Contacts of the strand formed by residues 232 - 236 (chain A) in PDB entry 2XE8
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 GLU 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PRO* 4.7 10.2 - - + +
207A PHE 3.1 3.8 + - - +
208A LEU* 3.5 20.2 - - + -
209A ALA 3.0 20.8 + - - -
230A VAL* 3.4 10.4 - - - +
231A ASN* 1.3 86.8 - - + +
233A MET* 1.3 62.5 + - - +
277A VAL* 4.0 1.3 - - - -
278A LYS* 3.5 27.3 - - + +
280A THR* 4.7 2.6 + - - -
326A ALA* 3.7 14.0 - - - +
329A ARG* 2.9 54.9 + - - +
330A ALA 5.5 0.2 + - - -
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Residues in contact with MET 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 4.3 0.9 - - - -
209A ALA* 3.2 16.6 - - + +
211A LEU* 3.9 22.9 - - + -
223A ILE* 4.1 11.0 - - + +
226A MET* 3.6 31.9 - - + -
227A LEU* 3.8 28.3 - - + +
230A VAL* 4.4 2.7 - - + -
232A GLU* 1.3 75.8 - - - +
234A ILE* 1.3 74.2 + - - +
235A ILE* 3.9 21.0 + - + -
277A VAL* 4.0 4.5 - - + +
278A LYS 3.0 8.3 + - - -
279A ILE* 3.4 17.7 - - + +
280A THR* 2.9 24.7 + - - -
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 4.0 14.5 - - + +
209A ALA 2.9 9.7 + - - +
210A ILE* 3.9 35.7 - - + -
211A LEU 2.9 27.0 + - - +
233A MET* 1.3 75.7 - - - +
235A ILE* 1.3 71.2 + - - +
236A GLY* 4.3 2.0 - - - +
280A THR* 3.4 22.9 - - - -
323A TYR* 3.6 62.4 - - + +
326A ALA* 4.3 6.1 - - + -
327A VAL* 5.2 0.4 - - + -
339A VAL* 4.9 1.3 - - + -
354A LEU* 5.3 0.7 - - + -
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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
----------------------------------------------------------
211A LEU* 3.3 5.8 - - + +
223A ILE* 5.2 8.1 - - + -
233A MET* 3.9 25.3 + - + -
234A ILE* 1.3 79.6 - - - +
236A GLY* 1.3 60.3 + - - +
239A MET* 3.9 26.5 - - + -
240A ALA* 3.8 3.8 - - - +
243A PHE* 3.9 42.4 - - + -
269A MET* 4.5 5.6 - - + -
279A ILE* 4.3 18.4 - - + -
280A THR 3.1 8.7 + - - +
281A LEU* 3.8 17.1 - - + +
282A PRO* 3.4 22.9 - - - +
323A TYR* 4.2 0.3 + - - -
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Residues in contact with GLY 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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211A LEU 2.9 10.2 + - - -
212A GLY* 3.3 13.5 - - - -
213A GLY 3.5 0.2 + - - -
234A ILE* 4.0 1.8 - - - +
235A ILE* 1.3 75.0 - - - +
237A GLY* 1.3 68.0 + - - -
239A MET* 3.2 19.4 - - - +
240A ALA* 4.3 4.9 - - - -
282A PRO* 4.7 0.7 - - - -
323A TYR* 4.0 14.4 - - - -
339A VAL* 4.5 10.1 - - - -
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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