Contacts of the strand formed by residues 503 - 512 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B ASN 2.9 24.7 + - - -
469B PHE* 2.8 44.7 + - + -
470B MET* 4.1 10.3 - - + -
471B PRO* 4.0 4.9 - - + -
472B GLU* 3.6 54.5 - - + -
495B PRO* 4.3 8.5 - - + -
496B ARG 3.1 21.8 - - - +
497B LYS* 3.6 35.7 - - + -
498B THR* 4.8 0.9 - - - -
501B SER 5.2 4.0 - - - -
502B GLY* 1.3 75.9 - - - -
504B PHE* 1.3 63.0 + - - +
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Residues in contact with PHE 504 (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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465B LEU* 4.4 7.2 - - + -
466B ILE 3.2 6.5 - - - +
467B GLN* 3.7 19.3 - - + -
469B PHE* 3.6 2.7 - - - -
493B THR* 4.9 1.7 + - - -
494B GLN 4.2 1.2 - - - +
495B PRO* 3.8 1.4 - - - +
496B ARG* 2.9 68.4 + - + +
497B LYS 3.9 9.0 - - - -
498B THR* 3.4 19.1 - - + -
503B PHE* 1.3 78.0 - - - +
505B VAL* 1.3 65.5 + - - +
506B PHE* 4.5 16.8 - + - -
491D SER* 3.4 34.5 - - - -
493D THR* 5.2 6.3 - - + -
508D ARG* 3.7 32.1 - - + +
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Residues in contact with VAL 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B CYS 3.9 0.9 - - - +
465B LEU* 3.8 3.1 - - - +
466B ILE* 2.9 46.7 + - + +
469B PHE* 4.1 6.9 - - + -
474B ILE* 4.3 16.6 - - + -
476B VAL* 4.2 18.4 - - + -
492B THR* 3.5 14.6 - - + -
493B THR* 2.9 38.1 - - - +
494B GLN 4.3 3.6 - - - +
495B PRO* 4.5 7.6 - - + -
504B PHE* 1.3 76.6 - - - +
506B PHE* 1.3 66.6 + - - +
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Residues in contact with PHE 506 (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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463B ALA* 6.1 1.6 - - + -
464B CYS 3.7 3.4 - - - -
465B LEU* 3.1 50.0 - - + -
491B SER 3.8 0.6 - - - +
492B THR* 3.3 3.9 - - - +
493B THR* 2.9 40.2 + - + +
504B PHE* 4.5 13.2 - + - -
505B VAL* 1.3 80.0 - - - +
507B SER* 1.3 59.6 + - - +
463D ALA* 3.8 25.6 - - + -
491D SER 5.8 0.2 - - - -
493D THR* 4.7 4.7 - - + -
506D PHE* 3.0 60.3 - + + -
507D SER 4.0 16.8 - - - -
508D ARG* 4.5 11.2 - - + -
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Residues in contact with SER 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ALA* 3.2 8.3 - - - +
464B CYS* 3.0 44.5 + - - -
476B VAL* 4.1 16.8 - - - +
478B TRP* 3.2 23.9 + - - -
490B HIS* 4.1 2.8 - - - +
491B SER 3.3 5.4 + - - -
492B THR* 3.4 19.5 + - - -
506B PHE* 1.3 75.5 - - - +
508B ARG* 1.3 64.5 + - - +
506D PHE* 3.9 3.6 - - - -
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Residues in contact with ARG 508 (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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461B THR* 3.7 8.1 + - + +
462B LEU 3.4 11.0 - - - +
489B ARG 4.4 0.5 - - - +
490B HIS* 3.2 4.9 - - - -
491B SER* 2.8 45.5 + - - +
507B SER* 1.3 76.4 + - - +
509B LEU* 1.3 62.2 + - - +
510B GLU* 3.1 45.9 + - - +
465D LEU* 4.7 7.4 - - + -
467D GLN* 3.0 32.8 + - - +
468D ASN* 4.2 5.3 + - - -
498D THR* 3.2 32.6 - - - +
504D PHE* 3.8 40.8 - - + -
506D PHE* 4.5 6.3 - - + -
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Residues in contact with LEU 509 (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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462B LEU* 3.1 26.8 + - + +
478B TRP* 3.4 61.4 - - + +
485B LEU* 3.9 18.8 - - + -
489B ARG* 3.5 39.9 - - + +
490B HIS* 4.1 2.7 - - + +
508B ARG* 1.3 75.0 - - - +
510B GLU* 1.3 74.5 + - - +
511B VAL* 3.4 17.2 - - + +
522B PHE* 5.1 3.8 - - + -
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Residues in contact with GLU 510 (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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460B ARG 4.3 4.7 - - - -
461B THR* 4.6 10.3 - - + +
489B ARG* 3.5 18.3 + - - +
508B ARG* 3.1 44.7 + - - +
509B LEU* 1.3 86.8 - - - +
511B VAL* 1.3 61.3 + - - +
468D ASN* 4.7 4.3 - - - +
498D THR* 4.4 7.0 - - - -
499D LYS* 3.9 25.9 + - - +
500D GLY* 4.9 5.0 + - - -
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Residues in contact with VAL 511 (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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459B LYS* 3.8 9.2 - - - +
460B ARG* 3.1 35.4 + - + +
462B LEU* 4.2 10.5 - - + -
489B ARG* 4.7 3.4 - - - +
509B LEU* 3.4 17.3 - - + +
510B GLU* 1.3 81.8 - - - +
512B THR* 1.3 88.4 + - - +
515B GLU* 3.9 10.3 - - - +
516B TRP* 4.4 10.8 - - + -
522B PHE* 3.4 44.4 - - + -
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Residues in contact with THR 512 (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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458B ASP* 4.2 5.6 - - + +
459B LYS* 5.8 2.6 - - + +
489B ARG* 5.1 4.3 + - - -
511B VAL* 1.3 84.2 - - - +
513B ARG* 1.3 72.9 + - + +
514B ALA* 3.8 17.7 - - + +
515B GLU* 2.9 36.2 + - - +
516B TRP* 3.6 4.0 - - - -
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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