Contacts of the strand formed by residues 252 - 257 (chain C) in PDB entry 5Z58
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 ALA 252 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C ASP 3.5 4.9 + - - -
224C GLY* 3.4 2.9 - - - -
225C VAL* 2.9 30.7 + - - +
250C ARG 4.2 0.2 + - - -
251C LEU* 1.3 73.6 - - - +
253C VAL* 1.3 58.1 + - - +
437C HIS* 3.9 24.0 - - + +
438C ILE* 4.2 11.0 - - + +
439C PRO* 4.1 17.5 - - + -
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Residues in contact with VAL 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C VAL* 3.7 17.9 - - + -
227C LEU* 5.5 4.3 - - + -
243C ILE* 5.4 11.0 - - + +
246C ALA* 4.8 5.8 - - + -
247C VAL* 4.1 23.3 - - + -
251C LEU 3.8 11.0 + - - +
252C ALA* 1.3 77.3 - - - +
254C THR* 1.3 77.5 + - - +
255C VAL* 4.9 3.8 - - + -
285C VAL* 5.8 0.2 - - + -
289C ILE* 4.1 24.7 - - + -
298C LEU* 5.7 12.5 - - + +
300C LEU* 3.9 22.8 - - + +
306C ASN* 4.9 2.8 - - - +
437C HIS* 5.6 1.1 + - - +
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Residues in contact with THR 254 (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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225C VAL 3.1 7.4 + - - +
226C VAL* 3.4 25.9 - - - +
227C LEU* 2.9 25.5 + - - +
253C VAL* 1.3 78.9 - - - +
255C VAL* 1.3 69.0 + - - +
300C LEU* 5.2 0.4 - - - -
306C ASN* 3.7 16.4 - - - +
433C MET* 3.5 26.5 - - + +
434C CYS* 5.2 0.3 - - - -
437C HIS* 4.2 17.3 - - + -
438C ILE* 4.1 23.2 - - + +
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Residues in contact with VAL 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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226C VAL* 4.7 0.2 - - - -
227C LEU* 2.8 21.1 - - + +
229C ILE* 4.2 15.5 - - + -
253C VAL* 4.9 3.8 - - + -
254C THR* 1.3 79.6 - - - +
256C CYS* 1.3 68.1 + - - +
257C ILE* 4.0 17.0 - - + -
281C ILE* 5.6 0.9 - - + -
282C VAL* 6.4 1.3 - - + -
285C VAL* 4.2 16.8 - - + -
300C LEU* 4.1 26.5 - - + -
306C ASN 3.0 10.8 + - - +
307C VAL* 3.2 14.7 - - + +
308C CYS 2.9 21.0 + - - -
433C MET* 3.6 5.0 - - - +
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Residues in contact with CYS 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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134C LEU* 5.6 2.5 - - + -
145C PHE* 4.2 17.0 - - - -
226C VAL* 4.1 15.0 - - + +
227C LEU 2.8 6.9 + - - -
228C PHE* 2.2 52.7 - - + +
255C VAL* 1.3 71.9 - - - +
257C ILE* 1.3 58.9 + - - +
258C ASN* 5.9 0.2 - - - -
308C CYS* 2.7 47.3 - - + -
310C SER* 3.2 23.1 - - - -
430C PHE* 5.8 2.0 - - - -
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Residues in contact with ILE 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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229C ILE 3.4 19.7 - - - +
231C ALA* 3.9 17.9 - - + +
255C VAL* 3.9 15.2 - - + -
256C CYS* 1.3 73.8 - - - +
258C ASN* 1.3 65.0 + - - +
260C ILE* 4.1 4.1 - - + +
278C LEU* 3.9 25.6 - - + -
281C ILE* 4.0 26.7 - - + -
282C VAL* 4.7 8.1 - - + -
307C VAL* 4.4 7.4 - - + -
308C CYS 3.0 13.7 + - - +
309C PHE* 4.1 16.2 - - + -
310C SER* 2.8 31.5 + - - +
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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