Contacts of the helix formed by residues 345 - 352 (chain 8) in PDB entry 3ZPV
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 345 (chain 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7597 ASP* 3.1 43.9 + - - +
7607 ASN* 4.0 20.0 - - + +
3388 VAL* 3.5 12.9 - - - +
3438 PHE* 3.8 3.6 - - - +
3448 GLN* 1.3 85.0 - - + +
3468 ILE* 1.3 64.0 + - - +
3478 ILE* 3.5 2.7 + - - +
3488 ALA* 3.1 20.6 + - - +
3498 TYR* 3.3 8.8 + - - +
7929 GLU* 3.3 22.7 - - - +
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Residues in contact with ILE 346 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3268 PHE* 3.3 35.4 - - + -
3318 ALA* 4.7 5.4 - - + +
3348 GLY* 3.6 22.2 - - - -
3358 ALA* 3.8 2.7 - - + +
3388 VAL* 3.7 1.7 - - - +
3458 THR* 1.3 69.4 - - - +
3478 ILE* 1.3 64.6 + - + +
3498 TYR* 3.4 9.7 + - - +
3508 HIS 3.0 21.8 + - - -
7859 ALA* 5.3 0.7 - - - +
7889 MET* 2.7 51.8 - - + +
7899 LEU* 3.9 29.8 - - + +
7929 GLU* 3.5 16.4 + - + +
7959 ALA* 4.1 6.1 - - + -
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Residues in contact with ILE 347 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7597 ASP* 3.8 22.4 - - + +
3198 MET* 4.0 6.7 - - + -
3248 PHE* 3.8 45.1 - - + -
3268 PHE* 4.0 11.2 - - + -
3458 THR* 3.1 6.9 - - - +
3468 ILE* 1.3 76.2 - - + +
3488 ALA* 1.3 65.0 + - - +
3508 HIS* 3.1 15.0 + - - +
3518 CYS* 3.1 18.2 + - - -
7929 GLU* 4.0 19.5 - - + +
7949 PHE* 3.9 14.4 - - + -
7959 ALA* 3.9 28.0 - - + -
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Residues in contact with ALA 348 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7597 ASP* 3.8 8.2 + - - +
3438 PHE* 4.0 21.1 - - + -
3448 GLN* 4.7 4.3 - - + +
3458 THR* 3.1 25.9 + - - +
3478 ILE* 1.3 77.4 - - - +
3498 TYR* 1.3 63.8 + - - +
3518 CYS* 3.4 14.2 + - - +
3528 THR* 3.6 17.0 - - - +
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Residues in contact with TYR 349 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3268 PHE* 4.9 3.4 - + - -
3308 LEU* 3.8 28.1 - - + +
3338 LYS* 3.4 30.3 - - + +
3348 GLY* 3.5 26.0 - - - +
3378 SER* 3.2 28.7 - - - -
3438 PHE* 3.8 25.5 - + + -
3458 THR 3.3 5.7 + - - +
3468 ILE* 3.5 15.7 - - - +
3478 ILE 3.2 0.6 - - - -
3488 ALA* 1.3 78.4 - - - +
3508 HIS* 1.3 68.2 + - - +
3528 THR* 3.0 25.9 + - - -
3538 GLN 3.7 19.4 + - - +
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Residues in contact with HIS 350 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3248 PHE* 3.7 28.0 - + + -
3258 VAL* 2.9 33.0 + - - +
3268 PHE* 3.7 28.5 - + + -
3308 LEU* 3.8 15.7 - - + +
3468 ILE 3.0 14.5 + - - +
3478 ILE* 3.1 11.2 + - - +
3498 TYR* 1.3 82.7 - - - +
3518 CYS* 1.3 58.5 + - - +
3538 GLN* 2.9 23.7 + - - +
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Residues in contact with CYS 351 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3198 MET* 5.9 2.9 - - - -
3208 ALA* 6.3 0.9 - - - -
3248 PHE* 4.0 26.0 - - - -
3478 ILE* 3.1 21.2 + - - -
3488 ALA* 3.7 12.1 - - - +
3498 TYR 3.2 0.2 - - - -
3508 HIS* 1.3 76.8 - - - +
3528 THR* 1.3 60.7 + - + +
3538 GLN 3.3 2.1 + - - -
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Residues in contact with THR 352 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3438 PHE* 3.7 28.4 - - + -
3488 ALA 3.6 13.0 - - - +
3498 TYR* 3.0 12.5 + - - -
3508 HIS 3.2 0.2 - - - -
3518 CYS* 1.3 80.1 - - + +
3538 GLN* 1.3 68.6 + - - +
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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