Contacts of the strand formed by residues 228 - 233 (chain A) in PDB entry 2XLR
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 LYS 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A LYS 3.1 6.7 + - - +
204A THR* 3.0 26.1 - - + +
205A VAL 2.9 28.5 + - - -
226A ALA 3.4 0.2 - - - -
227A LYS* 1.3 86.5 - - + +
229A LEU* 1.3 66.8 + - - +
230A ILE* 4.1 5.4 - - - -
245A ASN* 3.5 17.5 - - + +
247A ASP* 3.0 40.1 + - - -
249A ARG* 4.1 1.6 - - - +
268A GLU* 2.9 31.0 + - - +
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Residues in contact with LEU 229 (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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205A VAL* 3.4 19.7 - - + +
207A LEU* 4.8 10.1 - - + -
218A GLY 4.0 3.1 - - - +
221A CYS* 3.7 25.1 - - + -
222A TYR* 3.7 29.4 - - + -
226A ALA* 3.9 10.1 - - + -
228A LYS* 1.3 84.1 - - - +
230A ILE* 1.3 67.6 + - - +
245A ASN* 3.0 9.8 + - - +
246A TRP* 3.2 49.8 - - + -
247A ASP* 3.0 23.4 + - - +
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A THR* 3.8 26.9 - - + -
205A VAL 2.9 7.9 + - - +
206A LEU* 3.2 18.2 - - + -
207A LEU* 2.8 27.8 + - - +
228A LYS* 4.1 5.2 - - - -
229A LEU* 1.3 79.7 - - - +
231A SER* 1.3 70.6 + - - +
247A ASP* 3.4 22.2 - - - +
249A ARG* 3.8 24.9 - - + +
262A PHE* 4.0 11.4 - - + -
268A GLU* 4.1 20.6 - - + +
270A VAL* 4.0 20.2 - - + -
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.1 20.2 - - - -
209A GLY 4.9 2.0 - - - -
230A ILE* 1.3 78.2 - - - +
232A CYS* 1.3 60.4 + - - +
238A MET* 3.3 22.9 - - - +
246A TRP* 3.6 17.6 + - - -
247A ASP 3.0 4.6 + - - -
248A GLU* 3.1 24.9 - - - +
249A ARG* 2.9 25.1 + - - +
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Residues in contact with CYS 232 (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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206A LEU* 3.8 15.5 - - - -
207A LEU 3.0 17.0 + - - -
208A VAL* 3.8 18.2 - - - -
209A GLY 2.9 30.2 + - - +
231A SER* 1.3 75.0 - - - +
233A TYR* 1.3 61.7 + - - +
249A ARG 3.0 6.7 - - - +
250A PRO 3.4 21.8 - - - +
251A ASN* 3.8 6.9 - - - +
252A LEU* 3.8 23.1 - - - +
262A PHE* 4.2 8.3 - - + -
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Residues in contact with TYR 233 (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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209A GLY 4.9 1.6 - - - +
210A SER* 3.9 17.0 - - - +
232A CYS* 1.3 77.9 - - - +
234A ARG* 1.3 62.6 + - - +
235A THR 3.7 9.6 - - - -
236A ALA 3.3 35.9 - - - +
237A PRO* 3.7 40.6 - - + +
248A GLU* 4.2 11.9 - - + +
249A ARG* 2.8 39.5 + - - -
250A PRO* 3.9 22.6 - - + +
251A ASN* 3.2 22.9 + - - -
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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