Contacts of the strand formed by residues 493 - 501 (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 LEU 493 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436B ILE* 4.4 12.3 - - + -
450B ILE* 3.5 9.2 - - + -
452B ILE* 4.2 16.6 - - + -
480B ILE* 4.3 9.9 - - + +
481B LYS* 4.4 1.1 - - - -
484B PHE* 3.6 32.1 - - + +
487B LEU* 4.1 21.0 + - + -
488B ASP* 3.8 28.5 - - + +
491B ASN* 3.4 2.6 - - - +
492B LEU* 1.3 87.9 - - - +
494B GLN* 1.3 67.9 + - - +
495B PHE* 3.6 36.3 - - + -
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Residues in contact with GLN 494 (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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124B LYS* 3.2 31.4 + - - +
125B GLY* 4.1 9.1 - - - +
127B PHE* 4.6 0.4 - - + -
128B GLY* 3.7 27.2 - - - +
129B TYR 4.8 0.2 + - - -
449B PRO* 3.6 19.3 - - + -
450B ILE 2.9 11.3 + - - +
451B PRO* 3.2 9.5 - - + +
452B ILE* 2.7 26.9 + - - +
491B ASN* 3.1 30.1 + - - +
493B LEU* 1.3 77.0 + - - +
495B PHE* 1.3 63.9 + - - +
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Residues in contact with PHE 495 (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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132B ALA* 5.6 1.2 - - - +
452B ILE* 3.3 30.1 - - + -
454B ILE* 3.8 20.0 - - + -
477B TYR* 3.4 34.3 - + + -
480B ILE* 3.8 34.5 - - + -
481B LYS* 3.8 28.3 - - + -
488B ASP* 4.7 1.6 - - - -
493B LEU* 3.6 34.1 - - + -
494B GLN* 1.3 75.8 + - - +
496B ARG* 1.3 63.0 + - - +
497B LEU* 4.1 8.5 - - + +
513B SER* 5.9 0.2 - - - -
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Residues in contact with ARG 496 (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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132B ALA* 3.5 30.7 + - + +
135B LEU* 3.5 29.7 - - + +
136B THR* 3.0 46.1 + - - +
139B THR* 4.9 2.2 + - - -
408B PHE* 3.9 8.5 - - - -
452B ILE 2.9 10.2 + - - +
453B ALA* 3.4 7.9 - - + -
454B ILE* 2.8 27.9 + - - +
495B PHE* 1.3 76.3 - - - +
497B LEU* 1.3 74.2 + - - +
498B SER* 3.1 25.0 + - - -
508B ILE* 3.8 13.1 - - - +
510B GLU* 3.9 24.0 + - - +
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Residues in contact with LEU 497 (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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454B ILE* 3.3 23.3 - - + +
473B ALA* 3.6 33.4 - - + +
474B ARG* 3.9 20.6 - - + -
477B TYR* 4.2 10.8 - - + -
495B PHE* 4.1 19.3 - - + -
496B ARG* 1.3 83.9 - - - +
498B SER* 1.3 63.9 + - - +
510B GLU* 3.4 6.9 - - - +
511B VAL* 2.9 39.9 + - + +
512B ALA 4.1 2.9 - - - +
513B SER* 4.0 23.1 - - - -
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Residues in contact with SER 498 (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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408B PHE* 4.0 1.0 - - - -
453B ALA* 6.0 0.2 - - - +
454B ILE 3.0 6.8 + - - +
455B HIS* 2.7 31.8 + - - +
456B TYR 3.2 19.8 + - - -
473B ALA* 5.0 3.5 - - - +
496B ARG* 3.1 22.5 + - - -
497B LEU* 1.3 78.6 - - - +
499B VAL* 1.3 68.1 + - - +
508B ILE* 3.6 15.9 - - - -
509B GLU 3.1 15.7 - - - -
510B GLU* 4.0 2.2 - - - -
511B VAL* 4.2 3.1 - - - +
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Residues in contact with VAL 499 (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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455B HIS* 4.0 1.8 - - - -
456B TYR* 3.1 9.9 - - + +
458B TYR* 3.5 24.9 - - + -
466B ARG* 3.8 19.1 - - + +
469B THR* 3.8 34.8 - - + +
470B VAL* 4.2 18.4 - - + -
473B ALA* 4.9 4.3 - - + -
498B SER* 1.3 78.5 - - - +
500B GLN* 1.3 60.8 + - - +
508B ILE* 3.8 0.9 - - - -
509B GLU* 2.8 45.5 + - - +
511B VAL* 4.0 6.5 - - + -
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Residues in contact with GLN 500 (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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407B GLY 5.1 0.2 - - - +
408B PHE* 5.4 0.2 - - - -
409B ASP* 4.8 1.4 + - - -
410B GLU* 2.9 28.1 + - - +
455B HIS* 2.9 28.3 + - + +
456B TYR 3.0 4.9 + - - -
457B ARG* 3.0 55.2 + - - +
458B TYR* 3.0 9.3 + - - -
499B VAL* 1.3 78.9 - - - +
501B ALA* 1.3 72.9 + - - +
505B GLY 4.8 0.8 - - - +
506B SER* 2.8 24.7 + - - +
507B PRO 3.3 20.2 - - - +
508B ILE* 3.5 13.3 - - + +
509B GLU* 4.7 0.7 - - - -
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Residues in contact with ALA 501 (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* 2.9 20.4 + - - -
458B TYR* 3.4 24.8 + - + +
460B PRO* 3.7 27.4 - - + -
500B GLN* 1.3 74.1 - - - +
502B GLN* 1.3 62.7 + - - +
503B ASP* 3.3 7.2 + - + +
506B SER* 3.4 22.7 - - - +
507B PRO* 4.5 0.4 + - + -
509B GLU* 4.4 3.5 + - - +
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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