Contacts of the strand formed by residues 469 - 475 (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 GLN 469 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276K ARG* 3.6 6.5 - - - +
277K VAL* 3.4 28.9 - - + +
333K ASP 4.3 0.9 - - - +
334K MET* 2.9 8.1 - - - +
335K SER* 2.7 56.9 + - - +
467K MET* 3.3 4.5 - - - +
468K ARG* 1.3 114.3 + - - +
470K MET* 1.3 60.3 + - - +
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Residues in contact with MET 470 (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* 3.9 6.1 - - - +
275K ASN* 3.3 0.6 - - - -
276K ARG* 2.5 44.9 + - + +
332K PHE* 4.5 9.4 - - - -
333K ASP 3.4 7.4 + - - +
334K MET* 4.0 27.4 - - - -
432K PRO* 3.5 36.3 - - + -
455K VAL* 3.5 29.8 - - + -
456K VAL 4.4 7.4 - - - +
457K TRP* 3.8 25.6 - - + -
467K MET* 4.0 9.6 - - + -
469K GLN* 1.3 75.1 - - - +
471K ALA* 1.3 69.3 + - - +
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Residues in contact with ALA 471 (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* 4.8 2.0 - - + -
274K GLN* 3.1 16.2 - - - +
275K ASN* 3.2 18.8 - - + +
331K LEU 3.7 0.9 - - - +
332K PHE* 3.3 10.0 - - - +
333K ASP* 3.0 34.4 + - + +
470K MET* 1.3 83.2 - - - +
472K MET* 1.3 61.3 + - - +
473K LYS* 4.4 20.6 - - - +
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Residues in contact with MET 472 (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* 3.5 3.5 - - - -
273K VAL* 2.8 34.7 + - + -
274K GLN* 2.8 31.4 + - + +
313K TRP* 4.4 12.3 - - - -
330K VAL* 3.6 24.7 - - + -
331K LEU 3.9 2.7 - - - -
332K PHE* 3.3 34.8 - - + -
349K PHE* 3.6 29.2 - - + -
422K TRP* 4.1 20.6 - - + -
423K TRP* 4.3 8.1 - - + -
432K PRO* 5.4 1.3 - - + -
471K ALA* 1.3 73.2 - - - +
473K LYS* 1.3 60.7 + - - +
474K LEU* 4.5 5.6 - - + -
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Residues in contact with LYS 473 (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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262K ASP* 2.7 35.0 + - - +
265K SER* 3.9 4.0 + - - -
270K TRP* 3.4 30.2 - - + -
271K THR 3.4 4.9 - - - +
272K VAL* 3.8 21.3 - - + -
330K VAL* 3.2 6.7 - - - +
331K LEU* 2.9 43.4 + - + +
333K ASP* 3.2 43.8 + - + +
471K ALA* 4.4 13.2 - - + +
472K MET* 1.3 79.9 - - - +
474K LEU* 1.3 64.5 + - - +
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Residues in contact with LEU 474 (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* 2.8 18.8 + - + -
270K TRP* 3.4 3.3 - - - -
271K THR* 2.8 28.8 + - - +
273K VAL* 3.4 24.5 - - + -
319K VAL* 3.7 19.3 - - + -
322K LEU* 3.7 21.5 - - + -
323K THR* 4.6 1.3 - - + -
328K GLN* 4.0 20.6 - - + +
329K GLN 3.5 1.6 - - - -
330K VAL* 3.9 14.6 - - + -
349K PHE* 3.6 33.0 - - + -
472K MET* 4.5 3.1 - - + -
473K LYS* 1.3 81.6 - - - +
475K ARG* 1.3 63.8 + - - +
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Residues in contact with ARG 475 (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 1.1 - - - -
233K GLU* 3.3 21.6 + - - +
266K HIS* 3.2 24.2 + - - +
267K GLY* 4.4 4.9 + - - -
268K GLY 3.6 18.8 + - - -
269K GLY 3.9 7.2 - - - +
270K TRP* 3.3 33.7 - - + +
328K GLN* 3.4 5.3 - - - -
329K GLN* 2.6 67.6 + - + +
345K GLN* 4.7 3.4 + - - -
474K LEU* 1.3 77.0 - - - +
476K PRO* 1.3 77.0 - - + +
477K LYS 4.7 4.8 + - - +
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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