Contacts of the strand formed by residues 499 - 510 (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 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A PHE* 3.1 39.9 + - + +
497A ASN* 3.1 35.7 - - - +
498A GLY* 1.3 74.5 - - - +
500A THR* 1.3 61.5 + - - +
501A PRO* 3.6 10.2 - - + +
534A VAL* 5.8 5.6 - - + -
535A LYS 3.4 6.1 - - - -
536A TYR* 3.7 17.5 - - + -
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Residues in contact with THR 500 (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* 3.1 46.1 - - + +
45A LYS* 5.2 0.2 - - - -
492A ASN* 3.9 14.8 - - + +
493A TYR 3.7 9.0 - - - +
494A LEU* 3.5 18.2 - - + +
498A GLY 2.9 15.2 + - - -
499A VAL* 1.3 73.8 + - - +
501A PRO* 1.3 69.6 - - - +
502A TYR* 3.6 6.6 + - - -
534A VAL* 3.6 0.7 - - - +
535A LYS* 2.6 33.4 + - - +
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Residues in contact with PRO 501 (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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492A ASN* 3.5 1.0 - - - -
493A TYR* 3.0 49.8 + - + +
495A PHE* 4.4 14.8 - - + -
499A VAL* 3.6 11.0 - - + +
500A THR* 1.3 89.6 - - - +
502A TYR* 1.3 60.6 + - - +
534A VAL* 3.6 26.9 - - + -
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Residues in contact with TYR 502 (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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46A VAL 4.6 0.2 - - - -
47A PRO* 3.6 31.9 - - + -
48A GLN 4.2 0.9 - - - -
49A SER* 3.6 8.3 + - - -
491A VAL 3.1 12.3 - - - +
492A ASN* 3.2 22.0 - - - +
500A THR 3.8 10.3 - - - -
501A PRO* 1.3 76.8 - - - +
503A PHE* 1.3 70.0 + - - +
531A GLU* 2.6 32.8 + - + -
532A VAL* 3.3 2.6 - - - +
533A GLY* 2.7 71.1 + - - +
534A VAL 3.9 0.7 - - - -
535A LYS* 3.5 36.5 - - + -
546A THR* 4.7 1.6 + - - -
547A GLY 4.3 1.7 + - - -
548A ALA* 3.4 12.8 - - - +
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Residues in contact with PHE 503 (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* 4.7 0.2 - - - +
489A GLY 5.4 0.9 - - - -
490A GLY* 5.2 1.6 - - - -
491A VAL* 2.9 63.0 + - + +
502A TYR* 1.3 84.3 - - - +
504A SER* 1.3 71.8 + - - +
505A TYR* 5.7 0.4 - - + -
531A GLU 3.0 7.6 - - - +
532A VAL* 3.4 24.9 - - + +
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Residues in contact with SER 504 (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* 2.5 33.0 + - - -
48A GLN* 4.1 8.5 - - - +
488A ARG* 5.1 3.3 - - - -
489A GLY 3.2 13.7 - - - -
490A GLY* 3.4 9.4 - - - -
502A TYR* 4.9 0.2 - - - -
503A PHE* 1.3 84.2 - - - +
505A TYR* 1.3 64.1 + - - +
506A SER* 5.4 1.4 - - - -
529A GLN* 3.9 1.4 + - - +
530A TYR* 3.9 2.8 - - - -
531A GLU* 2.7 41.8 + - - +
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Residues in contact with TYR 505 (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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487A TRP* 3.3 42.6 - + + -
488A ARG* 3.1 8.8 - - - +
489A GLY 2.7 36.5 + - - +
503A PHE* 5.3 0.2 - - - -
504A SER* 1.3 73.0 - - - +
506A SER* 1.3 67.6 + - - +
507A GLU* 2.7 38.0 + - + -
528A LYS* 3.4 19.2 - - + +
529A GLN 3.5 14.8 - - - -
530A TYR* 3.2 47.7 + + + -
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Residues in contact with SER 506 (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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48A GLN* 4.1 10.1 + - - -
135A PRO* 3.0 41.0 + - - +
138A VAL* 5.4 1.7 - - - +
487A TRP 4.2 4.5 - - - -
488A ARG* 4.1 18.6 - - - +
504A SER* 5.4 1.6 - - - -
505A TYR* 1.3 80.0 - - - +
507A GLU* 1.3 76.3 + - - +
528A LYS* 3.6 2.6 - - - -
529A GLN* 3.1 34.2 + - - +
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Residues in contact with GLU 507 (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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135A PRO* 3.2 12.9 - - - +
137A SER* 3.8 14.7 + - - -
138A VAL* 4.1 4.3 + - - +
485A PHE* 4.2 3.6 - - - +
486A THR* 3.6 23.1 - - + +
487A TRP* 3.1 53.1 + - - +
488A ARG* 5.1 0.2 - - - +
505A TYR* 2.7 30.1 + - + +
506A SER* 1.3 84.5 + - - +
508A SER* 1.3 59.8 + - - +
527A GLY 3.0 9.9 - - - +
528A LYS* 3.1 22.0 + - - +
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Residues in contact with SER 508 (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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135A PRO* 3.7 18.7 - - - +
136A VAL 4.1 2.5 - - - -
137A SER* 3.1 16.2 - - - -
143A SER* 3.9 11.1 + - - -
144A SER 4.5 0.9 - - - -
145A PRO* 3.5 19.3 - - - +
486A THR* 4.1 5.1 - - - +
507A GLU* 1.3 76.7 - - - +
509A PHE* 1.3 62.3 + - - +
526A LYS* 3.3 6.2 - - - +
527A GLY* 2.6 46.2 + - - +
528A LYS* 5.6 0.5 + - - -
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Residues in contact with PHE 509 (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* 3.1 15.5 + - - -
141A GLY 3.7 1.8 - - - -
142A LYS* 3.2 43.5 - - + -
143A SER 2.8 24.7 + - - -
440A GLN* 3.6 8.7 - - - -
463A ASP* 3.6 31.4 - - + -
465A ALA* 4.1 9.2 - - + -
482A ASP* 5.1 1.6 - - + -
484A GLN* 3.5 42.4 - - + +
486A THR* 4.4 9.0 - - + -
508A SER* 1.3 77.2 - - - +
510A GLU* 1.3 63.5 + - - +
511A PRO* 3.6 19.5 - - + -
524A PRO* 4.4 7.4 - - + -
525A SER 3.4 10.5 - - - +
526A LYS* 4.3 3.1 - - + +
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Residues in contact with GLU 510 (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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96A ALA 4.6 1.2 - - - +
97A ALA* 3.6 9.9 - - - +
98A GLU* 3.1 44.0 + - + +
142A LYS* 6.0 0.2 - - + -
143A SER 3.6 11.9 - - - +
144A SER* 3.1 28.9 + - - -
145A PRO* 3.8 8.9 - - + +
509A PHE* 1.3 75.3 - - - +
511A PRO* 1.3 76.0 - - + +
512A SER* 5.2 0.5 - - - -
524A PRO* 3.7 3.6 - - - -
525A SER* 2.9 48.2 + - - +
554A LYS* 4.7 1.4 - - - -
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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