Contacts of the strand formed by residues 430 - 437 (chain A) in PDB entry 3L5J
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 LYS 430 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A PHE* 2.8 33.3 + - - +
311A TRP* 4.6 0.4 - - - -
390A ALA* 6.1 1.4 - - - +
391A VAL 4.6 6.5 + - - -
392A LEU* 3.9 15.9 - - - +
428A VAL* 3.4 3.2 - - - +
429A LYS* 1.3 83.4 - - + +
431A TYR* 1.3 66.6 + - - +
432A ILE* 4.2 10.1 - - + -
450A GLN* 3.3 35.4 + - + +
451A GLU 3.3 15.3 - - - +
452A ASP* 4.8 1.3 - - - -
453A GLY* 3.9 5.6 - - - +
477A VAL* 3.0 55.7 + - + +
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Residues in contact with TYR 431 (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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405A VAL* 4.1 13.2 - - + -
421A TRP* 3.2 36.3 + + + -
423A THR* 4.7 2.3 + - - -
424A PRO* 3.3 27.8 - - + +
428A VAL* 3.7 19.7 - - + +
430A LYS* 1.3 76.8 - - - +
432A ILE* 1.3 68.2 + - - +
433A LEU* 4.2 11.0 - - + -
450A GLN* 3.5 7.1 - - - +
451A GLU* 2.9 41.8 + - + +
452A ASP 3.3 15.7 - - - -
453A GLY* 3.4 22.2 + - - -
455A VAL 3.2 19.3 + - - -
474A VAL* 4.0 13.0 - - + -
475A THR 3.7 2.0 - - - -
476A PRO* 4.4 11.0 - - + -
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Residues in contact with ILE 432 (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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311A TRP* 3.6 66.0 - - + +
430A LYS* 4.2 6.1 - - - -
431A TYR* 1.3 81.0 - - - +
433A LEU* 1.3 64.4 + - - +
434A GLU* 4.1 15.0 - - + +
448A TRP* 4.2 6.5 - - + -
449A GLN 3.7 13.7 - - - +
450A GLN* 4.1 19.5 - - + +
473A THR 3.4 4.0 - - - +
474A VAL* 3.6 0.2 - - - -
475A THR* 2.9 41.5 + - - +
477A VAL* 4.2 13.5 - - + -
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Residues in contact with LEU 433 (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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419A VAL* 4.1 20.2 - - + -
421A TRP* 4.2 9.0 - - + -
431A TYR* 4.2 14.1 - - + +
432A ILE* 1.3 75.7 - - - +
434A GLU* 1.3 62.6 + - - +
435A TRP* 3.4 3.7 - - - -
448A TRP* 3.0 24.4 - - - -
449A GLN* 3.1 24.8 + - + +
451A GLU* 3.8 27.1 - - + -
458A THR* 3.7 23.1 - - + -
460A LEU* 3.9 26.7 - - + -
472A ILE* 5.1 1.3 - - + -
473A THR 3.4 4.3 - - - +
474A VAL* 4.1 14.4 - - + -
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Residues in contact with GLU 434 (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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311A TRP* 3.3 28.3 + - - -
312A TYR 4.7 2.3 - - - +
432A ILE* 4.1 9.9 - - + +
433A LEU* 1.3 77.8 - - - +
435A TRP* 1.3 66.2 + - - +
446A THR* 4.1 24.6 + - + +
447A ASP 3.3 7.4 - - - +
448A TRP* 4.1 12.3 - - + -
471A LEU 4.4 0.7 - - - -
472A ILE* 3.4 3.6 - - - +
473A THR* 2.8 47.2 + - - +
475A THR* 5.4 6.1 - - - +
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Residues in contact with TRP 435 (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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433A LEU 3.4 26.0 - - - -
434A GLU* 1.3 78.9 - - - +
436A CYS* 1.3 59.4 + - - +
446A THR* 4.0 3.7 - - - -
447A ASP* 2.9 64.8 + - + +
448A TRP* 3.6 22.0 - - - -
449A GLN* 3.6 18.8 - - + -
460A LEU* 3.6 41.7 - - + -
461A ARG 3.4 29.8 - - - -
462A GLY* 5.1 2.7 - - - -
463A ASN 5.5 0.8 + - - -
464A LEU* 3.5 16.9 - - + +
470A TYR* 3.7 26.3 - + + -
471A LEU 3.3 11.9 - - - +
472A ILE* 4.0 7.4 - - + -
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Residues in contact with CYS 436 (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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435A TRP* 1.3 75.5 - - - +
437A VAL* 1.3 62.4 + - - +
438A LEU* 3.6 14.3 + - - -
444A CYS* 2.0 51.1 - - - -
445A ILE 3.2 30.7 - - - +
446A THR* 3.9 2.0 - - - -
470A TYR* 3.4 9.3 - - - -
471A LEU* 2.8 33.7 + - - -
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Residues in contact with VAL 437 (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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436A CYS* 1.3 76.1 - - - +
438A LEU* 1.3 74.9 + - - +
439A SER* 3.4 10.7 + - - -
442A ALA* 4.9 1.6 - - - +
443A PRO 4.5 12.0 - - - +
444A CYS* 5.1 0.5 - - - -
445A ILE 4.9 0.6 + - - -
468A LYS* 3.8 37.2 - - + -
469A CYS 3.6 7.4 - - - +
470A TYR* 3.2 36.3 - - + +
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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