Contacts of the strand formed by residues 477 - 494 (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 THR 477 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A GLU* 3.9 18.6 - - + +
469A SER 3.2 7.2 - - - +
470A LEU* 2.8 30.8 - - + +
475A GLY 4.0 2.7 + - - -
476A THR* 1.3 74.9 + - - +
478A ASP* 1.3 60.9 + - - +
479A LYS* 3.9 31.5 + - + +
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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
----------------------------------------------------------
467A GLN* 5.7 0.2 - - - +
468A GLU* 3.2 1.7 - - - -
469A SER* 2.6 47.6 + - - +
476A THR* 4.0 16.0 + - - -
477A THR* 1.3 72.2 - - - +
479A LYS* 1.3 63.2 + - - +
515A VAL* 4.2 17.1 - - - +
519A GLY 4.0 16.1 - - - +
520A ASN* 5.3 0.5 - - - -
521A ILE* 3.7 26.9 - - + +
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Residues in contact with LYS 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A GLN* 3.2 13.5 - - - +
468A GLU* 3.2 36.3 - - + +
477A THR* 3.9 19.9 + - + +
478A ASP* 1.3 81.8 - - - +
480A ARG* 1.3 65.3 + - - +
481A ASP* 5.8 1.8 - - - +
521A ILE* 3.8 9.1 + - - +
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Residues in contact with ARG 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ALA 3.7 1.6 - - - +
466A ASP* 3.5 1.0 - - - -
467A GLN* 2.8 42.2 + - + +
479A LYS* 1.3 77.5 - - - +
481A ASP* 1.3 70.1 + - - +
482A ASP* 2.9 40.0 + - - +
512A SER 5.2 0.2 - - - -
521A ILE* 2.9 46.3 + - + -
522A PHE 3.4 15.4 + - - -
523A ALA* 3.4 28.1 - - - +
524A PRO* 3.8 1.2 - - - +
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Residues in contact with ASP 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ALA 3.4 0.2 - - - -
466A ASP* 2.9 41.3 - - - +
467A GLN 4.1 3.3 + - - +
479A LYS* 5.8 1.6 - - - +
480A ARG* 1.3 83.1 + - - +
482A ASP* 1.3 63.7 + - - +
483A LYS* 4.0 7.3 + - + +
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Residues in contact with ASP 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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463A ASP 3.5 0.3 - - - +
464A TRP* 3.5 3.5 - - - -
465A ALA* 2.6 56.5 + - + +
466A ASP* 4.3 0.9 - - - +
467A GLN* 5.1 1.0 + - - -
480A ARG* 2.9 41.5 + - - -
481A ASP* 1.3 73.9 - - - +
483A LYS* 1.3 64.7 + - - +
484A GLN* 4.1 5.4 + - - +
509A PHE* 5.1 2.9 - - + -
511A PRO* 3.9 13.5 - - + +
524A PRO* 3.1 35.8 - - + +
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Residues in contact with LYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A TYR* 3.0 25.5 + - + +
463A ASP 3.2 5.4 - - - -
464A TRP* 3.7 32.3 - - + +
481A ASP* 4.0 7.7 + - + +
482A ASP* 1.3 75.7 + - - +
484A GLN* 1.3 74.5 + - - +
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Residues in contact with GLN 484 (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 ARG 3.9 0.5 - - - +
462A TYR* 3.3 9.1 - - - -
463A ASP* 2.7 38.6 + - - +
482A ASP* 4.1 3.9 + - + -
483A LYS* 1.3 88.6 + - - +
485A PHE* 1.3 71.3 + - - +
486A THR* 5.0 0.8 + - + -
509A PHE* 3.5 51.1 - - + -
524A PRO* 4.7 18.3 - - - +
526A LYS* 2.9 39.8 + - - +
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Residues in contact with PHE 485 (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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460A GLY* 4.3 5.6 - - - -
461A ARG 3.1 35.4 - - - -
462A TYR* 3.7 22.8 - + + -
484A GLN* 1.3 82.4 - - - +
486A THR* 1.3 70.1 + - - +
487A TRP* 3.8 40.2 - + + -
507A GLU* 4.2 4.3 - - - +
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Residues in contact with THR 486 (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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137A SER* 3.5 25.9 + - - -
138A VAL* 4.0 5.8 - - - +
460A GLY* 3.1 0.9 - - - -
461A ARG* 2.6 42.9 + - - +
463A ASP* 4.6 2.6 + - - -
484A GLN* 5.0 1.4 + - + -
485A PHE* 1.3 87.0 - - - +
487A TRP* 1.3 60.0 + - - +
507A GLU* 3.6 41.3 - - + +
508A SER* 3.9 15.7 - - - +
509A PHE* 4.4 13.6 - - + -
528A LYS* 5.9 1.3 - - - +
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Residues in contact with TRP 487 (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 4.7 - - - +
458A LEU* 3.7 20.9 - - + -
459A GLY 3.1 16.4 - - - +
460A GLY* 3.5 6.5 - - - -
485A PHE* 3.8 23.6 - + + -
486A THR* 1.3 76.4 - - - +
488A ARG* 1.3 79.0 + - - +
489A GLY* 3.7 18.2 - - - -
505A TYR* 3.3 34.4 - + + +
506A SER 4.2 0.5 - - - -
507A GLU* 3.1 58.2 + - - +
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Residues in contact with ARG 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY 3.1 28.7 + - - -
37A THR* 4.3 2.0 - - - +
46A VAL* 5.2 0.8 - - - +
47A PRO* 4.3 20.6 - - + +
48A GLN* 2.6 49.2 + - - +
132A MSE 4.4 3.2 - - - +
138A VAL* 3.4 26.4 - - + +
139A LEU* 3.5 7.5 - - - +
446A GLN* 2.8 29.1 + - - -
457A THR* 4.5 9.0 - - + +
458A LEU* 3.3 4.4 - - - +
459A GLY 2.7 34.0 + - - +
487A TRP* 1.3 81.6 - - - +
489A GLY* 1.3 67.7 + - - +
504A SER* 5.1 2.9 - - - -
505A TYR 3.1 16.6 - - - +
506A SER* 4.1 12.3 - - - +
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Residues in contact with GLY 489 (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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457A THR 3.5 6.1 - - - -
458A LEU* 3.7 14.6 - - - -
487A TRP* 3.7 10.6 - - - -
488A ARG* 1.3 77.4 - - - +
490A GLY* 1.3 55.8 + - - -
503A PHE* 5.4 2.0 - - - -
504A SER* 3.2 2.6 - - - -
505A TYR* 2.7 41.6 + - - +
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Residues in contact with GLY 490 (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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47A PRO* 3.9 12.0 - - - +
456A VAL* 3.7 1.4 - - - +
457A THR* 2.7 39.2 + - - +
488A ARG* 5.0 0.4 - - - +
489A GLY* 1.3 75.1 - - - -
491A VAL* 1.3 69.8 + - - +
503A PHE* 3.3 13.7 - - - -
504A SER* 3.4 9.0 - - - -
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Residues in contact with VAL 491 (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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454A VAL* 4.7 13.5 - - + -
455A LEU 3.5 13.9 - - - +
456A VAL* 4.3 14.4 - - + -
457A THR 4.8 0.2 - - - +
490A GLY* 1.3 80.3 - - - +
492A ASN* 1.3 73.4 + - - +
493A TYR* 4.2 5.1 + - + +
502A TYR* 3.1 23.2 - - - -
503A PHE* 2.9 43.6 + - + -
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Residues in contact with ASN 492 (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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44A GLN 2.6 30.1 + - - +
45A LYS* 4.1 7.8 - - - +
46A VAL 3.4 14.6 + - - -
47A PRO* 3.3 29.4 - - - +
455A LEU* 2.8 45.6 + - + +
457A THR* 5.1 1.4 + - - -
490A GLY 4.8 0.2 - - - -
491A VAL* 1.3 81.5 - - - +
493A TYR* 1.3 59.5 + - - +
494A LEU* 3.2 5.6 + - + +
500A THR* 3.9 7.1 - - + +
501A PRO 3.5 3.4 - - - -
502A TYR* 3.2 23.4 - - - +
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Residues in contact with TYR 493 (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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453A LYS* 3.3 26.0 - - + +
454A VAL* 4.1 22.0 - - + +
491A VAL* 4.2 6.3 - - + +
492A ASN* 1.3 67.6 - - - +
494A LEU* 1.3 59.3 + - - +
495A PHE* 2.9 46.5 + + - -
500A THR* 3.7 3.5 - - - -
501A PRO* 3.0 39.7 + - + +
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Residues in contact with LEU 494 (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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44A GLN* 3.8 25.8 - - + +
45A LYS* 3.4 37.5 - - + -
450A GLN* 4.3 13.2 - - - +
453A LYS* 2.9 44.2 + - - +
455A LEU* 5.5 3.4 - - + -
492A ASN* 3.2 7.4 + - + +
493A TYR* 1.3 70.3 - - - +
495A PHE* 1.3 76.1 + - - +
496A ASP* 6.2 0.2 - - - -
498A GLY* 5.1 3.6 - - - +
500A THR* 3.5 26.5 - - + +
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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