Contacts of the strand formed by residues 258 - 263 (chain A) in PDB entry 1LCY
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 VAL 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A MET* 3.4 43.5 - - + -
234A LEU 3.6 13.2 - - - +
235A THR* 4.6 1.1 - - - -
257A GLY* 1.3 78.4 - - - +
259A LEU* 1.3 63.3 + - - +
260A ILE 3.7 0.9 + - - -
279A VAL* 3.4 5.6 - - - +
280A ILE* 2.8 45.9 + - + +
288A VAL* 4.3 6.7 - - + -
290A ASN* 3.2 39.0 - - - +
291A ALA* 3.6 4.7 - - - +
294A VAL* 4.2 8.3 - - + -
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Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A MET* 3.2 6.2 - - - -
234A LEU* 3.0 44.4 + - + +
236A LEU* 4.0 19.7 - - + +
244A LEU* 4.8 6.5 - - + -
251A PHE* 3.8 19.5 - - + -
258A VAL* 1.3 72.9 - - - +
260A ILE* 1.3 78.7 + - - +
261A HIS* 3.3 17.1 + - + +
277A GLY* 3.3 33.2 - - - +
278A ASP 3.4 7.2 - - - +
279A VAL* 3.6 12.1 - - + +
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Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A VAL* 4.8 3.8 - - + -
232A MET 3.6 1.8 - - - +
233A MET* 3.9 19.3 - - + -
258A VAL 4.8 0.2 - - - +
259A LEU* 1.3 75.1 - - - +
261A HIS* 1.3 61.9 + - - +
262A LYS 4.0 8.3 - - - +
263A VAL* 3.5 32.3 - - + -
274A LEU* 3.6 31.9 - - + -
275A ARG 3.6 13.7 - - - +
276A PRO* 3.9 2.5 - - + -
277A GLY 2.9 23.2 + - - -
278A ASP* 3.0 26.9 + - + +
280A ILE* 3.8 26.7 - - + -
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Residues in contact with HIS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A MET* 3.6 37.6 - - + +
191A LYS* 3.7 22.1 + - - +
192A VAL* 5.9 0.9 - - - -
232A MET* 2.6 46.4 + - + +
233A MET* 5.1 0.9 - - - -
234A LEU* 5.5 1.1 - - + +
259A LEU* 3.3 15.6 + - + +
260A ILE* 1.3 75.2 - - - +
262A LYS* 1.3 89.6 + - - +
276A PRO* 3.7 12.8 - - - +
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A HIS* 5.8 5.0 + - + -
170A PHE* 5.0 17.6 - - - +
231A VAL* 3.1 7.7 - - - +
232A MET* 2.7 54.8 + - + +
260A ILE* 3.5 1.5 - - - +
261A HIS* 1.3 112.0 - - + +
263A VAL* 1.3 66.7 + - - +
264A ILE* 4.2 2.5 - - + -
276A PRO* 4.3 7.4 - - + -
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLY 3.7 2.9 - - - -
231A VAL* 4.0 5.6 - - + -
260A ILE* 3.5 28.7 - - + -
262A LYS* 1.3 75.5 - - - +
264A ILE* 1.3 64.4 + - - +
265A LEU* 3.7 9.7 + - - +
267A SER* 4.0 0.2 - - - +
269A ALA* 3.8 10.1 - - + -
270A HIS* 3.3 44.4 - - + +
274A LEU* 3.5 25.4 - - + +
275A ARG* 4.0 6.7 - - - -
276A PRO* 4.1 10.3 - - + +
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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