Contacts of the strand formed by residues 257 - 262 (chain K) in PDB entry 1LWU
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 TYR 257 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247K TYR* 3.5 7.6 - - - -
248K ILE* 2.8 55.5 + - + +
250K PRO* 3.3 34.2 - - + +
254K SER* 6.2 3.4 - - - -
255K GLU 3.8 12.8 - - - -
256K PRO* 1.3 74.4 - - - +
258K LYS* 1.3 74.3 + - - +
259K VAL* 3.6 1.0 + - + -
293K GLU* 5.7 4.0 - - - +
314K LEU* 3.9 20.9 - - + +
318K THR* 2.9 39.6 - - + +
322K LEU* 4.7 6.2 - - - +
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Residues in contact with LYS 258 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220K VAL* 5.3 3.6 - - - -
222K CYS* 3.9 24.5 + - - -
223K ARG 4.5 8.7 + - - -
224K VAL* 5.8 0.2 - - - +
225K PRO* 6.0 1.0 - - - +
245K ALA* 3.8 26.9 + - + +
246K TYR 3.2 12.3 - - - +
247K TYR* 4.0 29.9 - - + +
257K TYR* 1.3 81.2 - - - +
259K VAL* 1.3 63.5 + - - +
293K GLU* 4.9 2.9 - - - +
297K ILE* 3.7 34.4 - - + +
298K ALA 5.2 4.3 - - - +
306K CYS* 4.5 3.8 - - - +
314K LEU* 4.1 5.9 - - - +
140L ASP* 3.3 30.7 + - + +
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Residues in contact with VAL 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K CYS* 3.9 22.9 - - - -
245K ALA* 3.6 1.0 - - - -
246K TYR* 2.9 31.9 + - - +
248K ILE* 3.8 34.3 - - + -
257K TYR* 4.4 1.3 - - + +
258K LYS* 1.3 74.9 - - - +
260K PHE* 1.3 64.3 + - - +
261K CYS* 3.6 1.7 + - - -
271K THR* 3.5 15.3 - - + -
272K VAL 3.5 22.2 - - - +
297K ILE* 3.7 10.3 - - - -
312K TYR* 3.9 0.9 - - - +
314K LEU* 3.7 21.8 - - + -
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Residues in contact with PHE 260 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K SER* 3.9 10.5 - - - -
244K GLU* 3.8 29.6 - - - -
259K VAL* 1.3 72.9 - - - +
261K CYS* 1.3 79.9 + - - +
262K ASP* 4.5 3.4 - - + -
271K THR* 4.1 0.5 - - - -
272K VAL* 3.0 42.6 + - + +
297K ILE* 3.5 29.9 - - + +
298K ALA* 3.8 9.2 - - + -
307K ASN 3.8 11.0 - - - -
309K PRO* 3.4 46.9 - - + -
312K TYR* 3.1 22.7 + - + +
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Residues in contact with CYS 261 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K CYS* 2.0 51.4 - - - -
235K ILE* 4.0 7.0 - - - -
243K SER* 3.4 3.6 - - - -
244K GLU 3.2 17.8 + - - -
246K TYR* 3.8 40.4 - - + -
259K VAL* 4.2 4.0 - - - -
260K PHE* 1.3 91.0 - - - +
262K ASP* 1.3 59.4 + - - +
263K MET* 3.4 13.7 - - + -
270K TRP 3.4 0.4 - - - -
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Residues in contact with ASP 262 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K SER* 3.5 7.1 + - - -
260K PHE* 4.0 4.0 + - + -
261K CYS* 1.3 70.5 - - - +
263K MET* 1.3 60.7 + - - +
264K GLU* 3.1 5.1 + - - +
265K SER* 2.8 38.6 + - - +
268K GLY* 3.2 3.8 - - - -
269K GLY 3.2 1.9 + - - -
270K TRP* 2.7 45.3 + - + +
272K VAL* 4.3 5.2 - - + -
473K LYS* 2.7 38.2 + - - -
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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