Contacts of the strand formed by residues 493 - 501 (chain A) in PDB entry 2FGY
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 LEU 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436A ILE* 4.5 6.5 - - + -
450A ILE* 3.6 13.2 - - + -
452A ILE* 4.2 15.7 - - + -
480A ILE* 4.3 10.5 - - + +
481A LYS* 4.4 0.7 - - - -
484A PHE* 3.8 31.0 - - + +
487A LEU* 4.0 21.7 + - + -
488A ASP* 3.9 28.3 - - + +
491A ASN* 3.3 3.6 - - - +
492A LEU* 1.3 88.2 - - - +
494A GLN* 1.3 69.6 + - - +
495A PHE* 3.6 37.4 - - + -
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Residues in contact with GLN 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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124A LYS* 3.4 25.5 + - - +
125A GLY* 4.1 9.7 - - - +
127A PHE* 4.6 0.9 - - + -
128A GLY* 3.7 31.5 - - - +
449A PRO* 3.6 20.4 - - + -
450A ILE 2.9 13.4 + - - +
451A PRO* 3.2 8.5 - - + +
452A ILE* 2.7 28.2 + - - +
491A ASN* 3.0 30.7 + - - +
493A LEU* 1.3 77.6 + - - +
495A PHE* 1.3 62.3 + - - +
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Residues in contact with PHE 495 (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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132A ALA* 5.7 0.9 - - - +
452A ILE* 3.3 29.8 - - + +
454A ILE* 3.7 24.9 - - + -
477A TYR* 3.5 31.9 - + + -
480A ILE* 3.9 31.4 - - + -
481A LYS* 3.7 29.8 - - + -
488A ASP* 4.5 2.0 - - - -
493A LEU* 3.6 34.3 - - + -
494A GLN* 1.3 75.1 + - - +
496A ARG* 1.3 62.1 + - - +
497A LEU* 4.2 8.1 - - + +
513A SER* 5.9 0.2 - - - -
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Residues in contact with ARG 496 (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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132A ALA* 3.6 30.6 + - + +
135A LEU* 3.4 31.1 + - + +
136A THR* 3.0 45.2 + - - +
139A THR* 4.8 2.6 + - - -
408A PHE* 4.0 6.5 - - - -
452A ILE 2.9 8.8 + - - +
453A ALA* 3.4 6.4 - - + -
454A ILE* 2.8 33.6 + - - +
495A PHE* 1.3 76.2 - - - +
497A LEU* 1.3 68.2 + - - +
498A SER* 3.1 27.6 + - - -
508A ILE* 3.8 14.5 - - - +
510A GLU* 3.9 22.1 + - + +
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Residues in contact with LEU 497 (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 ILE* 3.3 24.5 - - + +
473A ALA* 3.5 37.9 - - + +
474A ARG* 3.8 21.1 - - + -
477A TYR* 4.2 19.1 - - + -
495A PHE* 4.2 6.5 - - + -
496A ARG* 1.3 80.9 - - - +
498A SER* 1.3 65.3 + - - +
510A GLU* 3.4 7.4 - - - +
511A VAL* 2.9 45.1 + - + +
513A SER* 4.0 21.3 - - - -
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Residues in contact with SER 498 (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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408A PHE* 4.0 1.0 - - - -
454A ILE 2.9 8.0 + - - +
455A HIS* 2.6 33.4 + - - +
456A TYR* 3.1 21.0 + - - +
473A ALA* 4.9 3.3 - - - +
496A ARG* 3.1 27.7 + - - -
497A LEU* 1.3 78.8 - - - +
499A VAL* 1.3 68.7 + - - +
508A ILE* 3.7 9.2 - - - -
509A GLU 3.1 15.7 - - - -
510A GLU* 4.1 1.8 - - - -
511A VAL* 4.2 3.1 - - - +
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Residues in contact with VAL 499 (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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455A HIS* 3.9 1.9 - - - -
456A TYR* 3.1 8.1 - - + +
458A TYR* 3.5 23.6 - - + -
466A ARG* 3.8 20.4 - - + +
469A THR* 3.7 33.0 - - + +
470A VAL* 4.3 18.4 - - + -
473A ALA* 4.9 4.0 - - + -
498A SER* 1.3 80.2 - - - +
500A GLN* 1.3 64.3 + - - +
508A ILE* 3.7 1.0 - - - -
509A GLU* 2.7 45.1 + - - +
511A VAL* 4.0 5.6 - - + -
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Residues in contact with GLN 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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407A GLY 5.2 0.3 - - - +
408A PHE* 5.3 0.2 - - - -
409A ASP* 4.8 1.1 + - - -
410A GLU* 2.9 27.3 + - - +
455A HIS* 3.0 28.0 + - + +
456A TYR 3.0 5.3 + - - -
457A ARG* 3.1 36.9 + - - +
458A TYR* 3.1 23.5 + - - -
499A VAL* 1.3 79.9 - - - +
501A ALA* 1.3 73.8 + - - +
505A GLY 4.8 1.4 - - - +
506A SER* 2.8 26.5 + - - +
507A PRO 3.5 19.1 - - - +
508A ILE* 3.5 12.7 - - + +
509A GLU* 4.7 0.9 - - - -
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Residues in contact with ALA 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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457A ARG* 2.8 21.7 + - - -
458A TYR* 3.4 24.3 + - + +
460A PRO* 3.7 27.8 - - + -
500A GLN* 1.3 72.4 - - - +
502A GLN* 1.3 62.7 + - - +
503A ASP* 3.2 7.8 + - + +
506A SER* 3.3 24.0 + - - +
507A PRO* 4.5 0.4 + - + -
509A GLU* 4.4 3.7 + - - +
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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