Contacts of the helix formed by residues 357 - 369 (chain A) in PDB entry 3NZI
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 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A LEU* 4.0 10.1 - - - +
268A GLY 3.2 18.7 + - - -
270A SER* 3.2 19.8 + - - -
339A VAL* 3.2 25.1 - - - -
340A ILE* 3.1 18.8 + - - -
341A GLY 4.0 0.4 - - - -
356A PRO* 1.3 73.4 - - - +
358A ASP* 1.3 52.0 + - - +
360A ILE* 3.1 17.5 - - - +
361A LYS* 2.7 33.1 + - - +
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Residues in contact with ASP 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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268A GLY 3.3 12.3 - - - +
269A ARG* 3.4 6.9 + - - +
270A SER* 3.1 27.6 + - - +
271A SER* 3.3 31.7 + - - -
356A PRO* 3.2 2.1 - - + -
357A SER* 1.3 75.1 - - - +
359A LYS* 1.3 65.0 + - + +
361A LYS* 3.4 21.5 + - - +
362A LYS* 3.2 19.6 + - - +
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Residues in contact with LYS 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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251A ILE* 4.0 5.3 - - + +
313A ASP 5.0 8.5 + - - -
314A MET* 3.2 37.5 - - + -
315A ASP* 5.6 2.0 - - - +
355A ILE* 4.3 8.1 - - + -
356A PRO* 3.4 16.4 + - + +
357A SER 3.4 0.2 - - - -
358A ASP* 1.3 74.9 - - + +
360A ILE* 1.3 67.8 + - - +
362A LYS* 3.3 20.8 + - + +
363A PHE* 3.2 18.2 + - - +
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Residues in contact with ILE 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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207A PHE* 4.9 1.8 - - + -
216A VAL* 4.8 13.2 - - + -
251A ILE* 3.8 17.0 - - + +
267A LEU* 3.8 15.9 - - + -
339A VAL* 4.7 7.2 - - + -
341A GLY 4.2 2.7 - - - -
342A ILE* 3.4 42.8 - - + +
355A ILE* 3.9 10.3 - - + +
356A PRO 3.1 17.6 + - - +
357A SER* 3.1 17.5 + - - +
359A LYS* 1.3 76.5 - - - +
361A LYS* 1.3 64.0 + - - +
363A PHE* 2.9 13.3 + - - +
364A LEU* 2.8 37.6 + - + +
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Residues in contact with LYS 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 4.0 21.9 + - + -
268A GLY 4.7 3.2 + - - +
269A ARG* 3.9 30.7 - - - +
357A SER 2.7 15.6 + - - +
358A ASP* 3.4 25.0 + - - +
359A LYS 3.3 0.2 - - - -
360A ILE* 1.3 72.3 - - - +
362A LYS* 1.3 66.2 + - - +
364A LEU* 2.8 22.6 + - + +
365A THR* 3.1 20.6 + - - +
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Residues in contact with LYS 362 (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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358A ASP 3.2 10.2 + - - +
359A LYS* 3.3 24.3 - - + +
361A LYS* 1.3 78.6 - - - +
363A PHE* 1.3 64.9 + - - +
364A LEU 3.0 0.2 + - - -
365A THR* 3.0 13.9 + - - -
366A GLU* 3.1 49.6 + - + +
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Residues in contact with PHE 363 (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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216A VAL* 5.6 0.4 - - + -
244A ASP* 3.8 26.3 - - + +
246A ASP* 3.6 44.4 - - + +
251A ILE* 3.6 35.9 - - + -
252A ALA* 3.9 9.9 - - - -
253A LEU* 3.6 49.1 - - + -
359A LYS 3.2 2.3 + - - +
360A ILE 2.9 11.9 + - - +
362A LYS* 1.3 77.9 - - - +
364A LEU* 1.3 71.4 + - + +
366A GLU* 3.6 9.9 + - - +
367A SER* 3.5 18.7 + - - -
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Residues in contact with LEU 364 (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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209A VAL* 4.7 14.4 - - + -
214A LEU* 6.4 0.7 - - + -
216A VAL* 4.3 11.4 - - + -
253A LEU* 3.1 36.8 - - + -
267A LEU* 4.5 6.5 - - + -
360A ILE* 2.8 55.1 + - + +
361A LYS* 2.8 16.7 + - + +
363A PHE* 1.3 77.0 - - + +
365A THR* 1.3 60.8 + - - +
367A SER* 2.9 20.8 + - - -
368A HIS* 3.1 15.5 + - - +
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Residues in contact with THR 365 (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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361A LYS* 3.1 16.5 + - - +
362A LYS* 3.0 9.5 + - - -
364A LEU* 1.3 78.3 - - - +
366A GLU* 1.3 60.9 + - + +
367A SER 3.1 0.2 - - - -
368A HIS* 4.5 4.8 - - - +
369A ASP* 3.2 32.7 + - + +
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Residues in contact with GLU 366 (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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244A ASP* 4.6 3.7 - - - +
362A LYS* 3.1 53.7 + - + +
363A PHE* 3.9 8.7 - - - +
365A THR* 1.3 78.6 - - + +
367A SER* 1.3 56.9 + - - +
369A ASP* 3.3 15.8 - - - +
370A ARG* 3.6 9.9 - - - +
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Residues in contact with SER 367 (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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243A LYS* 4.9 2.3 + - - +
244A ASP* 3.1 36.2 + - - +
253A LEU* 4.9 9.0 - - - +
363A PHE* 3.5 12.0 + - - -
364A LEU* 2.9 12.2 + - - -
366A GLU* 1.3 78.7 - - - +
368A HIS* 1.3 66.7 + - - +
369A ASP 3.3 1.6 - - - -
370A ARG 3.5 16.6 - - - -
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Residues in contact with HIS 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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214A LEU* 6.1 4.5 - - + -
364A LEU 3.1 12.8 + - - +
365A THR* 4.5 4.7 - - - +
367A SER* 1.3 77.2 - - - +
369A ASP* 1.3 58.0 + - - +
370A ARG 3.5 4.7 + - - -
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Residues in contact with ASP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 3.2 20.0 + - + +
366A GLU* 3.3 18.9 - - - +
367A SER 4.1 0.2 - - - -
368A HIS* 1.3 75.0 + - - +
370A ARG* 1.3 69.9 + - - +
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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