Contacts of the strand formed by residues 450 - 458 (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 ILE 450 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A ILE* 3.6 29.8 - - + -
436A ILE* 4.1 28.7 - - + -
439A PHE* 3.7 32.8 - - + +
443A ASN* 4.5 2.2 - - + +
444A LEU* 3.9 34.1 - - + -
449A PRO* 1.3 75.1 - - - +
451A PRO* 1.3 65.8 - - - +
452A ILE* 3.7 11.5 + - + +
487A LEU* 4.4 7.2 - - + -
492A LEU 2.8 14.6 + - - +
493A LEU* 3.6 8.2 - - + -
494A GLN 2.9 23.9 + - - +
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Residues in contact with PRO 451 (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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127A PHE* 3.8 21.3 - - + -
128A GLY* 5.8 0.2 - - - -
131A THR* 3.8 26.0 - - + -
400A ARG 3.3 24.0 - - - +
401A TYR* 3.6 5.7 - - + +
402A ILE* 3.1 23.4 + - - +
439A PHE* 4.3 3.6 - - + -
443A ASN* 3.6 10.3 - - - +
449A PRO 3.5 9.0 - - - +
450A ILE* 1.3 86.7 - - + +
452A ILE* 1.3 62.4 - - - +
494A GLN* 3.2 13.0 - - + +
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Residues in contact with ILE 452 (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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401A TYR* 5.5 0.4 - - - -
402A ILE* 3.5 22.2 - - + +
404A VAL* 4.3 12.3 - - + -
436A ILE* 4.5 7.0 - - + -
450A ILE* 3.9 21.8 - - + +
451A PRO* 1.3 79.4 - - - +
453A ALA* 1.3 62.2 + - - +
454A ILE* 3.9 13.4 + - + -
480A ILE* 4.1 19.1 - - + -
493A LEU* 4.2 15.9 - - + -
494A GLN 2.7 8.6 + - - +
495A PHE* 3.3 43.5 - - + +
496A ARG* 2.9 25.9 + - - +
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Residues in contact with ALA 453 (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 LEU* 3.7 30.1 - - + -
401A TYR* 4.2 9.6 - - + -
402A ILE 2.8 15.0 + - - +
403A SER* 3.4 3.0 + - - -
404A VAL* 2.9 27.7 + - - +
408A PHE* 3.9 16.8 - - + -
451A PRO 4.3 0.4 - - - -
452A ILE* 1.3 74.3 - - - +
454A ILE* 1.3 61.4 + - - +
455A HIS* 4.0 0.8 + - - -
496A ARG* 3.4 9.9 - - + +
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Residues in contact with ILE 454 (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 VAL* 3.5 23.1 - - + +
452A ILE* 4.3 5.8 - - + +
453A ALA* 1.3 70.7 - - - +
455A HIS* 1.3 62.7 + - - +
456A TYR* 3.6 26.2 - - + -
473A ALA* 3.9 19.5 - - + +
476A ILE* 4.0 11.2 - - + -
477A TYR* 3.7 32.3 - - + +
480A ILE* 4.7 0.4 - - + -
495A PHE* 3.7 29.6 - - + -
496A ARG 2.8 11.8 + - - +
497A LEU* 3.3 14.9 - - + -
498A SER* 2.9 26.6 + - - +
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Residues in contact with HIS 455 (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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403A SER* 5.4 0.9 - - - +
404A VAL 3.1 9.5 + - - +
405A GLY* 3.4 2.4 - - - -
406A ASP* 2.8 31.3 + - - -
407A GLY 3.5 26.2 - - - +
408A PHE* 3.5 35.4 - + + -
453A ALA 5.0 0.7 - - - +
454A ILE* 1.3 76.8 - - - +
456A TYR* 1.3 62.4 + - - +
457A ARG* 4.0 8.6 - - - -
498A SER* 2.6 27.4 + - - -
499A VAL* 3.9 7.2 - - - -
500A GLN* 3.0 45.8 + - + +
508A ILE* 3.8 16.6 - - + -
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Residues in contact with TYR 456 (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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405A GLY* 3.4 17.0 - - - -
406A ASP* 3.5 15.5 - - - -
422A LEU* 2.7 31.7 + - - +
423A ASP* 3.5 14.3 - - - -
454A ILE* 3.6 23.8 - - + -
455A HIS* 1.3 78.0 - - - +
457A ARG* 1.3 66.1 + - - +
469A THR* 3.4 21.1 - - + -
472A LYS* 3.5 31.4 - - + -
473A ALA* 4.0 19.1 - - + -
476A ILE* 3.3 30.5 - - + +
498A SER 3.1 7.1 + - - -
499A VAL* 3.1 10.5 - - + +
500A GLN* 3.0 23.4 + - - +
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Residues in contact with ARG 457 (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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196A ARG* 4.9 1.6 - - - +
406A ASP* 2.8 31.3 + - + +
407A GLY 4.8 6.0 + - - -
409A ASP* 2.7 37.0 + - - +
455A HIS* 4.0 7.0 - - - -
456A TYR* 1.3 76.9 - - - +
458A TYR* 1.3 61.8 + - - +
469A THR* 3.8 10.3 + - - +
472A LYS* 5.4 3.1 + - - -
500A GLN* 3.1 41.3 + - - +
501A ALA 2.8 30.1 + - - -
502A GLN* 3.1 31.0 + - + +
503A ASP 3.1 11.9 + - - -
504A ILE* 4.1 2.6 - - - +
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Residues in contact with TYR 458 (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* 1.3 74.1 - - - +
459A ASP* 1.3 64.6 + - - +
460A PRO* 3.4 33.7 - - + +
465A SER* 3.5 8.1 - - - +
466A ARG* 3.7 36.7 + - + -
469A THR* 3.4 23.3 - - - +
499A VAL* 3.5 33.9 - - + -
500A GLN 3.1 14.8 + - - -
501A ALA* 3.4 25.1 + - + +
502A GLN* 2.8 30.8 + - - +
509A GLU* 2.7 25.0 + - - -
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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
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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