Contacts of the strand formed by residues 204 - 208 (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 THR 204 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C LYS* 1.3 74.2 - - - +
205C VAL* 1.3 61.9 + - - +
227C LYS* 4.6 13.0 + - - +
228C LYS* 3.3 29.0 + - + +
230C ILE* 4.0 24.2 - - + -
268C GLU* 5.1 0.9 - - - +
269C LYS* 3.7 24.9 + - - +
270C VAL* 3.9 3.3 - - + -
271C ASP* 2.5 47.4 + - - +
272C ALA 3.4 2.6 + - - +
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Residues in contact with VAL 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C PHE* 3.9 34.8 - - + +
203C LYS* 4.2 11.2 - - + +
204C THR* 1.3 79.2 - - - +
206C LEU* 1.3 67.5 + - - +
207C LEU* 4.0 9.7 + - + +
221C CYS* 4.6 8.1 - - - -
226C ALA* 4.7 1.8 - - + -
228C LYS 3.1 6.7 + - - +
229C LEU* 3.4 19.5 - - + +
230C ILE* 3.0 27.1 + - - +
272C ALA* 3.7 9.9 - - + +
274C ILE* 3.9 30.7 - - + -
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Residues in contact with LEU 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C THR 4.2 0.2 - - - -
205C VAL* 1.3 73.0 - - - +
207C LEU* 1.3 68.1 + - - +
208C VAL* 4.1 8.0 + - + -
230C ILE* 3.4 28.7 - - + +
232C CYS* 3.7 23.6 - - - -
252C LEU* 4.1 34.8 - - + -
260C ALA* 4.2 14.4 - - + -
262C PHE* 3.9 7.0 - - + -
270C VAL* 4.2 15.8 - - + +
272C ALA 3.1 13.2 + - - +
273C ILE* 4.3 16.6 - - + -
274C ILE* 2.8 30.0 + - - +
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Residues in contact with LEU 207 (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* 4.4 6.3 - - + +
206C LEU* 1.3 75.0 - - - +
208C VAL* 1.3 62.8 + - - +
209C GLY 3.8 0.6 + - - -
214C ALA* 4.3 12.1 - - + +
217C ILE* 4.1 12.1 - - + -
218C GLY* 3.6 37.2 - - - +
221C CYS* 5.5 0.9 - - - -
229C LEU* 4.4 16.8 - - + -
230C ILE 2.8 18.4 + - - +
231C SER* 3.2 9.9 - - - -
232C CYS* 3.0 25.8 + - - -
246C TRP* 4.4 11.0 - - + -
274C ILE* 3.5 17.7 - - + +
276C CYS* 4.1 23.3 - - - -
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Residues in contact with VAL 208 (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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178C PHE* 4.2 11.7 - - + -
206C LEU* 4.1 8.5 - - + -
207C LEU* 1.3 76.3 - - - +
209C GLY* 1.3 58.9 + - - +
232C CYS* 3.9 21.8 - - - -
251C ASN* 4.3 0.2 - - - +
252C LEU* 4.4 7.9 - - + -
273C ILE* 4.0 18.6 - - + -
274C ILE 3.0 6.4 + - - +
275C LEU* 3.9 31.4 - - + -
276C CYS* 2.7 35.3 + - - +
277C THR* 3.9 4.3 - - + +
501C NAP 3.6 26.0 - - + +
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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