Contacts of the strand formed by residues 270 - 276 (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 TRP 270 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232K CYS* 3.9 1.8 - - - -
261K CYS* 3.4 3.8 - - - -
262K ASP* 2.7 47.4 + - + +
265K SER* 3.5 23.0 + - - -
266K HIS* 3.2 25.4 + - + +
268K GLY* 3.6 9.2 - - - -
269K GLY* 1.3 76.8 - - - +
271K THR* 1.3 61.0 + - - +
272K VAL 3.4 1.0 + - - -
329K GLN* 3.3 38.6 - - + -
330K VAL 4.3 2.0 - - - -
331K LEU* 3.5 34.5 - - + -
345K GLN* 4.1 10.1 - - - -
473K LYS* 3.4 31.4 - - + -
474K LEU 3.4 19.5 - - - -
475K ARG* 3.3 40.6 - - + +
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Residues in contact with THR 271 (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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231K HIS* 3.1 24.8 + - - -
232K CYS* 3.2 28.5 + - - -
248K ILE* 4.3 11.7 - - + -
259K VAL* 3.5 30.1 - - + -
269K GLY 3.6 0.4 + - - -
270K TRP* 1.3 70.5 - - - +
272K VAL* 1.3 64.0 + - - +
273K VAL* 3.3 5.2 + - + +
314K LEU* 4.8 7.4 - - + -
322K LEU* 4.9 8.5 - - + -
473K LYS* 4.2 0.7 - - - -
474K LEU* 2.8 40.9 + - - -
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Residues in contact with VAL 272 (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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259K VAL* 3.5 13.3 - - - +
260K PHE* 3.0 36.3 + - + +
262K ASP* 4.3 3.8 - - + -
270K TRP 4.3 4.9 - - - +
271K THR* 1.3 70.2 - - - +
273K VAL* 1.3 58.1 + - - +
274K GLN 3.3 24.7 - - - +
275K ASN* 3.7 20.2 - - + -
312K TYR* 2.6 36.1 + - + +
471K ALA* 4.8 2.2 - - + -
472K MET 3.5 5.6 - - - +
473K LYS* 3.8 27.1 - - + -
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Residues in contact with VAL 273 (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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271K THR* 3.6 14.4 - - + +
272K VAL* 1.3 76.3 - - - +
274K GLN* 1.3 60.4 + - + +
312K TYR* 4.1 2.0 - - - -
313K TRP* 3.5 11.0 - - + -
314K LEU* 2.8 48.4 + - + +
319K VAL* 3.2 35.4 - - + -
322K LEU* 5.0 1.1 - - + -
472K MET* 2.8 20.3 + - + +
474K LEU* 3.4 37.5 - - + +
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Residues in contact with GLN 274 (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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272K VAL* 3.3 7.7 - - - +
273K VAL* 1.3 78.5 - - - +
275K ASN* 1.3 69.6 + - - +
276K ARG* 3.3 23.0 - - - +
283K PHE* 4.3 2.9 - - + -
312K TYR 3.2 11.9 - - - +
313K TRP* 3.3 26.5 - - + -
422K TRP* 6.1 0.2 - - + -
432K PRO* 3.4 16.0 - - - +
433K ASN* 3.1 28.6 - - - +
470K MET* 3.9 2.5 - - - +
471K ALA* 3.1 14.3 - - - +
472K MET* 2.8 50.3 + - + +
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Residues in contact with ASN 275 (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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272K VAL* 3.7 15.7 - - + +
274K GLN* 1.3 81.2 - - - +
276K ARG* 1.3 73.8 + - - +
277K VAL* 4.5 6.7 - - - +
309K PRO* 3.7 24.7 - - - +
310K GLY 2.9 26.4 + - - +
311K GLU* 3.1 26.5 - - - +
312K TYR* 3.1 15.5 + - + +
470K MET 3.3 9.1 - - - +
471K ALA* 3.2 18.0 - - - +
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Residues in contact with ARG 276 (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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274K GLN* 3.3 20.9 - - - +
275K ASN* 1.3 76.6 - - - +
277K VAL* 1.3 66.7 + - - +
279K GLY* 5.0 0.6 - - - -
281K SER 4.3 3.0 + - - -
283K PHE* 3.4 35.5 - - - +
311K GLU* 2.8 31.7 + - - +
433K ASN* 3.3 25.2 - - - +
434K GLY 2.8 30.1 + - - +
435K ARG* 5.1 0.2 - - - +
436K TYR* 3.6 32.3 - - + +
455K VAL* 3.6 14.6 - - + +
468K ARG 5.8 0.2 - - - -
469K GLN* 3.6 4.5 - - - +
470K MET* 2.5 47.2 + - + +
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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