Contacts of the helix formed by residues 348 - 360 (chain A) in PDB entry 1ZHH
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 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A ALA 3.6 2.0 + - - -
347A ASP* 1.3 76.0 - - - +
349A PRO* 1.3 75.5 - - - +
350A GLU* 3.5 13.0 + - - +
351A ARG* 3.0 34.2 + - - +
352A ILE* 3.1 14.5 + - - +
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Residues in contact with PRO 349 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A GLN* 3.8 26.8 + - - +
347A ASP 4.3 2.0 - - - +
348A SER* 1.3 87.7 - - - +
350A GLU* 1.3 56.6 + - - +
352A ILE* 3.4 1.6 + - - +
353A GLU* 3.0 31.4 + - - +
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Residues in contact with GLU 350 (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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348A SER* 3.1 11.5 + - - +
349A PRO* 1.3 80.0 - - - +
351A ARG* 1.3 57.4 + - - +
353A GLU* 3.5 5.7 + - - +
354A ALA* 3.0 29.2 + - + +
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Residues in contact with ARG 351 (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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341A GLU* 3.8 21.8 + - - +
342A ILE 5.0 5.1 + - - -
347A ASP* 4.0 25.6 + - + +
348A SER* 3.0 27.3 + - - +
350A GLU* 1.3 73.7 - - - +
352A ILE* 1.3 60.5 + - - +
354A ALA* 3.2 12.7 + - - +
355A LEU* 3.0 61.8 + - + +
358A ARG* 6.0 0.4 - - - +
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Residues in contact with ILE 352 (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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296A LEU* 4.2 15.3 - - + -
299A ILE* 4.2 17.9 - - + -
300A GLN* 3.7 40.6 - - + +
309A MET* 5.1 0.8 - - - +
343A VAL* 3.8 19.7 - - + -
347A ASP* 4.1 19.1 - - + +
348A SER 3.1 17.3 + - - +
349A PRO 4.0 3.8 - - - +
350A GLU 3.4 0.2 - - - -
351A ARG* 1.3 74.4 - - + +
353A GLU* 1.3 63.9 + - - +
355A LEU* 3.2 9.5 + - - +
356A LYS* 3.0 46.1 + - - +
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Residues in contact with GLU 353 (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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349A PRO 3.0 18.5 + - - +
350A GLU* 3.8 5.6 - - - +
352A ILE* 1.3 77.4 - - - +
354A ALA* 1.3 58.4 + - - +
356A LYS* 3.2 24.9 + - - +
357A LYS* 3.0 66.6 + - - +
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Residues in contact with ALA 354 (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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350A GLU* 3.0 15.9 + - + +
351A ARG* 3.2 18.4 + - - +
353A GLU* 1.3 76.8 - - - +
355A LEU* 1.3 61.5 + - + +
357A LYS* 3.4 11.0 + - - +
358A ARG* 3.1 23.4 + - - +
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Residues in contact with LEU 355 (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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309A MET* 3.7 17.0 - - - +
311A MET* 4.0 7.4 - - + +
341A GLU* 3.9 25.6 - - + -
342A ILE 4.6 2.2 - - - +
343A VAL* 3.6 32.1 - - + -
347A ASP* 5.3 0.2 - - - +
351A ARG* 3.0 62.1 + - + +
352A ILE* 3.2 10.1 + - - +
354A ALA* 1.3 77.9 - - - +
356A LYS* 1.3 56.1 + - - +
358A ARG* 3.3 14.1 + - - +
359A ALA* 2.9 30.5 + - - +
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Residues in contact with LYS 356 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A SER* 5.9 4.0 - - - +
296A LEU* 3.4 38.5 - - + +
297A ASP* 5.0 5.9 + - - -
300A GLN* 4.0 16.8 + - - +
309A MET* 4.0 7.6 - - + -
352A ILE* 3.0 23.8 + - - +
353A GLU* 3.2 29.6 + - - +
355A LEU* 1.3 74.6 - - - +
357A LYS* 1.3 59.0 + - - +
359A ALA* 3.4 0.6 + - - -
360A PHE* 3.0 51.2 + - + +
364A ASP* 4.7 1.1 - - - +
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Residues in contact with LYS 357 (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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353A GLU* 3.0 54.1 + - - +
354A ALA* 3.8 8.8 - - - +
355A LEU 3.3 0.2 - - - -
356A LYS* 1.3 75.5 - - + +
358A ARG* 1.3 58.0 + - - +
360A PHE* 3.4 1.9 - - - -
361A ARG* 2.9 31.7 + - - +
364A ASP* 5.5 2.9 - - - -
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Residues in contact with ARG 358 (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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53A ARG* 4.9 10.3 - - - +
311A MET* 3.7 19.8 - - - +
314A ASP* 5.1 1.0 + - - -
339A ASP* 3.5 36.0 + - - +
341A GLU* 3.0 36.1 + - - +
351A ARG* 5.8 0.6 - - - +
354A ALA 3.1 16.8 + - - +
355A LEU* 3.6 13.3 - - - +
356A LYS 3.2 0.2 - - - -
357A LYS* 1.3 75.3 - - - +
359A ALA* 1.3 64.1 + - - +
360A PHE 3.2 0.7 + - - -
361A ARG* 3.0 48.0 + - - +
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Residues in contact with ALA 359 (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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309A MET* 4.1 11.2 - - + -
310A ARG 3.7 22.9 - - - +
311A MET* 3.8 16.8 - - - +
312A ASN* 3.6 4.0 - - - +
313A ASP* 2.9 32.9 + - - +
355A LEU 2.9 17.6 + - - +
356A LYS 3.4 4.7 + - - +
358A ARG* 1.3 76.9 - - - +
360A PHE* 1.3 69.7 + - + +
361A ARG 3.5 0.2 - - - -
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Residues in contact with PHE 360 (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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84A ARG* 3.5 42.8 - - - -
292A GLY* 6.4 2.0 - - - -
296A LEU* 6.4 0.4 - - + -
309A MET* 5.3 4.0 - - + -
312A ASN* 3.6 31.6 - - + -
313A ASP* 3.1 9.6 - - - -
356A LYS* 3.0 39.0 + - + +
357A LYS* 3.4 4.5 - - - -
359A ALA* 1.3 85.8 - - + +
361A ARG* 1.3 64.3 + - - +
363A SER* 3.6 8.1 - - - +
364A ASP* 3.1 47.3 + - - +
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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