Contacts of the helix formed by residues 311 - 319 (chain B) in PDB entry 4ZG9
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 PRO 311 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B VAL* 4.3 4.5 - - + -
172B ASP 3.2 10.1 - - - +
173B GLY 3.6 18.1 - - - +
174B PHE* 3.8 32.8 - - + -
178B TYR* 4.1 8.5 + - + -
310B GLN* 1.3 94.6 - - + +
312B ASP* 1.3 62.9 + - - -
313B PHE 3.3 0.2 + - - -
314B SER* 3.9 0.9 - - - -
315B GLY* 3.0 21.0 + - - -
325B MET* 4.5 9.6 - - - +
328B PRO* 5.0 7.2 - - + +
329B LEU* 3.9 22.4 - - + -
332B ILE* 5.3 4.9 - - + -
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Residues in contact with ASP 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ASP* 3.0 45.6 + - + +
173B GLY* 3.8 4.0 - - - -
309B GLU* 3.3 11.9 + - - +
311B PRO* 1.3 74.7 - - - +
313B PHE* 1.3 69.1 + - - +
315B GLY 3.1 8.5 + - - -
316B HIS* 2.9 25.5 + - - -
360B HIS* 3.7 1.0 - - - -
362B MET* 3.4 10.7 - - - +
475B HIS* 2.3 16.5 + - - -
904B ZN 1.9 38.8 - - - -
911B EDO 4.1 0.5 + - - -
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B GLU* 3.2 36.9 + - + +
310B GLN* 3.8 22.4 - - + +
311B PRO 3.3 0.2 - - - -
312B ASP* 1.3 83.8 + - - +
314B SER* 1.3 69.3 + - - +
316B HIS* 3.3 13.7 + + - +
317B LYS* 3.6 30.7 + - + +
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Residues in contact with SER 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B GLN* 2.9 29.2 + - - -
311B PRO 4.2 0.4 - - - -
313B PHE* 1.3 88.0 - - - +
315B GLY* 1.3 56.1 + - - +
317B LYS* 3.0 8.6 + - - -
318B TYR* 2.9 41.9 + - - -
325B MET* 3.1 22.5 - - - +
328B PRO* 3.6 15.8 - - - +
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Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TYR* 5.0 2.5 - - - -
311B PRO 3.0 15.5 + - - -
312B ASP 3.1 4.9 + - - -
314B SER* 1.3 72.6 - - - +
316B HIS* 1.3 59.9 + - - +
319B GLY* 3.0 28.6 + - - -
325B MET* 3.2 18.5 - - - +
362B MET* 3.8 17.7 - - - +
473B GLY* 3.6 8.7 - - - -
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Residues in contact with HIS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ASP* 2.9 33.2 + - - -
313B PHE* 3.8 8.3 - + - +
314B SER 3.2 0.4 - - - -
315B GLY* 1.3 75.7 - - - +
317B LYS* 1.3 58.0 + - - +
362B MET* 3.9 2.0 - - + +
470B PHE 5.0 0.2 - - - -
471B PHE* 4.1 12.3 - - + +
472B GLN 2.4 34.5 + - - -
473B GLY 2.9 26.2 + - - +
474B ASP* 3.5 22.5 + - - -
475B HIS* 3.4 13.2 - + - -
904B ZN 2.3 32.8 - - - -
911B EDO 3.6 4.6 + - - -
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Residues in contact with LYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B PHE* 3.6 28.5 + - + +
314B SER* 3.0 10.0 + - - +
316B HIS* 1.3 81.3 - - - +
318B TYR* 1.3 102.4 + - + +
469B CYS 5.7 0.2 - - - +
470B PHE 4.2 18.5 - - - +
471B PHE 4.5 0.7 - - - -
472B GLN* 3.4 18.9 + - - +
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Residues in contact with TYR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B SER* 2.9 30.1 + - - +
317B LYS* 1.3 122.1 + - + +
319B GLY* 1.3 67.8 + - - +
322B GLY* 3.5 15.6 + - - -
324B GLU* 3.5 59.5 - - + +
325B MET* 4.2 9.6 - - + -
364B ASP* 5.1 0.9 - - - +
472B GLN* 3.8 18.9 - - - +
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Residues in contact with GLY 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B GLY* 3.0 21.4 + - - -
317B LYS 3.7 0.8 - - - -
318B TYR* 1.3 84.4 - - - +
320B PRO* 1.3 76.1 - - - +
321B PHE 3.3 3.2 + - - -
322B GLY* 3.3 2.1 + - - -
325B MET* 3.2 17.7 - - - +
364B ASP* 4.3 3.6 - - - -
472B GLN* 3.6 16.8 - - - +
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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