Contacts of the strand formed by residues 367 - 377 (chain B) in PDB entry 2ZL6
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 GLY 367 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293B THR* 3.3 9.5 - - - +
294B SER 2.8 32.1 + - - -
334B GLN* 4.2 7.0 - - - -
365B GLY 3.4 0.4 + - - -
366B SER* 1.3 74.4 - - - +
368B ASN* 1.3 59.1 + - - -
369B TYR* 3.3 14.4 - - - -
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Residues in contact with ASN 368 (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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291B ARG* 2.9 42.1 + - - +
292B GLY* 3.4 14.2 + - - -
293B THR* 3.0 24.3 + - + +
302B THR* 5.5 3.2 + - - +
334B GLN* 2.8 29.9 + - - +
335B PHE* 5.1 3.3 + - - -
367B GLY* 1.3 72.1 - - - -
369B TYR* 1.3 62.7 + - - +
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Residues in contact with TYR 369 (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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290B ILE* 5.6 0.5 - - - +
291B ARG* 3.3 11.2 - - - -
292B GLY 2.9 34.5 + - - +
294B SER* 4.1 4.0 - - - -
299B ILE* 5.8 1.1 - - + -
332B MET* 3.7 43.5 - - + -
333B THR 3.3 7.6 - - - +
334B GLN* 3.6 32.3 + - + +
335B PHE* 5.9 0.4 - - - -
341B THR* 4.8 11.8 + - + -
364B ILE* 3.5 23.2 - - + +
365B GLY* 2.7 36.7 + - - -
366B SER 3.9 4.3 + - - -
367B GLY 3.3 20.9 - - - -
368B ASN* 1.3 74.9 - - - +
370B VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 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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426A PRO* 4.4 7.0 - - + -
289B LYS* 4.7 8.5 - - + +
290B ILE 3.4 5.6 - - - +
291B ARG* 3.9 10.3 - - - +
304B LEU* 3.6 31.9 - - + -
331B ASN 3.8 0.2 - - - +
332B MET* 3.4 1.9 - - - -
333B THR* 2.9 54.9 + - - +
334B GLN* 5.1 0.6 - - - +
335B PHE* 4.1 27.5 - - + -
369B TYR* 1.3 75.8 - - - +
371B GLY* 1.3 68.1 + - - +
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Residues in contact with GLY 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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289B LYS* 3.1 10.5 - - - +
290B ILE* 2.8 36.2 + - - +
330B ILE* 3.6 17.7 - - - -
331B ASN 3.2 8.7 - - - -
332B MET* 3.8 6.9 - - - -
370B VAL* 1.3 76.5 - - - +
372B VAL* 1.3 61.4 + - - -
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Residues in contact with VAL 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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372A VAL* 6.0 6.5 - - + -
247B PRO* 4.3 20.4 - - + -
287B VAL 4.5 1.6 - - - +
288B ALA 3.5 9.0 - - - +
289B LYS* 3.9 27.6 - - + -
330B ILE* 3.5 4.6 - - - +
331B ASN* 2.8 44.0 + - + +
371B GLY* 1.3 73.8 - - - +
373B LEU* 1.3 78.8 + - - +
374B SER* 3.2 1.1 + - - -
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Residues in contact with LEU 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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246B ALA* 4.5 3.6 - - + -
247B PRO* 4.8 7.8 - - - +
288B ALA* 2.9 36.2 + - + +
321B PRO* 4.7 9.2 - - + -
323B LEU* 3.9 24.7 - - + -
328B TRP* 3.8 33.0 - - + -
329B HIS 3.9 5.2 - - - +
330B ILE* 4.1 9.9 - - + +
372B VAL* 1.3 83.8 - - - +
374B SER* 1.3 61.8 + - - +
375B TRP 3.8 14.6 - - - +
376B ILE* 4.1 4.9 - - + -
425B MET* 3.8 29.0 - - + +
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Residues in contact with SER 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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331A ASN* 2.9 25.1 + - - -
333A THR* 3.2 18.7 + - - +
340A GLN* 3.1 17.6 + - - -
248B LEU* 6.1 0.3 - - - +
329B HIS 2.9 17.2 + - - -
331B ASN* 4.3 4.5 - - - -
372B VAL* 3.2 6.9 + - - -
373B LEU* 1.3 75.5 - - - +
375B TRP* 1.3 61.8 + - - +
425B MET* 4.2 5.3 - - - +
426B PRO* 3.3 19.8 - - - +
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Residues in contact with TRP 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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333A THR* 4.1 9.9 - - + -
337A HIS 5.4 0.4 - - - +
338A SER* 3.8 12.3 - - - -
339A SER* 3.3 40.4 - - - +
340A GLN* 3.8 6.0 + - + +
329B HIS* 2.9 67.4 + + + +
342B GLN* 3.0 34.9 + - - -
373B LEU* 3.8 1.4 - - - +
374B SER* 1.3 94.4 - - - +
376B ILE* 1.3 88.9 + - - +
377B SER* 4.1 4.0 - - - -
425B MET* 4.2 3.8 - - - -
426B PRO* 3.4 24.5 - - + +
427B GLY* 4.0 7.9 - - - +
428B PRO* 4.1 4.9 - - + -
5C FUC 3.3 26.0 - - - -
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Residues in contact with ILE 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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323B LEU* 4.2 9.6 - - + -
326B CYS* 4.1 15.3 - - + -
327B ASP 3.3 14.1 - - - +
328B TRP* 4.5 0.7 - - + -
329B HIS* 3.9 1.1 - - - -
373B LEU* 4.1 16.2 - - + -
375B TRP* 1.3 88.7 - - - +
377B SER* 1.3 63.0 + - - +
387B VAL* 4.0 9.4 - - + -
389B LEU* 3.8 34.8 - - + -
425B MET* 3.7 26.5 - - + -
426B PRO 3.1 2.8 + - - -
427B GLY* 3.3 23.9 - - - -
428B PRO* 3.3 1.6 - - - +
431B TYR* 3.5 25.0 - - + -
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Residues in contact with SER 377 (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 CYS* 3.3 8.7 - - - +
327B ASP* 2.8 27.1 + - - +
329B HIS* 2.7 28.9 - - - -
375B TRP* 4.1 9.0 - - - -
376B ILE* 1.3 76.8 - - - +
378B PRO* 1.4 72.4 - - - +
387B VAL* 3.9 5.6 - - - -
428B PRO* 4.1 7.2 - - - -
431B TYR* 4.1 5.2 - - - -
4C GAL 2.7 25.5 + - - -
5C FUC 5.2 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