Contacts of the helix formed by residues 324 - 334 (chain A) in PDB entry 2ZB8
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 ASN 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A ILE* 3.6 23.2 - - + +
320A ASN 2.9 21.4 + - - -
321A GLY 2.8 11.7 + - - +
323A GLU* 1.3 94.5 + - - +
325A MET* 1.3 57.8 + - - +
326A GLY 3.3 2.7 - - - -
327A ALA* 3.2 16.7 + - + +
328A ALA* 2.9 28.7 + - - +
343A VAL* 5.0 0.7 - - - -
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Residues in contact with MET 325 (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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6A VAL* 4.2 7.6 - - + -
46A LEU* 3.6 31.0 - - + -
47A SER 4.0 1.6 - - - +
48A VAL* 3.8 20.4 - - + +
103A TRP* 3.5 55.4 - - + -
322A LEU* 3.0 35.1 + - + +
323A GLU 3.4 1.0 - - - -
324A ASN* 1.3 76.8 - - - +
326A GLY* 1.3 58.6 + - - +
328A ALA* 3.3 5.4 + - - +
329A PHE* 2.9 29.2 + - - +
343A VAL* 3.5 31.6 - - + -
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Residues in contact with GLY 326 (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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6A VAL* 5.6 0.2 - - - +
19A VAL 4.7 0.9 - - - -
20A ALA* 3.7 16.3 - - - -
23A PHE* 3.6 36.4 - - - +
323A GLU 4.8 2.2 + - - -
324A ASN 3.3 0.4 - - - -
325A MET* 1.3 76.6 - - - +
327A ALA* 1.3 64.8 + - - +
329A PHE* 3.3 2.1 + - - +
330A GLN* 3.0 24.1 + - - +
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Residues in contact with ALA 327 (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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20A ALA* 3.8 16.4 - - + +
319A ILE* 4.9 4.3 - - + -
323A GLU 5.3 0.8 + - - +
324A ASN* 3.2 25.7 + - + +
326A GLY* 1.3 74.4 - - - +
328A ALA* 1.3 52.7 + - - +
330A GLN* 3.3 4.4 + - - +
331A SER* 2.7 37.0 + - - -
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Residues in contact with ALA 328 (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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48A VAL* 3.8 5.4 - - + +
319A ILE* 3.9 25.0 - - + +
324A ASN 2.9 17.4 + - - +
325A MET 3.6 4.5 - - - +
326A GLY 3.2 0.2 - - - -
327A ALA* 1.3 73.9 - - - +
329A PHE* 1.3 60.0 + - - +
331A SER* 3.3 1.6 + - - -
332A MET* 2.9 31.5 + - - +
341A GLN* 3.9 11.5 - - + +
343A VAL* 3.6 26.0 - - + -
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Residues in contact with PHE 329 (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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18A PRO* 3.6 20.6 - - + -
19A VAL 5.8 0.4 - - - -
23A PHE* 4.2 25.4 - + + -
48A VAL* 4.0 20.3 - - + +
49A ASP 3.5 23.8 - - - -
52A MET* 3.7 14.6 - - + -
53A ARG* 3.7 26.0 - - + -
56A MET* 3.5 21.8 - - - -
68A TRP* 5.8 0.2 - + - -
103A TRP* 5.2 2.2 - + + -
325A MET 2.9 17.5 + - - +
326A GLY 3.8 4.0 - - - +
328A ALA* 1.3 76.4 - - - +
330A GLN* 1.3 66.1 - - - +
332A MET* 3.3 19.4 + - + +
333A MET* 3.0 44.7 + - + +
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Residues in contact with GLN 330 (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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18A PRO 3.8 15.0 + - - +
19A VAL* 3.6 21.5 - - - +
20A ALA* 2.9 34.7 + - - +
21A GLU* 4.5 2.6 + - - +
326A GLY 3.0 16.2 + - - +
327A ALA* 3.6 4.9 - - - +
329A PHE* 1.3 83.8 - - - +
331A SER* 1.3 63.7 + - - +
333A MET* 3.4 3.9 + - - +
334A THR* 2.9 36.5 + - + +
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Residues in contact with SER 331 (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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319A ILE* 4.7 8.9 - - - +
327A ALA 2.7 22.9 + - - -
328A ALA* 3.6 7.6 - - - -
329A PHE 3.2 0.2 - - - -
330A GLN* 1.3 74.6 - - - +
332A MET* 1.3 62.7 + - - +
334A THR* 3.1 13.5 + - - -
335A GLY 3.1 0.2 + - - -
336A GLY* 2.8 43.9 + - - -
341A GLN* 4.4 7.4 + - - -
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Residues in contact with MET 332 (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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48A VAL* 3.9 6.3 - - + +
49A ASP 3.3 41.5 - - - +
50A PRO* 3.5 22.4 - - + -
328A ALA 2.9 20.8 + - - +
329A PHE* 3.6 26.0 - - + +
331A SER* 1.3 72.7 - - - +
333A MET* 1.3 73.2 + - + +
334A THR 3.1 1.0 + - - -
335A GLY 3.1 9.2 + - - -
337A ASN* 3.3 20.8 - - - +
341A GLN* 3.9 22.3 + - + -
700A NAP 3.2 38.0 - - - +
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Residues in contact with MET 333 (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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18A PRO* 4.1 12.3 - - + -
50A PRO* 4.0 8.1 - - - -
53A ARG* 4.1 21.3 - - + -
256A ILE* 4.0 28.5 - - + +
259A TYR* 4.4 7.4 - - + -
260A ASN* 4.3 22.6 + - - +
329A PHE* 3.0 48.9 + - + +
330A GLN 3.8 5.2 - - - +
332A MET* 1.3 97.3 - - + +
334A THR* 1.3 64.0 + - + +
700A NAP 3.2 25.6 + - - +
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Residues in contact with THR 334 (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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18A PRO* 5.8 2.5 - - + +
209A LYS* 4.9 10.8 + - - -
330A GLN* 2.9 28.2 + - + +
331A SER* 3.1 8.8 + - - -
333A MET* 1.3 85.3 - - + +
335A GLY* 1.3 59.5 + - - +
336A GLY* 3.6 1.2 + - - -
700A NAP 4.8 3.6 - - - -
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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