Contacts of the strand formed by residues 468 - 475 (chain D) in PDB entry 2FGJ
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 468 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467D ASP* 1.3 84.6 - - + +
469D THR* 1.3 64.6 + - - +
470D PHE* 4.2 19.9 + - + -
490D LEU 3.8 0.9 - - - +
491D SER* 3.2 4.0 - - - -
492D ILE* 2.7 52.6 + - + +
494D GLN* 5.7 1.6 - - - +
515D ILE* 4.7 13.9 - - + -
526D VAL* 5.1 2.5 - - + -
527D LEU 3.4 7.9 - - - +
528D ILE* 4.6 9.4 - - + -
626D ILE* 3.7 42.6 - - + -
656D THR* 3.7 28.3 - - + +
658D ILE* 4.6 4.9 - - + -
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Residues in contact with THR 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D ASP* 4.5 4.9 + - - -
468D ILE* 1.3 79.3 + - - +
470D PHE* 1.3 65.4 + - - +
471D ARG* 3.6 40.3 + - + +
490D LEU 3.3 7.2 - - - +
491D SER* 4.0 14.8 + - - +
525D GLN 3.5 1.9 - - - +
526D VAL* 3.2 8.8 - - - +
527D LEU* 2.9 53.9 + - + +
530D GLY 5.9 0.3 + - - -
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Residues in contact with PHE 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D ILE* 4.6 12.1 - - + -
469D THR* 1.3 75.9 - - - +
471D ARG* 1.3 66.5 + - - +
473D ILE* 3.6 19.7 - - + -
488D ILE* 3.6 21.3 - - + +
489D ASN* 3.3 2.1 - - - -
490D LEU* 2.5 70.4 + - + +
492D ILE* 5.3 0.7 - - + -
511D LEU* 3.4 39.7 - - + -
514D LEU* 4.0 11.0 - - + -
515D ILE* 3.6 27.6 - - + -
525D GLN 3.7 2.9 - - - -
526D VAL* 3.8 25.4 - - + -
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Residues in contact with ARG 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D THR* 3.6 23.2 - - + +
470D PHE* 1.3 78.2 - - - +
472D ASN* 1.3 72.6 + - + +
473D ILE* 3.2 3.1 + - - +
488D ILE 3.7 0.6 + - - -
489D ASN* 3.7 6.1 - - + +
524D GLY* 3.3 15.9 - - - -
525D GLN* 3.3 23.0 + - - +
527D LEU* 3.6 36.4 - - + +
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Residues in contact with ASN 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D ARG* 1.3 71.7 - - - +
473D ILE* 1.3 61.0 + - - +
474D ARG* 5.1 1.4 - - - +
487D ASN* 3.7 16.5 - - - +
488D ILE 3.2 4.7 + - - -
489D ASN* 2.8 38.8 + - - +
523D ASN* 3.4 17.5 - - - +
524D GLY* 3.4 6.6 + - - -
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Residues in contact with ILE 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470D PHE* 3.6 17.3 - - + -
471D ARG 3.2 3.1 - - - +
472D ASN* 1.3 75.9 - - - +
474D ARG* 1.3 60.0 + - - +
485D LEU* 4.1 3.0 - - + +
486D ASP 3.8 1.7 - - - -
487D ASN 3.3 6.8 + - - -
488D ILE* 3.2 45.9 + - + +
514D LEU* 4.4 12.8 - - + -
521D PRO* 3.7 28.3 - - + -
523D ASN 3.1 13.2 - - - +
524D GLY* 3.8 7.0 - - - -
525D GLN 3.5 18.4 - - - +
526D VAL* 3.4 31.9 - - + -
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Residues in contact with ARG 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D ASN 5.2 1.1 - - - +
473D ILE* 1.3 76.5 - - - +
475D PHE* 1.3 61.3 + - - +
476D ARG* 3.3 25.7 - - - +
483D VAL* 3.6 22.1 - - - +
485D LEU* 3.3 8.5 - - - +
486D ASP* 3.3 28.7 - - - +
487D ASN* 3.9 2.5 - - - +
521D PRO* 3.5 5.8 - - - +
522D GLU* 3.2 51.5 + - + +
523D ASN* 2.8 41.9 + - + +
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Residues in contact with PHE 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474D ARG* 1.3 75.5 - - - +
476D ARG* 1.3 77.0 + - - +
477D TYR* 3.7 44.4 - + - -
483D VAL* 4.0 2.0 - - - -
484D ILE* 3.0 26.3 + - + -
485D LEU* 3.0 29.1 + - + +
510D THR* 3.9 20.2 - - + -
514D LEU* 4.0 22.9 - - + -
519D TYR* 3.4 36.6 - + + -
520D ILE 3.3 27.4 - - - -
521D PRO* 3.9 8.3 - - + -
522D GLU* 4.7 4.7 - - - -
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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