Contacts of the helix formed by residues 275 - 278 (chain I) in PDB entry 4ZZ7
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 SER 275 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I HIS* 4.7 4.2 - - - -
92I LYS* 3.9 28.3 + - - -
96I ASP* 3.0 32.9 + - - +
149I ASN 5.8 0.2 - - - -
150I PHE* 5.2 1.1 - - - -
273I PHE 3.5 0.2 + - - -
274I GLY* 1.3 71.0 - - - -
276I SER* 1.3 62.8 + - - +
278I GLU* 2.8 35.9 + - - +
279I ARG* 3.2 28.7 + - - -
320I PHE* 4.4 3.2 - - - +
321I GLY 5.8 0.2 - - - +
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Residues in contact with SER 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I HIS* 5.5 1.7 - - - -
92I LYS* 5.9 0.9 - - - +
273I PHE 2.9 12.9 + - - -
275I SER* 1.3 77.3 - - - +
277I GLY* 1.3 57.3 + - - +
278I GLU* 3.1 15.1 + - - +
320I PHE* 3.6 13.1 - - - +
321I GLY* 3.0 39.0 + - - -
322I PRO 3.7 13.0 + - - -
323I VAL* 4.8 2.9 - - - +
385I GLY* 3.0 5.4 - - - -
386I PRO* 2.9 32.7 - - - +
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Residues in contact with GLY 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I ALA 3.4 16.8 + - - -
273I PHE 3.5 5.3 + - - -
274I GLY 3.0 11.2 + - - -
276I SER* 1.3 75.2 - - - +
278I GLU* 1.3 48.7 + - - +
279I ARG* 2.8 19.6 + - - +
282I ALA* 3.5 17.8 - - - +
384I PHE* 3.8 15.0 - - - -
385I GLY 3.4 16.0 + - - +
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Residues in contact with GLU 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I HIS* 3.4 25.5 + - - +
148I PHE* 3.6 14.4 - - + -
149I ASN* 3.0 22.3 + - + +
150I PHE* 4.9 0.5 - - - -
275I SER* 2.8 24.6 + - - +
276I SER* 3.1 9.8 - - - +
277I GLY* 1.3 66.5 - - - +
279I ARG* 1.3 60.0 + - - +
322I PRO 3.6 11.4 - - - +
323I VAL* 3.2 12.4 - - + -
324I ILE* 2.6 40.9 + - - +
328I HIS* 3.6 5.7 - - - -
384I PHE* 3.5 37.9 - - + +
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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