Contacts of the strand formed by residues 367 - 377 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A THR* 3.2 9.3 - - - +
294A SER 2.8 31.1 + - - -
334A GLN* 4.1 8.1 - - - -
365A GLY 3.4 0.6 + - - -
366A SER* 1.3 75.5 - - - +
368A ASN* 1.3 61.8 + - - -
369A TYR* 3.3 12.8 - - - -
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Residues in contact with ASN 368 (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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291A ARG* 2.9 43.2 + - - +
292A GLY* 3.3 15.6 + - - -
293A THR* 3.0 24.4 + - + +
302A THR* 5.5 3.4 + - - +
334A GLN* 3.0 29.5 + - - +
335A PHE* 5.2 3.1 + - - -
367A GLY* 1.3 72.1 - - - -
369A TYR* 1.3 61.6 + - - +
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Residues in contact with TYR 369 (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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290A ILE* 4.1 0.7 - - - +
291A ARG* 3.3 7.3 - - - -
292A GLY 2.9 34.6 + - - +
294A SER* 4.1 4.9 - - - -
299A ILE* 5.8 0.7 - - + -
332A MET* 3.6 45.9 - - + +
333A THR 3.3 7.9 - - - +
334A GLN* 3.5 34.2 + - + +
341A THR* 4.7 12.3 + - - -
364A ILE* 3.5 22.8 - - + +
365A GLY* 2.6 36.0 + - - -
366A SER 3.8 5.0 + - - -
367A GLY 3.3 22.4 - - - -
368A ASN* 1.3 75.8 - - - +
370A VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 370 (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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289A LYS* 4.5 6.5 - - + -
290A ILE 3.4 9.4 - - - +
291A ARG* 3.0 34.8 - - - +
304A LEU* 4.8 4.5 - - + +
331A ASN 3.7 0.7 - - - +
332A MET* 3.4 1.4 - - - -
333A THR* 2.8 42.9 + - - +
334A GLN* 5.1 0.6 - - - +
335A PHE* 3.8 23.1 - - + -
369A TYR* 1.3 74.6 - - - +
371A GLY* 1.3 66.8 + - - +
520A ACT 3.7 33.7 - - + +
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Residues in contact with GLY 371 (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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289A LYS* 3.0 10.1 - - - +
290A ILE* 2.8 38.5 + - - +
330A ILE* 3.6 17.7 - - - -
331A ASN 3.2 8.7 - - - -
332A MET* 3.8 6.9 - - - -
370A VAL* 1.3 76.7 - - - +
372A VAL* 1.3 61.9 + - - -
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Residues in contact with VAL 372 (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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247A PRO* 4.6 15.5 - - + -
287A VAL 4.6 4.9 - - - +
288A ALA 3.6 9.9 - - - +
289A LYS* 3.9 26.7 - - + -
330A ILE* 3.9 2.9 - - - -
331A ASN* 2.8 49.5 + - + +
370A VAL* 6.2 0.2 - - + -
371A GLY* 1.3 74.5 - - - +
373A LEU* 1.3 76.6 + - - +
374A SER* 3.2 1.2 + - - -
372B VAL* 6.0 7.0 - - + -
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Residues in contact with LEU 373 (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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246A ALA* 4.7 2.7 - - + -
247A PRO* 5.1 7.5 - - + +
288A ALA* 2.9 36.4 + - + +
321A PRO* 4.8 7.9 - - + -
323A LEU* 3.9 22.0 - - + -
328A TRP* 3.7 36.6 - - + -
329A HIS 3.9 11.4 - - - +
330A ILE* 4.2 10.1 - - + +
372A VAL* 1.3 83.6 - - - +
374A SER* 1.3 59.0 + - - +
375A TRP 3.9 10.3 - - - +
376A ILE* 4.1 7.6 - - + -
425A MET* 3.8 28.7 - - + +
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Residues in contact with SER 374 (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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329A HIS 2.9 15.7 + - - -
331A ASN* 4.3 4.3 - - - -
372A VAL* 3.2 6.5 + - - -
373A LEU* 1.3 72.8 - - - +
375A TRP* 1.3 63.5 + - - +
425A MET* 4.3 7.6 - - - +
426A PRO* 3.9 13.5 - - - +
331B ASN* 3.0 24.9 + - - -
333B THR* 3.2 22.2 + - - +
340B GLN* 3.0 21.5 + - - -
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Residues in contact with TRP 375 (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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329A HIS* 2.9 75.8 + + + +
342A GLN* 3.0 33.2 + - - -
373A LEU* 3.9 1.9 - - - +
374A SER* 1.3 95.6 - - - +
376A ILE* 1.3 81.7 + - - +
377A SER* 4.0 4.0 - - - -
425A MET* 4.4 3.4 - - - -
426A PRO* 3.4 24.0 - - + +
427A GLY* 4.1 1.6 - - - +
428A PRO* 4.0 12.6 - - + -
333B THR* 4.2 5.4 - - + -
337B HIS 5.6 0.4 - - - +
338B SER* 3.7 20.6 - - - -
339B SER* 3.3 49.1 - - - +
340B GLN* 3.7 2.4 - - + +
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Residues in contact with ILE 376 (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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323A LEU* 4.2 9.2 - - + -
326A CYS* 4.1 15.3 - - + -
327A ASP 3.3 14.1 - - - +
328A TRP* 4.5 0.4 - - + -
329A HIS* 4.0 0.7 - - - -
373A LEU* 4.1 17.0 - - + -
375A TRP* 1.3 84.3 - - - +
377A SER* 1.3 62.8 + - - +
387A VAL* 4.0 9.4 - - + -
389A LEU* 3.7 35.4 - - + -
425A MET* 3.6 27.1 - - + -
426A PRO 3.1 3.6 + - - -
427A GLY* 3.4 2.9 - - - -
428A PRO* 3.2 21.5 - - - +
431A TYR* 3.5 24.9 - - + -
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Residues in contact with SER 377 (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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326A CYS* 3.3 8.3 - - - +
327A ASP* 2.8 28.5 + - - +
329A HIS* 2.7 30.1 + - - -
375A TRP* 4.0 8.7 - - - -
376A ILE* 1.3 76.9 - - - +
378A PRO* 1.3 82.4 + - - +
387A VAL* 3.7 5.2 - - - -
428A PRO* 4.2 6.3 - - - -
431A TYR* 4.1 4.7 - - - -
338B SER* 5.5 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