Contacts of the strand formed by residues 503 - 512 (chain D) in PDB entry 1F6A
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 PHE 503 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468D ASN 2.9 24.3 + - - -
469D PHE* 2.8 43.6 + - + -
470D MET* 4.1 11.2 - - + -
471D PRO* 4.0 4.0 - - + -
472D GLU* 3.7 54.3 - - + -
495D PRO* 4.4 7.9 - - + -
496D ARG* 3.2 21.8 - - - +
497D LYS* 3.7 36.3 - - + -
498D THR* 4.8 0.9 - - - -
501D SER 5.1 3.6 - - - -
502D GLY* 1.3 74.9 - - - -
504D PHE* 1.3 64.1 + - - +
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Residues in contact with PHE 504 (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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491B SER* 3.6 33.0 - - - -
493B THR* 5.3 5.8 - - + -
508B ARG* 3.8 31.0 - - + +
465D LEU* 4.4 7.6 - - + -
466D ILE 3.2 7.0 - - - +
467D GLN* 3.7 19.7 - - + -
469D PHE* 3.6 2.7 - - - -
493D THR* 4.9 2.0 + - - -
494D GLN 4.2 1.6 - - - +
495D PRO* 3.8 1.0 - - - +
496D ARG* 2.9 67.9 + - + +
497D LYS 3.9 9.0 - - - -
498D THR* 3.4 21.1 - - + -
503D PHE* 1.3 79.4 - - - +
505D VAL* 1.3 65.8 + - - +
506D PHE* 4.5 16.4 - + - -
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Residues in contact with VAL 505 (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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464D CYS 3.9 0.9 - - - +
465D LEU* 3.8 3.3 - - - +
466D ILE* 2.9 47.3 + - + +
469D PHE* 4.1 6.9 - - + -
474D ILE* 4.3 17.3 - - + -
476D VAL* 4.2 18.4 - - + -
492D THR* 3.5 14.1 - - + -
493D THR* 2.9 39.3 - - - +
494D GLN 4.3 2.7 - - - +
495D PRO* 4.5 8.1 - - + -
504D PHE* 1.3 76.7 - - - +
506D PHE* 1.3 67.0 + - - +
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Residues in contact with PHE 506 (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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463B ALA* 3.7 26.5 - - + -
493B THR* 4.8 3.4 - - + -
506B PHE* 3.0 60.8 - + + -
507B SER 3.9 16.8 - - - -
508B ARG* 4.5 9.6 - - + -
463D ALA* 6.1 1.6 - - + -
464D CYS 3.7 4.3 - - - -
465D LEU* 3.1 50.5 - - + -
491D SER 3.8 0.6 - - - +
492D THR* 3.3 3.9 - - - +
493D THR* 2.8 40.6 + - + +
504D PHE* 4.5 14.1 - + - -
505D VAL* 1.3 79.8 - - - +
507D SER* 1.3 59.5 + - - +
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Residues in contact with SER 507 (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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506B PHE* 4.0 4.9 - - - -
463D ALA* 3.2 7.4 - - - +
464D CYS* 3.0 43.9 + - - -
466D ILE* 6.2 0.7 - - - -
476D VAL* 4.1 16.5 - - - +
478D TRP* 3.2 23.3 + - - -
490D HIS* 4.1 2.6 - - - +
491D SER 3.3 4.9 + - - -
492D THR* 3.4 19.7 + - - -
506D PHE* 1.3 76.1 - - - +
508D ARG* 1.3 63.4 + - - +
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Residues in contact with ARG 508 (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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465B LEU* 4.6 8.1 - - + -
467B GLN* 2.9 35.1 + - - +
468B ASN* 4.1 5.7 + - - -
498B THR* 3.2 31.6 - - - +
504B PHE* 3.7 41.4 - - + -
506B PHE* 4.5 6.3 - - + -
461D THR* 3.8 7.4 - - + +
462D LEU 3.4 11.0 - - - +
489D ARG 4.4 0.3 - - - +
490D HIS* 3.2 5.2 - - - -
491D SER* 2.8 44.1 + - - +
507D SER* 1.3 76.4 + - - +
509D LEU* 1.3 62.9 + - - +
510D GLU* 3.1 44.8 + - - +
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Residues in contact with LEU 509 (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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462D LEU* 3.1 26.0 + - + +
478D TRP* 3.3 61.4 - - + +
485D LEU* 3.9 19.1 - - + -
489D ARG* 3.5 40.2 - - + +
490D HIS* 4.1 2.7 - - + +
508D ARG* 1.3 76.5 - - - +
510D GLU* 1.3 76.2 + - - +
511D VAL* 3.3 17.5 + - + +
522D PHE* 5.1 4.5 - - + -
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Residues in contact with GLU 510 (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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468B ASN* 4.5 5.2 - - - +
498B THR* 4.4 5.9 - - - -
499B LYS* 4.0 26.0 + - - +
500B GLY* 4.9 5.4 + - - -
460D ARG 4.3 4.9 - - - -
461D THR* 4.6 10.5 - - + +
489D ARG* 3.5 18.5 + - - +
508D ARG* 3.1 44.9 + - - +
509D LEU* 1.3 86.8 - - - +
511D VAL* 1.3 61.6 + - - +
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Residues in contact with VAL 511 (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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459D LYS* 3.8 9.4 - - - +
460D ARG* 3.1 35.9 + - + +
462D LEU* 4.2 10.3 - - + -
485D LEU* 6.3 0.2 - - + -
489D ARG* 4.7 3.4 - - - +
509D LEU* 3.3 18.8 - - + +
510D GLU* 1.3 81.0 - - - +
512D THR* 1.3 86.8 + - - +
515D GLU* 3.9 11.0 - - + +
516D TRP* 4.4 11.9 - - + -
522D PHE* 3.4 43.5 - - + -
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Residues in contact with THR 512 (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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458D ASP* 4.2 6.5 - - + +
459D LYS* 5.8 2.5 - - + +
489D ARG* 5.1 5.0 + - - -
511D VAL* 1.3 82.9 - - - +
513D ARG* 1.3 73.1 + - + +
514D ALA* 3.8 17.3 - - + +
515D GLU* 2.9 36.2 + - - +
516D TRP* 3.7 4.9 - - - -
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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