Contacts of the strand formed by residues 233 - 239 (chain A) in PDB entry 5XOC
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 CYS 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A PHE* 3.3 1.1 - - - +
232A TRP* 1.3 114.3 - - + +
234A SER* 1.3 66.4 + - - +
235A ILE* 4.0 22.4 - - - -
249A HIS* 3.7 1.4 - - - +
250A ALA* 2.8 43.5 + - - +
398A LEU* 4.6 7.6 - - + -
399A HIS 3.1 15.5 - - - +
400A LEU* 3.7 9.6 - - + -
401A ASN* 3.7 6.3 + - - +
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Residues in contact with SER 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A CYS* 1.3 73.9 + - - +
235A ILE* 1.3 63.2 + - - +
236A SER* 5.5 0.2 - - - -
247A THR* 4.0 12.1 - - - -
248A PHE 3.3 4.5 - - - -
249A HIS* 2.8 30.5 + - - -
397A GLU 3.5 1.0 - - - +
398A LEU* 3.3 5.4 - - - +
399A HIS* 2.9 44.4 + - - +
401A ASN* 3.8 12.9 + - - +
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Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A CYS* 4.0 14.4 - - - -
234A SER* 1.3 79.9 - - - +
236A SER* 1.3 64.0 + - - +
247A THR* 3.4 4.3 - - - +
248A PHE* 2.8 43.6 + - + +
255A MET* 3.7 37.5 - - + -
257A VAL* 4.0 11.7 - - + -
269A PHE* 3.8 19.1 - - + -
296A LEU* 4.0 11.7 - - + -
396A ILE* 3.8 38.6 - - + -
397A GLU 3.3 4.7 - - - +
398A LEU* 4.2 7.6 - - + -
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A SER 4.3 0.5 - - - -
235A ILE* 1.3 72.0 - - - +
237A TYR* 1.3 61.7 + - - +
238A TYR* 3.5 15.3 - - - -
243A ARG* 3.4 24.5 + - - +
247A THR* 3.1 29.1 + - - +
396A ILE* 3.3 5.6 - - - -
397A GLU* 2.9 38.2 + - - -
399A HIS* 5.8 3.9 + - - -
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Residues in contact with TYR 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ILE 4.3 0.6 + - - -
236A SER* 1.3 74.1 - - - +
238A TYR* 1.3 76.4 + - - +
239A GLU* 2.8 43.5 + - + +
243A ARG* 3.1 12.1 + - - +
244A VAL* 3.0 51.9 + - + +
246A GLU 5.1 0.6 + - - -
269A PHE* 4.2 11.9 - - + -
271A LEU* 3.8 41.5 - - + -
274A LEU* 3.6 14.8 - - + -
287A ARG* 3.2 19.8 + - - +
290A ILE* 4.9 0.7 - - - +
376A PHE* 5.4 0.2 - + - -
394A CYS* 3.8 26.0 - - + -
395A TRP 3.5 10.5 - - - -
396A ILE* 4.0 8.1 - - + -
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A SER* 3.5 18.7 - - - -
237A TYR* 1.3 89.7 - - - +
239A GLU* 1.3 64.0 + - - +
240A LEU 4.1 0.9 - - - +
241A ASN 4.5 4.9 - - - -
242A GLN 3.3 24.5 - - - -
243A ARG* 3.3 33.0 + - + +
244A VAL 4.4 0.2 - - - +
393A PRO 3.7 0.3 - - - +
395A TRP* 2.8 86.9 + + + +
397A GLU* 3.6 22.8 + - + -
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A TYR* 2.8 37.4 + - + +
238A TYR* 1.3 73.7 - - - +
240A LEU* 1.3 65.6 + - - +
241A ASN 3.0 0.9 + - - -
242A GLN* 2.9 34.2 + - - +
244A VAL* 3.9 11.3 - - + +
276A ASN* 2.8 26.8 + - - +
279A ARG* 2.6 40.4 + - - +
283A VAL* 3.4 16.2 - - + +
287A ARG* 3.3 3.8 + - - -
393A PRO 3.2 13.7 - - - +
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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