Contacts of the strand formed by residues 360 - 364 (chain A) in PDB entry 1ZJA
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 THR 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A TRP 2.6 27.3 + - - +
8A LYS* 3.6 3.6 + - - -
10A ALA 3.6 10.1 - - - +
12A PHE* 3.5 34.8 - - + -
276A MET* 3.9 13.4 - - - -
318A TRP* 2.8 19.0 + - - -
319A ASN 2.8 8.8 + - - -
320A THR* 3.1 4.8 - - - +
321A PHE 2.8 20.7 + - - -
359A GLY* 1.3 72.2 - - - -
361A PRO* 1.3 61.9 - - - +
362A PHE* 3.4 12.2 - - + -
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Residues in contact with PRO 361 (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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10A ALA 3.6 12.3 - - - +
11A VAL* 3.9 6.8 - - + +
12A PHE* 2.9 29.2 + - - +
321A PHE* 3.3 10.5 - - + +
354A THR* 3.6 33.7 - - + +
355A LEU* 4.0 17.5 - - + -
357A GLN 5.6 0.2 - - - +
359A GLY 3.3 10.5 - - - +
360A THR* 1.3 85.1 - - - +
362A PHE* 1.3 60.6 + - - +
363A ILE* 4.1 1.1 - - + -
470A ARG* 3.3 26.0 - - - +
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Residues in contact with PHE 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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12A PHE* 3.4 40.4 - + + -
13A TYR 5.2 0.2 - - - -
14A GLN* 5.0 9.0 - - + +
50A TRP* 3.8 33.7 - + + -
97A MET* 4.1 5.6 - - - -
276A MET* 3.9 14.1 - - + -
278A PHE* 3.6 23.8 - + + -
320A THR* 3.6 28.5 - - + -
321A PHE 3.0 10.8 + - - +
322A PHE* 3.8 25.0 - - + +
323A LEU 4.9 1.2 + - - -
324A GLY 4.7 3.2 + - - +
354A THR* 4.6 4.9 - - - +
360A THR* 3.4 27.4 - - + -
361A PRO* 1.3 74.5 - - - +
363A ILE* 1.3 64.6 + - - +
364A PHE 3.8 1.7 + - - -
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Residues in contact with ILE 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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11A VAL* 4.0 17.0 - - + -
12A PHE 2.8 12.6 + - - +
13A TYR* 3.3 20.0 - - + -
14A GLN* 2.9 24.3 + - - -
44A LEU* 5.5 2.0 - - + -
46A ILE* 4.4 5.4 - - + -
354A THR* 4.6 13.0 - - + -
355A LEU* 4.4 7.9 - - + -
361A PRO 5.5 0.4 - - - -
362A PHE* 1.3 73.9 - - - +
364A PHE* 1.3 70.5 + - - +
365A GLN 3.7 0.2 + - - -
367A ASP* 4.7 3.6 - - + -
368A GLU* 4.3 15.7 - - + +
463A TYR* 3.8 38.6 - - + +
467A ILE* 3.9 22.9 - - + -
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Residues in contact with PHE 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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14A GLN* 3.5 35.7 - - + +
16A TYR* 4.3 11.9 - + + -
324A GLY* 3.7 18.3 + - - +
325A ASN* 3.6 12.6 - - - -
326A HIS* 3.7 19.5 - - + -
330A ARG* 3.6 22.9 - - - -
362A PHE 3.8 3.0 + - - -
363A ILE* 1.3 77.0 - - - +
365A GLN* 1.3 90.3 - - + +
366A GLY 3.2 0.2 + - - -
367A ASP* 2.9 37.2 + - - +
417A ALA* 3.1 43.7 - - + -
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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