 4.1 12.1 - - + -
439B GLU* 3.8 26.7 - - + -
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Residues in contact with ILE 351 (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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311B ALA* 4.3 11.9 - - + +
314B LEU* 3.7 22.8 - - + +
316B VAL* 3.8 25.6 - - + -
339B THR* 4.4 2.9 - - + -
340B ARG 3.7 18.4 - - - +
341B LYS 5.0 2.0 - - - -
342B PRO* 3.6 35.4 - - + -
350B PHE* 1.3 75.4 - - - +
352B VAL* 1.3 78.2 + - - +
353B GLU* 4.0 14.8 - - + -
414B HIS 3.8 0.9 - - - +
415B LEU* 3.7 3.1 - - - +
416B CYS* 3.0 37.7 + - - +
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ARG* 3.2 33.0 + - - +
341B LYS 5.5 0.2 + - - -
350B PHE* 4.0 7.3 - - + -
351B ILE* 1.3 77.2 - - - +
353B GLU* 1.3 71.0 + - - +
354B ALA* 5.0 0.2 - - + -
413B VAL* 4.2 14.8 - - + -
414B HIS 3.5 4.0 - - - +
415B LEU* 4.0 18.8 - - + -
436B ILE 4.7 0.4 - - - +
439B GLU* 3.8 26.9 - - + +
440B ILE* 3.8 27.8 - - + +
443B ALA* 3.6 25.8 - - + -
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Residues in contact with GLU 353 (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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316B VAL* 3.4 15.3 - - - +
317B ILE* 2.9 17.8 + - - +
318B GLY* 2.9 18.0 + - - -
322B ILE* 3.8 16.5 - - + +
338B ILE 3.3 9.9 - - - +
339B THR* 2.7 27.1 + - + +
351B ILE* 4.0 13.5 - - + +
352B VAL* 1.3 77.5 - - - +
354B ALA* 1.3 62.6 + - - +
412B MET* 4.7 0.4 - - - +
413B VAL* 3.4 6.6 - - - +
414B HIS* 2.7 67.5 + - + +
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Residues in contact with ALA 354 (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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322B ILE* 4.9 3.5 - - - +
337B SER* 3.1 6.3 - - - -
338B ILE* 2.9 47.4 + - + +
352B VAL* 5.0 0.4 - - + -
353B GLU* 1.3 76.4 - - - +
355B GLY* 1.3 57.8 + - - +
412B MET* 3.3 7.6 - - - +
413B VAL* 4.9 2.7 - - + -
443B ALA* 4.0 19.3 - - + +
444B LEU* 4.4 10.1 - - + -
447B VAL* 3.7 17.3 - - + +
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Residues in contact with GLY 355 (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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322B ILE* 4.2 5.8 - - - +
326B LEU* 4.1 14.4 - - - -
336B ALA 3.5 8.7 - - - -
337B SER* 4.1 6.1 - - - -
354B ALA* 1.3 74.7 - - - +
356B VAL* 1.3 60.4 + - - +
410B VAL 4.5 0.2 - - - -
411B VAL* 3.4 6.8 - - - +
412B MET* 2.7 36.9 + - - +
444B LEU* 5.1 0.5 - - - +
447B VAL* 4.7 4.3 - - - +
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Residues in contact with VAL 356 (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 LEU* 4.0 4.1 - - - +
334B PHE* 4.2 14.8 - - + -
335B ALA* 3.2 5.4 - - - +
336B ALA* 2.9 40.7 + - + +
355B GLY* 1.3 73.9 - - - +
357B ALA* 1.3 66.1 + - - +
397B TRP* 5.0 4.7 - - + -
409B MET* 3.9 26.0 - - + -
410B VAL 3.2 11.4 - - - +
411B VAL* 4.6 5.6 - - + -
444B LEU* 6.4 0.4 - - + -
447B VAL* 4.0 33.7 - - + +
448B ALA* 6.2 0.2 - - - -
451B LEU* 4.1 15.0 - - + -
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Residues in contact with ALA 357 (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 LEU* 4.4 13.4 - - + +
330B PHE* 5.2 2.0 - - + -
332B PRO* 3.8 21.3 - - + -
334B PHE* 3.2 9.6 - - - +
335B ALA* 4.4 4.7 - - + -
356B VAL* 1.3 77.4 - - - +
358B PHE* 1.3 60.6 + - - +
362B ILE* 3.8 10.5 - - + -
409B MET* 3.2 8.7 - - - +
410B VAL* 2.8 42.0 + - + -
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Residues in contact with PHE 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B PRO* 3.4 0.7 - - - +
333B ASP* 2.8 24.8 + - - +
334B PHE* 2.9 21.6 + - + +
357B ALA* 1.3 74.2 - - - +
359B GLY* 1.3 82.7 + - - +
362B ILE* 4.0 1.8 - - - -
402B ILE* 4.5 13.2 - - + -
403B GLU* 4.4 14.4 - - - -
407B TYR* 4.0 21.8 - - + -
408B GLN* 3.1 35.4 - - - -
409B MET* 4.1 9.9 - - + -
451B LEU* 3.8 28.5 - - + -
454B TYR* 4.3 9.9 - + + -
455B LEU* 4.0 25.4 - - + -
458B LYS* 4.6 12.1 - - - -
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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