Contacts of the helix formed by residues 314 - 321 (chain A) in PDB entry 1ZEB
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 ARG 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A THR* 3.5 27.7 + - - +
149A THR* 4.2 3.8 - - + -
273A ASP* 4.0 13.1 + - - +
274A MET 2.8 36.2 + - - -
275A LYS* 3.8 6.2 - - - +
276A TYR* 3.4 61.4 + - + +
312A GLY 3.3 0.6 - - - -
313A GLY* 1.3 78.7 - - - +
315A ILE* 1.3 66.5 + - - +
316A ASP 3.1 0.9 - - - -
317A HIS* 3.0 35.1 + - - +
318A GLY* 3.0 18.7 + - - -
321A GLU* 4.6 3.0 + - - -
330A GLU* 3.5 21.6 + - - +
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Residues in contact with ILE 315 (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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41A GLY* 3.8 21.1 - - - -
42A ASP 3.2 12.1 - - - +
43A GLY 4.2 2.7 - - - -
44A MET* 4.1 13.0 - - + +
48A THR* 4.0 16.2 - - + -
312A GLY 3.4 16.6 - - - +
314A ARG* 1.3 77.5 - - - +
316A ASP* 1.3 62.8 + - - +
318A GLY 3.2 0.5 + - - -
319A HIS* 3.1 22.6 + - + +
327A ALA* 3.6 12.6 - - - +
330A GLU* 3.6 13.3 - - + +
331A THR* 3.5 47.6 - - - +
334A PHE* 4.1 16.2 - - + -
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Residues in contact with ASP 316 (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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42A ASP* 2.8 34.3 + - - +
92A SEP 2.7 15.3 + - - -
313A GLY 3.9 7.4 + - - +
315A ILE* 1.3 74.3 - - - +
317A HIS* 1.3 65.8 + - - +
319A HIS 3.2 2.6 + - - -
320A HIS* 2.9 39.3 + - - -
358A HIS* 3.2 3.8 - - - -
360A HIS* 2.8 29.5 + - - -
432A HIS* 3.0 2.8 + - - -
901A ZN 2.0 38.8 - - - -
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Residues in contact with HIS 317 (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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92A SEP 5.4 0.4 + - - -
149A THR* 3.9 13.2 - - + +
150A ARG* 4.8 1.1 - - - -
153A HIS* 4.1 20.6 + + - -
273A ASP* 3.1 28.3 - - - -
276A TYR* 3.2 16.4 - - + +
313A GLY 3.9 9.8 + - - -
314A ARG* 3.0 38.4 + - - +
316A ASP* 1.3 88.7 + - + +
318A GLY* 1.3 66.9 + - - +
320A HIS* 3.3 12.1 + + - +
321A GLU* 3.1 28.6 + - - +
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Residues in contact with GLY 318 (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 TYR* 3.2 8.8 + - - -
314A ARG 3.0 12.3 + - - -
315A ILE 3.6 3.8 - - - -
317A HIS* 1.3 75.4 - - - +
319A HIS* 1.3 58.3 + - - +
321A GLU* 3.2 6.6 + - - +
322A SER 3.2 2.9 + - - -
323A ARG 2.9 33.2 + - - -
326A ARG* 4.0 7.6 - - - -
327A ALA* 3.7 18.4 - - - -
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Residues in contact with HIS 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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43A GLY 3.9 4.5 - - - -
48A THR* 2.7 32.6 + - + +
315A ILE* 3.1 15.3 + - + -
316A ASP 3.6 4.3 - - - +
318A GLY* 1.3 75.8 - - - +
320A HIS* 1.3 54.9 + - - +
322A SER* 2.7 23.6 + - - -
324A ALA* 4.9 0.2 - - - -
327A ALA* 3.4 20.5 - - + +
328A LEU* 4.8 1.1 - - + -
360A HIS* 3.3 42.8 - + + +
362A PHE* 3.4 32.2 - + - -
393A TYR* 2.5 32.4 + + + -
430A GLU* 3.2 16.0 - - - +
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Residues in contact with HIS 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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316A ASP* 2.9 37.3 + - - -
317A HIS* 3.3 13.9 + + - +
319A HIS* 1.3 74.5 - - - +
321A GLU* 1.3 60.0 + - + +
322A SER 3.1 0.6 + - - -
360A HIS* 3.6 4.2 - + - -
397A PRO* 3.6 4.0 - - - +
428A ASP 4.1 0.9 - - - +
429A GLU* 3.4 38.7 + - + +
430A GLU* 2.6 50.8 + - - -
431A THR* 4.8 0.4 - - - -
432A HIS* 3.2 21.3 - + - -
901A ZN 2.1 30.4 - - - -
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Residues in contact with GLU 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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276A TYR* 2.7 30.2 + - - -
314A ARG* 4.6 3.8 + - - -
317A HIS* 3.1 9.1 + - - +
318A GLY* 3.6 7.2 - - - +
319A HIS 3.2 0.2 - - - -
320A HIS* 1.3 77.2 - - + +
322A SER* 1.3 67.3 + - - +
323A ARG* 3.0 20.8 + - + +
326A ARG* 2.9 34.1 + - - -
397A PRO* 3.5 2.1 - - - +
420A ARG* 2.8 42.3 + - - +
428A ASP 5.6 0.2 - - - -
429A GLU* 5.7 2.7 - - - +
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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