Contacts of the helix formed by residues 308 - 315 (chain B) in PDB entry 4ZTZ
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 ASP 308 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B PRO* 5.4 3.1 - - - +
306B LEU* 2.7 13.1 + - - +
307B GLY* 1.3 84.7 - - - +
309B HIS* 1.3 59.5 + - - +
310B GLU 3.7 1.1 - - - -
311B LEU* 4.3 5.6 - - + -
312B LEU* 3.2 39.9 + - + +
332B VAL* 3.7 25.3 - - + +
333B PRO 3.2 25.9 - - - +
334B CYS* 4.3 6.4 - - - +
335B VAL* 4.2 12.6 - - - +
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Residues in contact with HIS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ARG* 4.4 20.2 - - - +
306B LEU* 4.9 2.9 - - + +
307B GLY 2.8 13.2 + - - +
308B ASP* 1.3 73.6 - - - +
310B GLU* 1.3 72.5 + - + +
312B LEU* 3.2 10.2 + - - +
313B HIS* 2.9 38.3 + + + +
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 5.8 2.7 - - + -
187B HIS* 3.7 27.0 - - - +
190B LEU* 3.7 27.8 - - + -
306B LEU* 5.9 8.2 - - + +
308B ASP* 4.7 0.2 - - - +
309B HIS* 1.3 88.7 + - + +
311B LEU* 1.3 57.6 + - + +
313B HIS* 3.2 18.6 + - - +
314B MET* 2.9 40.4 + - - +
335B VAL* 6.2 1.7 - - + +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 3.9 39.3 - - + +
193B TYR* 4.5 16.4 - - + -
242B PHE* 4.0 14.8 - - + -
308B ASP* 4.3 7.9 + - + +
309B HIS 3.3 0.8 - - - -
310B GLU* 1.3 78.6 - - - +
312B LEU* 1.3 63.3 + - + +
314B MET* 3.4 7.7 + - - -
315B TYR* 3.2 26.3 + - + -
322B LEU* 3.3 23.4 - - + +
332B VAL* 6.2 0.4 - - + -
333B PRO* 3.9 26.7 - - + +
335B VAL* 3.7 31.6 - - + +
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Residues in contact with LEU 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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308B ASP* 3.2 39.2 + - + +
309B HIS* 3.2 11.1 + - - +
311B LEU* 1.3 80.6 - - + +
313B HIS* 1.3 60.2 + - - +
315B TYR 3.4 21.2 - - - +
316B PRO* 3.7 6.1 - - - +
319B VAL* 5.3 12.6 - - + +
322B LEU* 4.5 11.9 - - + -
332B VAL* 4.0 19.1 - - + -
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Residues in contact with HIS 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 HIS* 2.9 28.6 + + + +
310B GLU* 3.2 22.5 + - - +
312B LEU* 1.3 76.1 - - - +
314B MET* 1.3 64.2 + - - +
316B PRO* 3.8 13.4 - - - +
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Residues in contact with MET 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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187B HIS* 3.7 22.4 - - + -
190B LEU* 3.9 22.0 - - - +
191B GLU* 3.8 38.4 - - + -
310B GLU* 2.9 33.9 + - - +
311B LEU* 3.8 7.9 - - - +
312B LEU 3.3 0.2 - - - -
313B HIS* 1.3 79.7 - - - +
315B TYR* 1.3 89.2 + - + +
316B PRO* 3.5 6.9 - - - +
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Residues in contact with TYR 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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190B LEU 4.9 4.5 + - - -
191B GLU 4.2 15.2 + - - -
193B TYR* 5.6 2.5 - + + -
194B VAL* 3.6 22.1 + - + +
311B LEU* 3.2 20.3 + - + +
312B LEU* 3.4 10.0 - - - +
314B MET* 1.3 110.1 - - + +
316B PRO* 1.3 63.6 - - - +
317B GLY 3.4 2.2 + - - -
318B ASN 4.1 9.6 - - - +
319B VAL* 3.5 18.5 - - - +
321B LYS* 3.6 32.1 - - + -
322B LEU* 3.5 28.0 - - + +
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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
------------------------------------------------------------
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