Contacts of the strand formed by residues 469 - 475 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276H ARG* 3.6 6.3 - - - +
277H VAL* 3.4 28.1 - - + +
333H ASP 4.3 0.9 - - - +
334H MET* 2.9 7.8 - - - +
335H SER* 2.7 56.4 + - - +
467H MET* 3.5 3.6 - - - +
468H ARG* 1.3 114.3 + - - +
470H MET* 1.3 62.9 + - - +
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Residues in contact with MET 470 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274H GLN* 3.9 6.1 - - - +
275H ASN* 3.3 0.2 - - - -
276H ARG* 2.6 44.9 + - + +
332H PHE* 4.5 4.9 - - - -
333H ASP 3.4 6.0 + - - +
334H MET* 4.1 22.0 - - - -
432H PRO* 3.5 34.8 - - + -
455H VAL* 3.6 31.4 - - + -
456H VAL 4.4 7.9 - - - +
457H TRP* 3.8 24.5 - - + -
467H MET* 4.0 15.5 - - + -
469H GLN* 1.3 74.7 - - - +
471H ALA* 1.3 74.0 + - - +
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Residues in contact with ALA 471 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H VAL* 4.9 2.2 - - + -
274H GLN* 3.1 15.9 - - - +
275H ASN* 3.3 19.3 - - + +
331H LEU 3.7 0.5 - - - +
332H PHE* 3.3 10.6 - - - +
333H ASP* 3.0 34.7 + - + +
470H MET* 1.3 83.1 - - - +
472H MET* 1.3 62.1 + - - +
473H LYS* 4.4 20.0 - - - +
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Residues in contact with MET 472 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H VAL* 3.5 3.1 - - - -
273H VAL* 2.8 39.2 + - + -
274H GLN* 2.9 30.8 + - + +
313H TRP* 4.5 12.3 - - - -
319H VAL* 5.9 0.2 - - + -
330H VAL* 3.6 24.9 - - + -
331H LEU 3.9 2.7 - - - -
332H PHE* 3.3 34.5 - - + -
349H PHE* 3.6 28.3 - - + -
422H TRP* 4.1 20.9 - - + -
423H TRP* 4.3 7.4 - - + -
432H PRO* 5.4 1.1 - - + -
471H ALA* 1.3 73.6 - - - +
473H LYS* 1.3 55.8 + - - +
474H LEU* 4.4 6.1 - - + -
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Residues in contact with LYS 473 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H ASP* 2.7 33.4 + - - +
265H SER* 3.9 4.2 + - - -
270H TRP* 3.4 28.9 - - + -
271H THR 3.3 4.7 - - - +
272H VAL* 3.8 21.1 - - + -
273H VAL 4.4 0.2 - - - +
330H VAL* 3.2 7.0 - - - +
331H LEU* 2.9 43.0 + - + +
333H ASP* 3.2 43.8 + - + +
471H ALA* 4.4 13.2 - - + +
472H MET* 1.3 81.3 - - - +
474H LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 474 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H HIS* 2.8 18.6 + - + -
270H TRP* 3.4 3.4 - - - -
271H THR* 2.8 28.6 + - - +
273H VAL* 3.4 24.5 - - + -
319H VAL* 3.7 19.7 - - + -
322H LEU* 3.7 22.4 - - + -
323H THR* 4.6 2.0 - - + -
328H GLN* 4.0 19.3 - - + +
329H GLN 3.5 1.1 - - - -
330H VAL* 3.8 15.5 - - + -
349H PHE* 3.6 32.5 - - + -
472H MET* 4.4 2.9 - - + -
473H LYS* 1.3 81.9 - - - +
475H ARG* 1.3 62.6 + - - +
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Residues in contact with ARG 475 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231H HIS* 3.1 1.3 - - - +
233H GLU* 3.2 20.5 + - - +
266H HIS* 3.2 22.6 + - - +
267H GLY* 4.4 4.9 + - - -
268H GLY 3.6 20.4 + - - -
269H GLY 3.8 6.5 - - - +
270H TRP* 3.3 33.2 - - + +
328H GLN* 3.4 5.5 - - - -
329H GLN* 2.7 68.3 + - + +
345H GLN* 4.8 3.6 + - - -
474H LEU* 1.3 78.1 - - - +
476H PRO* 1.3 76.1 - - + +
477H LYS 4.7 4.0 + - - +
506H NDG 4.2 16.4 + - - -
507H GAL 6.1 1.0 - - - -
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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