Contacts of the strand formed by residues 326 - 333 (chain A) in PDB entry 2ZH2
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 PHE 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A LYS* 3.4 43.5 - - + -
283A PHE 3.1 20.9 - - - +
284A ARG* 3.5 46.9 - - + -
285A LYS* 3.9 4.0 - - - +
321A LYS 4.0 0.3 - - - +
322A ALA* 3.6 1.0 - - - -
323A SER* 2.7 35.5 + - - +
325A GLU* 1.3 110.4 - - + +
327A CYS* 1.3 68.0 + - - +
328A TYR* 4.2 11.4 - - + -
411A TYR* 4.4 7.6 - + - -
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Residues in contact with CYS 327 (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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281A VAL 3.5 0.7 - - - +
282A LYS* 3.4 5.9 - - - +
283A PHE* 3.0 57.2 + - + -
285A LYS* 3.5 33.4 - - - -
293A LEU* 4.2 7.9 - - - -
297A LEU* 4.1 15.5 - - + -
321A LYS 3.2 5.6 - - - +
322A ALA* 4.0 17.9 - - - -
326A PHE* 1.3 73.1 - - - +
328A TYR* 1.3 66.7 + - - +
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Residues in contact with TYR 328 (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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280A ALA* 4.7 10.1 - - + -
281A VAL 3.2 4.5 - - - +
282A LYS* 3.8 33.6 + - + -
297A LEU* 5.3 0.3 - - - +
320A PHE* 2.9 8.8 - - - +
321A LYS* 2.7 45.4 + - + +
323A SER* 3.9 19.5 - - - -
325A GLU* 3.9 9.0 + - - -
326A PHE* 4.2 14.4 - - + -
327A CYS* 1.3 79.4 - - - +
329A LEU* 1.3 65.2 + - - +
330A LEU* 3.5 17.5 - - + -
415A ILE* 5.9 1.3 - - + -
420A LEU* 5.5 0.4 - - + -
423A GLU* 2.7 41.9 + - + -
424A PRO* 3.1 21.0 - - + +
425A VAL* 3.5 19.1 - - + -
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Residues in contact with LEU 329 (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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280A ALA* 3.0 5.0 - - - -
281A VAL* 2.8 42.3 + - + +
283A PHE* 3.9 19.7 - - + -
297A LEU* 4.0 24.5 - - + +
300A ALA* 3.8 19.5 - - + -
301A SER* 3.6 18.4 - - - +
304A ILE* 3.7 27.4 - - + -
319A ALA 3.5 3.6 - - - -
320A PHE* 3.8 7.9 - - + -
328A TYR* 1.3 80.2 - - - +
330A LEU* 1.3 62.4 + - - +
331A PHE* 3.7 19.5 - - + -
408A ILE* 4.6 3.6 - - + -
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Residues in contact with LEU 330 (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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279A PHE 3.6 3.1 - - - +
280A ALA* 3.9 10.5 - - + -
318A SER* 3.2 1.4 - - - -
319A ALA* 2.8 41.5 + - + +
320A PHE* 4.3 4.9 - - - +
321A LYS 4.8 0.7 - - - +
328A TYR* 3.5 31.6 - - + +
329A LEU* 1.3 79.7 - - - +
331A PHE* 1.3 79.3 + - - +
420A LEU* 5.6 0.2 - - + -
425A VAL* 4.0 13.0 - - + -
428A GLU* 3.6 30.5 - - + -
429A LEU* 3.5 32.1 - - + +
432A MET* 4.0 7.2 - - - -
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Residues in contact with PHE 331 (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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277A ALA 3.6 1.1 - - - +
278A VAL* 3.3 7.6 - - - +
279A PHE* 2.9 66.9 + + + +
281A VAL* 4.1 8.7 - - + -
301A SER* 3.7 20.6 - - - -
304A ILE* 3.4 34.1 - - + -
305A PHE* 4.1 7.4 - + - -
308A LEU* 3.9 19.5 - - + -
315A PRO* 6.1 0.2 - - + -
317A ARG 3.8 6.3 - - - +
318A SER* 3.5 25.6 - - - -
329A LEU* 3.7 34.3 - - + -
330A LEU* 1.3 83.4 - - - +
332A GLU* 1.3 61.0 + - - +
333A CYS* 5.0 0.2 - - - -
432A MET* 4.0 3.8 - - - +
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Residues in contact with GLU 332 (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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274A ARG* 2.7 45.1 + - - -
276A THR* 2.8 33.3 + - - +
277A ALA 3.1 3.6 - - - -
278A VAL* 3.8 6.2 - - + +
315A PRO* 3.5 3.1 - - - +
316A LEU* 2.7 53.1 + - + +
317A ARG* 3.5 11.2 + - - +
331A PHE* 1.3 76.2 - - - +
333A CYS* 1.3 56.6 + - - +
432A MET* 3.9 18.7 - - + +
433A MET* 3.7 17.4 - - - +
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Residues in contact with CYS 333 (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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276A THR* 2.8 25.9 - - - -
277A ALA* 2.9 19.2 + - + +
279A PHE* 4.3 5.8 - - - -
308A LEU* 3.8 28.3 - - - -
313A PHE* 3.3 15.7 - - - +
314A MET 3.6 4.5 - - - -
315A PRO* 3.7 22.4 - - - -
316A LEU* 4.3 1.3 - - - +
332A GLU* 1.3 77.3 - - - +
334A GLN* 1.3 62.8 + - - +
335A ILE 4.1 3.6 - - - +
385A PRO* 4.3 22.2 - - + -
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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