Contacts of the strand formed by residues 454 - 471 (chain A) in PDB entry 1FCP
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 VAL 454 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ALA 3.8 0.7 - - - +
450A GLN* 3.5 2.0 - - - -
451A TRP* 2.7 53.3 + - + +
452A ASP 2.7 11.0 + - - +
453A LYS* 1.3 83.3 - - - +
455A LEU* 1.3 63.2 + - - +
456A VAL* 3.8 8.1 + - + +
491A VAL* 4.7 13.0 - - + -
492A ASN 4.1 2.2 - - - -
493A TYR* 4.1 24.2 - - + +
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 5.3 1.6 - - + -
45A LYS* 3.2 60.3 - - + +
448A GLN* 4.3 19.7 - - + +
449A ALA 3.3 19.5 - - - +
450A GLN* 3.5 28.0 - - + +
453A LYS 3.9 0.6 - - - -
454A VAL* 1.3 74.0 - - - +
456A VAL* 1.3 60.0 + - - +
457A THR* 4.2 8.5 + - - +
491A VAL* 3.5 5.2 - - - +
492A ASN* 2.8 46.5 + - + +
494A LEU* 5.5 4.3 - - + -
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Residues in contact with VAL 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ASP* 3.7 2.1 - - - +
448A GLN* 3.9 0.3 - - - -
449A ALA* 2.7 54.0 + - + +
451A TRP* 5.8 2.5 - - + +
454A VAL* 4.8 9.2 - - + +
455A LEU* 1.3 75.6 - - - +
457A THR* 1.3 69.1 + - - +
458A LEU* 4.2 7.5 + - + -
490A GLY 3.7 10.5 - - - +
491A VAL* 4.3 14.4 - - + +
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Residues in contact with THR 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 5.0 1.8 - - + -
45A LYS 4.3 7.6 + - - -
47A PRO* 3.7 36.4 - - + +
446A GLN* 4.1 23.3 - - + +
447A ASP 3.6 10.5 - - - +
448A GLN* 4.3 14.9 + - + +
455A LEU* 4.2 8.5 - - - +
456A VAL* 1.3 76.6 + - - +
458A LEU* 1.3 65.2 + - - +
488A ARG* 4.5 9.6 - - + +
489A GLY* 3.5 0.6 - - - -
490A GLY 2.7 38.2 + - - +
491A VAL* 4.8 0.2 - - - +
492A ASN* 5.1 1.4 + - - -
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Residues in contact with LEU 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLN* 3.5 4.8 - - - +
447A ASP* 3.0 31.6 + - + +
456A VAL* 4.2 8.9 + - + +
457A THR* 1.3 77.8 - - - +
459A GLY* 1.3 62.5 + - - +
487A TRP* 3.7 21.3 - - + -
488A ARG* 3.3 18.8 - - - +
489A GLY* 3.7 11.9 - - - -
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Residues in contact with GLY 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.8 8.1 - - - -
445A VAL 3.1 13.9 - - - -
446A GLN* 3.9 7.2 - - - -
458A LEU* 1.3 82.9 - - - +
460A GLY* 1.3 55.5 + - - -
487A TRP* 3.1 7.4 - - - +
488A ARG* 2.7 37.6 + - - +
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Residues in contact with GLY 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.7 6.9 - - - +
444A TYR* 3.2 4.2 - - - +
445A VAL* 2.8 33.4 + - - +
446A GLN* 5.2 0.2 - - - +
459A GLY* 1.3 74.6 - - - -
461A ARG* 1.3 61.3 + - - +
485A PHE* 4.3 9.9 - - - -
486A THR 3.1 12.1 - - - -
487A TRP* 3.5 7.4 - - - -
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Residues in contact with ARG 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER 3.2 20.2 - - - +
138A VAL 3.6 7.4 - - - +
139A LEU 2.9 27.4 + - - -
140A TYR* 3.2 8.9 + - - +
141A GLY* 3.2 13.6 - - - -
379A ASP* 2.9 40.4 + - - +
440A GLN* 3.6 6.3 - - - +
442A GLY* 3.8 10.4 - - - +
443A VAL 3.2 11.7 - - - +
444A TYR* 3.4 21.5 - - + -
460A GLY* 1.3 75.8 - - - +
462A TYR* 1.3 64.5 + - - +
463A ASP* 2.6 39.6 + - - +
484A GLN 3.9 0.3 - - - +
485A PHE* 3.1 10.3 - - - -
486A THR* 2.6 38.3 + - - +
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Residues in contact with TYR 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A THR 3.8 0.7 - - - +
442A GLY* 3.2 2.9 - - - -
443A VAL* 2.9 46.4 + - + +
461A ARG* 1.3 74.1 - - - +
463A ASP* 1.3 65.2 + - - +
464A TRP* 3.4 50.3 - + - -
483A LYS* 3.0 37.8 + - + +
484A GLN* 3.3 18.4 - - - -
485A PHE* 3.7 22.4 - + + -
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Residues in contact with ASP 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER 4.3 1.2 - - - +
141A GLY* 3.4 13.5 - - - -
440A GLN* 3.3 16.2 - - - +
441A THR 3.3 4.4 - - - +
461A ARG* 2.6 58.2 + - - +
462A TYR* 1.3 75.4 - - - +
464A TRP* 1.3 65.7 + - - +
465A ALA* 3.7 0.6 - - - +
482A ASP 3.5 0.5 - - - +
483A LYS* 3.2 6.2 - - - -
484A GLN 2.7 34.5 + - - +
486A THR* 4.6 2.4 + - - -
509A PHE* 3.6 31.2 - - + -
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Residues in contact with TRP 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LYS 3.4 3.3 - - - +
440A GLN* 3.2 6.2 - - - -
441A THR* 2.8 61.3 + - + +
443A VAL* 4.1 29.4 - - + -
462A TYR* 3.4 33.2 - + - -
463A ASP* 1.3 72.4 - - - +
465A ALA* 1.3 59.2 + - - +
466A ASP* 3.5 17.8 + - - +
482A ASP 3.5 2.9 - - - -
483A LYS* 3.7 32.5 - - + +
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Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 5.1 3.8 - - + -
439A LYS 3.5 5.8 - - - -
440A GLN* 4.2 12.1 - - + +
463A ASP 3.7 0.4 - - - -
464A TRP* 1.3 70.7 - - - +
466A ASP* 1.3 60.2 + - - +
467A GLN* 5.5 0.5 - - - +
480A ARG 3.7 2.3 - - - +
481A ASP* 3.4 1.0 - - - -
482A ASP* 2.6 53.6 + - + +
509A PHE* 4.1 13.5 - - + -
511A PRO* 4.0 21.0 - - + +
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Residues in contact with ASP 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLN* 3.6 1.9 - - - +
439A LYS* 2.8 57.8 + - + +
464A TRP* 4.1 19.0 - - - +
465A ALA* 1.3 78.6 + - - +
467A GLN* 1.3 59.7 + - - +
480A ARG 3.5 0.4 - - - -
481A ASP* 2.9 40.9 - - - +
482A ASP 4.0 1.0 + - - +
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Residues in contact with GLN 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LYS 3.6 13.9 - - - +
438A GLN* 4.5 9.1 - - + +
465A ALA 5.5 0.4 - - - +
466A ASP* 1.3 76.6 - - - +
468A GLU* 1.3 66.9 + - - +
469A SER* 5.6 5.9 + - - -
478A ASP 5.7 0.2 - - - +
479A LYS* 3.2 5.5 - - - +
480A ARG* 2.8 48.5 + - + +
481A ASP* 4.6 2.1 - - - +
482A ASP* 5.1 0.6 + - - -
511A PRO* 4.2 16.2 - - - +
512A SER 2.7 27.8 + - - -
513A SER* 3.7 21.3 - - - +
521A ILE* 4.0 15.6 - - + +
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Residues in contact with GLU 468 (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 LEU 3.6 2.8 - - - +
436A ASN* 4.8 0.2 - - - -
437A LYS* 2.9 64.2 + - + +
467A GLN* 1.3 81.4 - - - +
469A SER* 1.3 63.1 + - - +
470A LEU* 6.0 1.9 - - + +
477A THR* 3.9 14.9 - - + +
478A ASP 3.2 6.7 - - - -
479A LYS* 3.2 32.7 - - + +
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Residues in contact with SER 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ILE* 3.1 15.8 - - - +
435A LEU 3.4 3.8 - - - -
436A ASN* 2.9 27.0 + - - +
467A GLN* 5.6 5.4 + - - -
468A GLU* 1.3 74.1 - - - +
470A LEU* 1.3 59.3 + - - +
471A ASN* 5.9 0.3 - - - +
476A THR* 3.8 0.7 + - - +
477A THR* 3.2 7.5 - - - -
478A ASP* 2.6 49.5 + - - +
513A SER 6.2 0.2 - - - -
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Residues in contact with LEU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ILE* 3.1 7.7 - - - +
435A LEU* 2.7 53.8 + - + +
468A GLU* 5.4 2.4 - - + +
469A SER* 1.3 74.2 + - - +
471A ASN* 1.3 62.9 + - - +
472A ARG* 3.5 38.1 + - + +
475A GLY* 4.5 9.2 - - - +
476A THR 3.3 8.7 - - - +
477A THR* 2.8 28.7 - - + +
4B GMH 4.4 10.1 - - - +
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Residues in contact with ASN 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TYR* 5.1 5.5 - - - -
433A ARG 3.7 4.4 + - - +
434A ILE* 3.2 26.3 - - + +
469A SER* 4.1 0.8 - - - +
470A LEU* 1.3 72.3 - - - +
472A ARG* 1.3 52.4 + - - +
473A VAL* 2.6 38.0 + - - +
474A ALA* 3.0 20.2 + - - +
475A GLY* 2.7 26.5 + - - -
476A THR* 3.0 29.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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