Contacts of the strand formed by residues 450 - 458 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B ILE* 3.7 28.9 - - + -
436B ILE* 4.1 29.2 - - + -
439B PHE* 3.7 33.2 - - + +
443B ASN* 4.4 2.2 - - + +
444B LEU* 3.9 33.7 - - + -
449B PRO* 1.3 74.8 - - - +
451B PRO* 1.3 64.5 - - + +
452B ILE* 3.7 11.4 + - + +
487B LEU* 4.2 7.9 - - + -
492B LEU 2.9 12.9 + - - +
493B LEU* 3.5 8.1 - - + -
494B GLN 2.9 22.4 + - - +
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Residues in contact with PRO 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B PHE* 3.9 20.6 - - + -
128B GLY* 5.7 0.7 - - - -
131B THR* 3.7 24.9 - - + -
400B ARG 3.2 24.7 - - - +
401B TYR* 3.6 4.8 - - + +
402B ILE* 3.0 23.4 + - - +
439B PHE* 4.2 4.9 - - + -
443B ASN* 3.7 9.9 - - - +
449B PRO 3.6 8.0 - - - +
450B ILE* 1.3 86.7 - - + +
452B ILE* 1.3 62.0 + - - +
494B GLN* 3.2 13.5 - - + +
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Residues in contact with ILE 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B ILE* 3.4 20.2 - - + +
404B VAL* 4.2 22.9 - - + -
436B ILE* 4.4 10.5 - - + -
450B ILE* 4.0 13.7 - - + +
451B PRO* 1.3 80.8 - - - +
453B ALA* 1.3 61.6 + - - +
454B ILE* 3.9 3.3 + - + -
480B ILE* 4.0 21.1 - - + -
493B LEU* 4.2 21.1 - - + -
494B GLN 2.7 9.4 + - - +
495B PHE* 3.3 41.2 - - + +
496B ARG* 2.9 25.9 + - - +
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Residues in contact with ALA 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 3.7 30.1 - - + -
401B TYR* 4.2 9.1 - - + -
402B ILE 2.8 14.4 + - - +
403B SER* 3.4 3.4 + - - -
404B VAL* 3.0 27.9 + - - +
408B PHE* 4.0 15.9 - - + -
451B PRO 4.2 0.2 - - - -
452B ILE* 1.3 73.2 - - - +
454B ILE* 1.3 60.4 + - - +
455B HIS* 4.0 0.8 + - - +
496B ARG* 3.4 11.0 - - + +
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Residues in contact with ILE 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B VAL* 3.5 23.1 - - + +
452B ILE* 4.3 6.7 - - + -
453B ALA* 1.3 73.0 - - - +
455B HIS* 1.3 61.4 + - - +
456B TYR* 3.7 25.8 - - + -
473B ALA* 3.9 19.7 - - + +
476B ILE* 4.0 11.7 - - + -
477B TYR* 3.6 39.3 - - + +
495B PHE* 3.8 20.6 - - + -
496B ARG 2.8 11.9 + - - +
497B LEU* 3.3 13.6 - - + +
498B SER* 3.0 26.6 + - - +
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Residues in contact with HIS 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B SER* 5.4 0.7 - - - +
404B VAL 3.1 9.3 + - - +
405B GLY* 3.5 1.0 - - - -
406B ASP* 2.8 32.5 + - - -
407B GLY* 3.4 28.9 - - - +
408B PHE* 3.5 32.4 - + + -
453B ALA 5.1 0.7 - - - +
454B ILE* 1.3 76.2 - - - +
456B TYR* 1.3 61.2 + - - +
457B ARG* 4.0 8.7 - - - -
498B SER* 2.7 26.2 + - - -
499B VAL* 4.0 8.3 - - - -
500B GLN* 2.9 45.5 + - + +
508B ILE* 3.8 16.2 - - + -
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Residues in contact with TYR 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B GLY* 3.4 16.9 + - - -
406B ASP* 3.5 17.7 - - - +
422B LEU* 2.8 33.3 + - - +
423B ASP* 3.7 13.2 - - - -
454B ILE* 3.7 23.1 - - + -
455B HIS* 1.3 78.3 - - - +
457B ARG* 1.3 65.9 + - - +
469B THR* 3.3 21.1 - - + -
472B LYS* 3.6 28.9 - - + -
473B ALA* 4.1 19.3 - - + -
476B ILE* 3.2 31.0 - - + +
498B SER 3.2 7.5 + - - -
499B VAL* 3.1 10.2 - - + +
500B GLN* 3.0 22.7 + - - -
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Residues in contact with ARG 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ARG* 4.9 1.6 - - - +
406B ASP* 2.8 31.4 + - + +
407B GLY 4.8 5.8 + - - -
409B ASP* 2.7 36.2 + - - +
455B HIS* 4.0 8.1 - - - -
456B TYR* 1.3 77.1 - - - +
458B TYR* 1.3 61.9 + - - +
469B THR* 3.7 10.9 + - - +
472B LYS* 5.5 2.4 + - - -
500B GLN* 3.0 43.7 + - - +
501B ALA 2.9 29.5 + - - -
502B GLN* 3.3 25.4 + - + +
503B ASP 3.1 17.8 + - - -
504B ILE* 4.2 2.4 - - - +
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Residues in contact with TYR 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B ARG* 1.3 73.0 - - - +
459B ASP* 1.3 62.1 + - - +
460B PRO* 3.6 30.4 - - + +
465B SER* 3.5 8.7 - - - +
466B ARG* 3.7 37.6 + - + -
469B THR* 3.4 25.1 - - - +
499B VAL* 3.5 33.2 - - + -
500B GLN 3.0 14.2 + - - -
501B ALA* 3.4 28.2 + - + +
502B GLN* 2.9 30.8 + - - +
509B GLU* 2.7 24.6 + - - -
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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