Contacts of the helix formed by residues 396 - 407 (chain A) in PDB entry 1Z8G
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 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A HIS* 3.6 29.4 - + - -
256A ASN* 3.4 38.8 - - - -
258A ILE* 3.7 28.0 - - + -
335A LYS* 3.7 35.4 - - + -
391A THR* 3.4 27.6 - - + -
392A LYS 3.3 18.6 - - - -
393A VAL* 2.8 9.0 + - - +
395A ASP* 1.3 81.6 - - - +
397A ARG* 1.3 64.4 + - - +
398A GLU 3.3 2.7 - - - -
399A TRP* 3.1 14.4 + - + -
400A ILE* 2.9 24.7 + - + +
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Residues in contact with ARG 397 (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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91A GLU* 2.9 32.9 + - - +
92A GLU* 3.9 2.2 - - - +
94A GLY* 4.2 2.4 - - - -
278A LEU* 4.9 6.0 - - + +
279A PRO* 2.9 43.8 + - + +
280A ALA* 3.9 8.2 - - - +
281A ALA* 3.5 34.1 - - - +
282A GLY 5.4 0.9 - - - +
393A VAL* 3.4 4.1 + - + +
394A SER* 3.5 30.1 + - - +
395A ASP 3.7 0.6 - - - -
396A PHE* 1.3 77.7 - - - +
398A GLU* 1.3 74.2 + - + +
400A ILE* 3.2 8.4 + - - +
401A PHE* 3.0 54.3 + - + -
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Residues in contact with GLU 398 (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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88A LEU* 6.1 0.5 - - - +
91A GLU* 4.8 6.2 - - - +
129A GLN* 4.1 40.8 + - - +
396A PHE 3.3 0.4 - - - -
397A ARG* 1.3 86.8 + - + +
399A TRP* 1.3 66.7 + - - +
401A PHE* 3.7 26.3 - - - +
402A GLN* 3.0 29.8 + - - +
405A LYS* 5.9 0.5 + - - -
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Residues in contact with TRP 399 (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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238A VAL* 3.6 29.4 - - + -
239A TYR 3.9 4.9 - - - -
240A HIS* 3.4 43.9 - + + +
258A ILE* 4.2 24.7 - - + -
259A ALA* 4.1 9.9 - - - -
260A LEU* 3.7 27.4 - - + -
396A PHE* 3.1 20.5 + + + +
398A GLU* 1.3 77.8 - - - +
400A ILE* 1.3 71.3 + - + +
402A GLN* 3.9 2.8 - - - +
403A ALA* 2.9 34.5 + - + +
416A GLN* 2.9 29.2 + - + +
417A LEU* 3.5 23.6 - - - -
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Residues in contact with ILE 400 (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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96A LEU* 4.4 3.6 - - + -
193A LEU* 3.8 23.6 - - + -
199A LEU* 3.9 33.4 - - + -
258A ILE* 4.4 4.9 - - + -
260A LEU* 4.3 5.4 - - + -
278A LEU* 4.1 29.2 - - + -
393A VAL* 4.2 8.5 - - + -
396A PHE 2.9 24.6 + - - +
397A ARG* 3.5 7.4 - - - +
399A TRP* 1.3 90.9 - - + +
401A PHE* 1.3 66.0 + - - +
403A ALA* 3.3 1.9 + - - +
404A ILE* 3.2 35.6 + - + +
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Residues in contact with PHE 401 (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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91A GLU* 3.7 49.4 - - + +
95A PHE 3.7 9.9 - - - -
96A LEU* 3.5 35.0 - - + -
278A LEU* 3.8 24.2 - - + -
397A ARG* 3.0 58.0 + - + +
398A GLU* 3.7 23.8 - - - +
400A ILE* 1.3 76.6 - - - +
402A GLN* 1.3 60.3 + - - +
404A ILE* 3.6 4.5 + - - +
405A LYS* 3.1 35.3 + - - +
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Residues in contact with GLN 402 (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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398A GLU* 3.0 20.0 + - - +
399A TRP* 4.2 2.7 - - - +
401A PHE* 1.3 75.1 - - - +
403A ALA* 1.3 61.3 + - - +
405A LYS* 3.2 23.6 + - - +
406A THR* 2.8 59.7 + - - +
416A GLN* 6.0 5.2 - - - +
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Residues in contact with ALA 403 (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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197A TRP* 4.8 1.4 - - - -
238A VAL* 4.1 17.8 - - + +
260A LEU* 3.6 24.0 - - + -
399A TRP* 2.9 24.8 + - + +
400A ILE 3.3 0.4 + - - +
402A GLN* 1.3 75.8 - - - +
404A ILE* 1.3 58.0 + - - +
406A THR* 4.7 0.4 - - - -
407A HIS* 2.9 42.1 + - - +
416A GLN* 4.5 12.5 - - + +
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Residues in contact with ILE 404 (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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96A LEU* 3.7 36.3 - - + -
97A ARG* 3.6 27.4 - - - +
193A LEU* 4.8 1.1 - - + -
197A TRP* 3.8 43.5 - - + +
260A LEU* 4.0 16.4 - - + -
400A ILE* 3.2 24.2 + - + +
401A PHE* 4.0 4.7 - - - +
403A ALA* 1.3 75.7 - - - +
405A LYS* 1.3 63.6 + - + +
408A SER* 3.2 24.8 + - - -
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Residues in contact with LYS 405 (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* 3.9 18.0 - - - +
91A GLU* 2.9 32.3 + - - -
97A ARG* 6.5 0.9 - - - -
398A GLU* 5.9 0.4 + - - -
401A PHE* 3.1 24.9 + - - +
402A GLN* 3.2 27.0 + - - +
404A ILE* 1.3 80.4 - - + +
406A THR* 1.3 64.9 + - - +
408A SER* 3.6 13.9 + - - -
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Residues in contact with THR 406 (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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402A GLN* 2.8 44.0 + - - +
403A ALA* 4.7 0.2 - - - -
405A LYS* 1.3 73.7 - - - +
407A HIS* 1.3 88.0 + - + +
408A SER* 3.8 1.2 + - - -
416A GLN* 4.3 8.0 + - - +
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Residues in contact with HIS 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TRP* 3.8 11.9 - - - -
236A ALA* 5.6 1.0 - - - +
238A VAL* 3.9 34.3 - - + +
262A HIS* 4.7 0.9 + - - -
403A ALA* 2.9 23.0 + - - +
404A ILE 3.9 2.2 - - - -
406A THR* 1.3 94.2 + - + +
408A SER* 1.3 64.4 + - - +
409A GLU 3.1 4.5 + - - -
410A ALA* 3.2 28.3 + - + +
414A VAL* 3.3 28.8 - - + +
415A THR 4.5 1.3 - - - -
416A GLN* 2.8 30.9 + - - +
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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