Contacts of the strand formed by residues 261 - 266 (chain A) in PDB entry 1LKF
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 TRP 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A TYR 3.6 7.4 - - - -
72A ASP* 3.9 1.3 - - - -
188A TYR* 3.3 26.2 - - - +
194A LEU* 3.7 16.0 - - + +
196A GLY 3.3 20.0 - - - +
197A ARG 2.8 28.1 + - - +
199A SER 2.9 28.5 + - - -
201A ALA 3.4 22.2 - - - -
202A TYR 4.5 0.2 - - - -
203A ALA* 3.3 44.6 - - + -
206A ASN* 3.3 19.1 - - + +
254A ILE* 4.2 8.3 - - + -
255A ARG* 3.4 28.0 - - - -
256A TRP* 3.5 41.2 - + + -
260A TYR* 1.3 74.5 - - - +
262A ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 262 (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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187A THR 3.9 16.8 - - - +
188A TYR 3.4 12.8 - - - +
189A GLY* 4.4 1.3 - - - +
194A LEU* 4.8 1.8 - - - -
253A GLN 3.8 0.2 - - - +
254A ILE* 3.2 6.7 - - - -
255A ARG* 3.0 34.9 + - + +
260A TYR* 4.1 10.3 - - + -
261A TRP* 1.3 76.3 - - - +
263A GLY* 1.3 61.9 + - - +
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Residues in contact with GLY 263 (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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184A PHE* 4.4 2.4 - - - -
188A TYR 2.9 10.3 + - - -
189A GLY* 3.3 7.4 - - - -
190A ASN 2.9 36.2 + - - -
194A LEU* 4.8 3.2 - - - +
252A TYR* 3.8 7.9 - - - -
253A GLN 3.1 9.0 - - - -
254A ILE* 4.1 3.3 - - - +
262A ALA* 1.3 76.6 - - - +
264A ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 264 (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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184A PHE* 5.3 7.9 - - + -
190A ASN* 3.9 4.3 + - - -
251A LEU 3.5 2.8 - - - +
252A TYR* 3.5 3.5 - - - -
253A GLN* 2.7 51.1 + - + +
263A GLY* 1.3 74.6 - - - +
265A ASN* 1.3 61.5 + - - +
266A TYR* 4.1 12.1 - - + +
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Residues in contact with ASN 265 (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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78A TRP* 2.9 31.1 + - - -
181A ARG* 3.2 28.7 + - - +
184A PHE* 6.2 0.4 - - - -
190A ASN* 3.6 29.7 - - - +
192A LEU* 4.4 0.7 - - - -
250A ASP* 2.8 32.5 + - - +
251A LEU 3.4 5.8 - - - +
252A TYR* 3.7 9.7 - - + +
264A ALA* 1.3 73.7 - - - +
266A TYR* 1.3 60.8 + - - +
267A LYS* 3.4 6.5 + - - +
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Residues in contact with TYR 266 (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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250A ASP* 3.2 6.9 - - - -
251A LEU* 2.8 49.3 + - + +
253A GLN* 3.6 39.9 + - + -
264A ALA* 4.4 12.0 - - + +
265A ASN* 1.3 71.5 - - - +
267A LYS* 1.3 63.9 + - - +
269A PHE* 3.5 42.9 + + + -
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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