Contacts of the strand formed by residues 228 - 233 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C LYS 3.2 5.2 + - - +
204C THR* 4.0 22.9 - - + +
205C VAL* 3.1 24.4 + - - +
226C ALA* 3.4 1.1 - - - +
227C LYS* 1.3 86.5 - - + +
229C LEU* 1.3 72.9 + - - +
230C ILE* 4.3 4.7 - - - -
245C ASN* 3.4 18.4 - - + +
247C ASP* 3.2 38.9 + - - -
249C ARG* 4.2 1.2 - - - +
268C GLU* 3.0 29.2 + - - +
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Residues in contact with LEU 229 (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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205C VAL* 3.4 19.1 - - + +
207C LEU* 4.4 12.3 - - + -
218C GLY 3.9 4.9 - - - +
221C CYS* 3.7 26.2 - - + -
222C TYR* 3.7 28.9 - - + +
226C ALA* 4.2 7.0 - - + -
228C LYS* 1.3 81.2 - - - +
230C ILE* 1.3 66.7 + - - +
245C ASN* 2.9 11.9 + - - +
246C TRP* 3.1 46.2 - - + -
247C ASP* 3.0 23.4 + - - +
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Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR* 4.0 22.7 - - + -
205C VAL 3.0 7.3 + - - +
206C LEU* 3.4 18.6 - - + -
207C LEU* 2.8 28.2 + - - +
228C LYS* 4.3 4.5 - - - -
229C LEU* 1.3 80.1 - - - +
231C SER* 1.3 70.5 + - - +
246C TRP* 4.8 0.4 - - - -
247C ASP* 3.3 21.1 - - - +
249C ARG* 3.9 22.4 - - - +
262C PHE* 4.1 10.5 - - + -
268C GLU* 3.9 31.9 - - + +
270C VAL* 4.2 13.9 - - + -
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Residues in contact with SER 231 (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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207C LEU* 3.2 22.2 - - - -
209C GLY 4.7 2.7 - - - -
230C ILE* 1.3 79.2 - - - +
232C CYS* 1.3 61.6 + - - +
238C MET* 3.5 26.1 - - - +
246C TRP* 3.3 21.1 + - - +
247C ASP 3.0 5.7 + - - +
248C GLU* 3.4 14.6 - - - +
249C ARG* 2.9 23.9 + - - -
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Residues in contact with CYS 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C LEU* 3.7 22.9 - - - -
207C LEU 3.0 11.6 + - - -
208C VAL* 3.9 17.3 - - - -
209C GLY 3.0 29.0 + - - +
231C SER* 1.3 74.8 - - - +
233C TYR* 1.3 61.6 + - - +
248C GLU* 5.8 0.2 - - - -
249C ARG 3.0 6.3 - - - +
250C PRO 3.4 22.7 - - - +
251C ASN* 4.0 6.3 - - - +
252C LEU* 3.9 21.8 - - - +
262C PHE* 4.2 8.3 - - + -
501C NAP 5.0 0.2 - - - -
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Residues in contact with TYR 233 (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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209C GLY 4.9 1.6 - - - +
210C SER* 3.9 17.0 - - - +
232C CYS* 1.3 76.0 - - - +
234C ARG* 1.3 61.3 + - - +
235C THR 3.8 9.6 - - - -
236C ALA 3.4 35.0 - - - +
237C PRO* 3.6 40.9 - - + +
248C GLU* 4.2 13.2 - - + +
249C ARG* 2.9 35.2 + - - -
250C PRO* 3.9 22.6 - - + +
251C ASN* 3.1 23.3 + - - +
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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