Contacts of the helix formed by residues 252 - 257 (chain C) in PDB entry 5ZR1
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 ARG 252 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C ASN* 3.9 22.4 - - - +
217C ASP* 3.2 28.2 + - - +
218C ASN* 3.2 22.6 + - - -
221C ILE* 3.4 25.9 - - - +
250C ASN 3.9 2.0 + - - +
251C LEU* 1.3 77.7 - - - +
253C GLN* 1.3 66.5 + - - +
254C SER* 3.3 11.0 + - - +
255C THR* 3.1 16.8 + - - +
256C ILE* 3.5 10.9 + - - +
461D GLU* 3.6 28.0 - - + +
499D PHE* 6.3 0.2 - - + -
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Residues in contact with GLN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C GLU 5.7 0.4 + - - -
252C ARG* 1.3 73.0 - - - +
254C SER* 1.3 61.2 + - - +
255C THR 3.3 0.9 + - - -
256C ILE* 3.4 15.5 + - - +
257C ARG* 3.3 36.4 + - - +
454D LYS 4.2 13.5 + - - -
457D LYS* 3.8 24.3 - - - +
458D ASN* 3.9 20.4 - - + +
461D GLU* 2.9 21.5 + - - +
250E TYR* 3.8 13.9 + - - +
297E ASP* 3.0 31.0 + - - +
298E ASN* 4.6 6.3 + - - -
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Residues in contact with SER 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ILE* 5.4 4.7 - - - +
252C ARG* 4.5 9.7 + - - +
253C GLN* 1.3 77.4 - - - +
255C THR* 1.3 64.3 + - - +
257C ARG* 3.7 29.6 + - - +
258C LEU* 3.7 15.8 + - - +
458D ASN* 5.2 1.5 + - - -
461D GLU* 4.5 1.0 + - - -
260E ASP* 5.1 2.1 - - - +
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Residues in contact with THR 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C ASP* 2.4 36.2 + - - +
220C ILE* 4.2 33.9 - - + -
221C ILE* 4.0 13.5 - - + +
251C LEU* 4.6 8.1 - - + -
252C ARG* 3.1 12.4 + - - +
254C SER* 1.3 79.5 + - - +
256C ILE* 1.3 59.4 + - - +
257C ARG 3.2 0.2 - - - -
258C LEU* 3.0 11.0 + - + +
259C LEU* 2.9 34.2 + - + +
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Residues in contact with ILE 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C GLU* 3.3 41.1 - - + +
251C LEU* 4.1 21.3 - - + +
252C ARG 3.6 14.6 - - - +
253C GLN* 3.4 21.0 + - - +
255C THR* 1.3 77.3 - - - +
257C ARG* 1.3 60.2 + - - +
259C LEU* 3.2 17.9 + - + +
260C LYS* 3.3 15.9 + - + +
457D LYS* 5.2 0.4 - - - +
297E ASP 3.9 20.2 - - - +
298E ASN* 4.5 8.1 - - - +
299E LEU* 3.7 27.3 - - + +
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Residues in contact with ARG 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C GLN* 3.3 27.8 + - - +
254C SER* 3.7 31.4 - - - +
255C THR 3.2 0.4 - - - -
256C ILE* 1.3 77.3 - - - +
258C LEU* 1.3 56.2 + - - +
260C LYS* 4.0 1.7 + - - +
261C ARG* 3.3 23.8 + - - -
458D ASN* 3.1 32.3 + - - +
250E TYR* 3.7 7.9 + - - -
254E ASP* 5.2 1.4 + - - -
256E PHE 5.5 0.4 - - - -
257E ALA* 3.5 32.2 - - - +
260E ASP* 3.7 34.3 + - - +
261E LEU* 5.1 2.2 - - - -
264E PHE* 3.3 18.8 - - + -
297E ASP* 3.6 35.8 + - + +
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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