Contacts of the strand formed by residues 318 - 325 (chain A) in PDB entry 2ZB5
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 SER 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A HIS* 2.8 29.3 + - - -
316A GLY 4.1 4.5 + - - -
317A VAL* 1.3 82.9 + - - +
319A PHE* 1.3 62.0 + - - +
336A TRP* 3.8 31.7 - - - +
337A VAL 3.4 13.0 + - - -
338A PRO* 3.8 8.7 - - - +
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Residues in contact with PHE 319 (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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288A MET* 4.7 3.1 - - + -
299A LEU* 3.6 28.3 - - + -
300A CYS 3.3 16.8 - - - +
301A HIS* 4.0 7.2 - - + -
306A ILE* 3.3 28.7 - - + -
317A VAL* 4.3 12.1 - - + -
318A SER* 1.3 82.7 - - - +
320A GLN* 1.3 59.5 + - - +
321A LEU 3.7 0.3 + - - -
336A TRP* 3.3 5.7 - - - -
337A VAL* 2.8 31.1 + - - +
339A LEU* 4.5 20.9 - - + -
349A LEU* 4.1 12.1 - - + -
351A LEU* 3.7 23.8 - - + -
413A LEU* 4.4 12.1 - - + -
425A ILE* 3.6 26.7 - - + -
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Residues in contact with GLN 320 (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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255A PHE* 4.1 2.4 - - - -
278A GLN* 3.1 20.1 + - - +
284A LEU* 2.9 28.8 - - + +
298A ALA 3.4 5.7 - - - +
299A LEU* 3.4 2.1 - - - -
300A CYS* 3.0 38.6 + - + +
319A PHE* 1.3 70.7 - - - +
321A LEU* 1.3 61.7 + - - +
322A VAL* 3.9 16.7 + - + +
334A GLN* 2.7 29.1 + - - +
335A SER 3.4 11.7 - - - +
336A TRP* 3.8 42.0 - - + +
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Residues in contact with LEU 321 (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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297A ALA* 4.7 2.9 - - + -
298A ALA 3.4 18.4 - - - +
299A LEU* 3.6 17.3 - - + -
319A PHE 3.7 1.2 + - - -
320A GLN* 1.3 72.3 - - - +
322A VAL* 1.3 69.2 + - - +
323A LYS* 5.1 3.4 - - + +
333A MET* 3.8 11.3 - - - +
334A GLN* 3.1 5.2 - - - +
335A SER* 2.7 33.4 + - - +
337A VAL* 3.7 25.4 - - + -
365A TRP* 5.1 2.2 - - + -
415A VAL* 3.6 30.7 - - + -
417A LEU* 4.4 21.5 - - + -
423A LEU* 4.2 14.6 - - + -
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Residues in contact with VAL 322 (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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255A PHE* 3.6 50.9 - - + -
276A LEU* 3.8 22.9 - - + -
296A LEU* 3.8 1.9 - - + +
297A ALA* 3.3 5.5 - - - -
298A ALA* 3.0 33.6 + - + +
300A CYS* 5.3 0.2 - - - -
320A GLN* 3.9 16.8 - - + +
321A LEU* 1.3 79.5 - - - +
323A LYS* 1.3 63.8 + - - +
324A LEU* 4.2 16.6 - - + -
333A MET 3.7 4.7 - - - +
334A GLN* 4.2 11.9 - - + +
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Residues in contact with LYS 323 (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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295A LYS* 4.4 19.3 - - + -
296A LEU 3.4 9.4 - - - +
321A LEU* 5.2 4.7 - - + +
322A VAL* 1.3 75.6 - - - +
324A LEU* 1.3 68.3 + - - +
331A THR* 3.4 28.7 + - - +
332A ASP* 3.2 6.6 - - - -
333A MET* 2.9 55.5 + - + +
417A LEU* 2.9 63.1 + - + +
418A SER* 3.5 8.1 - - - +
423A LEU* 6.2 0.2 - - - +
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Residues in contact with LEU 324 (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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255A PHE* 3.4 37.0 - - + +
257A VAL* 4.0 11.0 - - + +
274A ASN* 3.5 21.8 - - - +
275A TYR* 3.9 10.1 - - - +
276A LEU* 3.8 27.6 - - + +
295A LYS* 3.3 3.7 - - - +
296A LEU* 2.7 45.3 + - + +
322A VAL* 4.2 12.8 - - + -
323A LYS* 1.3 84.6 - - - +
325A GLY* 1.3 60.5 + - - +
328A LYS* 6.0 1.6 - - - +
332A ASP* 3.5 13.7 - - + +
333A MET 5.2 1.3 - - - +
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Residues in contact with GLY 325 (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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257A VAL* 4.0 2.6 - - - +
274A ASN* 2.9 22.0 + - - +
294A LEU 3.7 9.9 - - - -
295A LYS* 3.8 5.2 - - - -
324A LEU* 1.3 75.3 - - - +
326A VAL* 1.3 64.7 + - - -
327A TRP 2.8 14.8 + - - -
329A SER* 6.0 0.2 - - - -
331A THR* 5.4 3.1 + - - -
332A ASP* 2.9 16.1 + - - -
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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