Contacts of the strand formed by residues 473 - 482 (chain A) in PDB entry 1L7R
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 ALA 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A ALA 3.4 0.2 - - - +
417A ASP* 3.0 13.3 + - - +
418A GLN* 2.7 35.9 + - + +
419A ARG* 4.5 1.1 - - + +
422A HIS* 3.5 33.2 - - + +
465A VAL* 3.4 15.7 - - + -
466A ASP 3.7 4.7 - - - -
467A VAL* 4.2 11.4 - - + +
471A GLY 3.2 5.7 + - - +
472A ARG* 1.3 71.4 - - - +
474A ILE* 1.3 59.8 + - - +
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Residues in contact with ILE 474 (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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258A TYR* 4.5 1.8 - - - +
296A ASP 3.9 19.7 - - - +
297A ARG* 4.5 12.3 - - + +
415A PRO* 3.5 42.4 - - + +
416A ALA 3.7 0.9 - - - -
417A ASP* 4.1 12.6 - - + +
465A VAL* 3.4 2.7 - - - -
466A ASP* 2.9 41.7 + - + +
468A PHE* 3.6 31.2 - - + -
472A ARG* 3.9 17.5 - - + -
473A ALA* 1.3 73.0 - - - +
475A ALA* 1.3 70.3 + - - +
476A LEU* 3.6 4.5 + - + +
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Residues in contact with ALA 475 (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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258A TYR* 2.6 30.2 + - + -
402A LEU 4.3 3.8 - - - +
404A GLY* 4.6 6.3 - - - +
414A GLY 4.1 14.1 - - - +
415A PRO* 3.6 1.2 - - - +
416A ALA 3.1 10.8 + - - +
418A GLN* 3.4 28.0 - - + +
463A LYS* 4.3 11.9 - - + -
464A LEU 3.9 5.2 - - - -
465A VAL* 4.3 4.9 - - - -
473A ALA 3.7 1.4 + - - -
474A ILE* 1.3 80.0 - - - +
476A LEU* 1.3 53.1 + - - +
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Residues in contact with LEU 476 (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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257A TRP* 4.4 8.0 - - - +
258A TYR* 3.3 36.0 - - - +
340A MET* 4.0 7.4 - - + -
404A GLY* 5.5 2.3 - - - -
405A THR* 6.1 0.3 - - - +
464A LEU* 2.9 31.6 + - + +
466A ASP* 4.1 9.0 - - + +
474A ILE* 4.0 10.8 - - + +
475A ALA* 1.3 76.7 - - - +
477A CYS* 1.3 63.0 + - - +
509A ALA 4.8 0.3 - - - +
510A THR* 3.9 22.9 + - + +
512A ASN* 3.7 32.3 - - + +
514A PHE* 3.3 37.9 - - + -
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Residues in contact with CYS 477 (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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257A TRP 5.8 0.7 - - - +
404A GLY* 6.1 2.0 - - - -
405A THR* 6.4 2.2 - - - -
445A VAL* 3.9 30.1 - - - -
463A LYS* 3.5 1.8 - - - +
464A LEU* 2.8 45.2 + - - +
476A LEU* 1.3 81.7 - - - +
478A ASP* 1.3 65.7 + - - +
507A MET* 3.2 22.2 - - - +
508A LEU* 5.0 2.2 - - + -
509A ALA 3.6 16.6 - - - +
510A THR* 4.1 8.7 - - - -
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Residues in contact with ASP 478 (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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404A GLY* 4.1 21.0 - - - -
405A THR* 4.5 9.7 + - - +
461A THR* 6.5 0.2 - - - -
462A ALA 3.2 14.4 - - - +
463A LYS* 3.8 21.7 - - + +
477A CYS* 1.3 80.6 - - - +
479A GLY* 1.3 64.5 + - - +
506A ASP 4.1 0.7 - - - +
507A MET* 3.6 20.1 + - - -
508A LEU* 4.1 12.4 - - - +
528A ASN* 3.3 26.6 + - - +
531A LYS* 4.9 3.1 - - - +
532A TYR* 4.1 13.2 + - - -
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Residues in contact with GLY 479 (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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461A THR* 3.4 6.4 - - - +
462A ALA 3.0 28.6 + - - +
478A ASP* 1.3 83.3 - - - +
480A ILE* 1.3 61.3 + - - +
505A ILE* 3.4 10.1 - - - -
506A ASP 3.2 19.5 - - - -
507A MET* 3.8 2.2 - - - +
532A TYR* 4.8 6.5 - - - -
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Residues in contact with ILE 480 (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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155A GLY* 3.0 29.6 + - - +
157A ALA* 4.0 15.7 - - + +
459A ASP* 3.6 31.2 - - + +
460A PHE 3.4 13.2 - - - +
461A THR* 3.6 19.3 - - + -
479A GLY* 1.3 75.0 - - - +
481A VAL* 1.3 68.3 + - - +
505A ILE* 3.5 7.8 - - - +
506A ASP 4.2 6.4 + - - +
527A SER* 5.3 3.8 - - - -
528A ASN 5.3 0.9 - - - +
532A TYR* 3.6 54.7 - - + +
533A ASP 5.2 0.4 - - - +
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Residues in contact with VAL 481 (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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155A GLY* 3.8 7.2 - - - +
459A ASP* 3.3 3.8 - - - -
460A PHE* 2.9 47.4 + - + +
480A ILE* 1.3 78.9 - - - +
482A ARG* 1.3 71.2 + - - +
483A MET* 3.5 6.6 + - - +
485A TYR 4.9 1.6 - - - +
486A ARG* 4.1 24.2 - - + +
503A VAL* 4.1 16.4 - - + -
504A ALA 3.7 21.1 - - - +
505A ILE* 3.7 15.0 - - + -
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Residues in contact with ARG 482 (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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152A TYR* 5.9 1.0 - - - -
155A GLY 2.9 17.0 + - - +
156A GLY 3.4 16.6 + - - +
157A ALA* 3.6 22.1 - - + +
158A LEU* 3.8 2.4 - - - +
457A ASP* 4.2 1.8 - - - +
459A ASP* 2.8 41.8 + - - +
480A ILE* 4.2 1.0 - - - +
481A VAL* 1.3 70.4 - - - +
483A MET* 1.3 55.6 + - - +
484A ARG* 4.1 9.4 - - + +
485A TYR* 2.8 49.4 + - + +
486A ARG 3.4 3.5 + - - -
533A ASP* 2.9 47.5 + - - -
535A ASN* 3.5 19.3 + - - +
542A ILE* 3.6 27.7 - - - +
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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