Contacts of the strand formed by residues 509 - 519 (chain F) in PDB entry 3GUT
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 VAL 509 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355F PHE* 4.2 4.5 - - - -
400F ASN* 3.8 37.6 + - + +
407F HIS* 3.1 25.6 + - - -
506F ASP* 3.6 24.9 + - + +
507F LEU 3.5 1.6 + - - -
508F SER* 1.3 95.0 - - - +
510F VAL* 1.3 62.2 + - - +
536F ALA* 3.9 14.4 - - + -
537F ILE 2.9 18.2 - - - +
538F TYR* 3.8 21.8 - - + -
544F ASN* 5.9 3.6 - - - +
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Residues in contact with VAL 510 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355F PHE* 4.3 15.7 - - + -
397F LEU* 3.6 38.1 - - + -
398F VAL 3.5 7.9 - - - +
400F ASN* 5.3 1.3 - - - -
407F HIS* 3.4 35.7 - - + +
409F HIS* 4.9 2.0 - - + +
439F ILE* 4.7 7.0 - - + -
509F VAL* 1.3 75.0 - - - +
511F ARG* 1.3 73.5 + - - +
536F ALA* 3.4 0.3 - - - +
537F ILE* 2.6 53.0 + - + +
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Residues in contact with ARG 511 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397F LEU* 3.3 5.1 - - - -
398F VAL* 2.8 44.3 + - + +
399F THR 3.4 20.9 - - - +
400F ASN* 3.5 26.5 + - + +
401F GLY 4.9 3.6 + - - -
404F ILE* 4.4 16.1 - - - +
510F VAL* 1.3 83.0 - - - +
512F LEU* 1.3 66.7 + - - +
533F VAL* 4.1 21.7 + - - +
534F SER* 2.9 36.4 + - - +
535F ASP* 4.1 7.4 + - - +
536F ALA* 3.8 16.6 - - + +
537F ILE* 5.3 1.3 - - - -
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Residues in contact with LEU 512 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348F PRO* 4.3 14.6 - - + -
367F LEU* 3.8 25.4 - - + -
380F PRO* 4.7 7.6 - - + -
395F VAL* 4.1 7.2 - - + -
396F GLN 3.5 1.6 - - - -
397F LEU* 3.5 28.0 - - + -
398F VAL* 4.4 0.2 - - - -
411F LEU* 3.9 22.9 - - + -
437F LEU* 5.2 6.1 - - + -
439F ILE* 5.1 0.4 - - + -
511F ARG* 1.3 76.5 - - - +
513F MET* 1.3 60.9 + - - +
514F PHE* 4.0 27.1 - - + -
533F VAL* 3.4 4.5 - - - +
534F SER* 2.9 38.1 + - - +
537F ILE* 4.3 11.7 - - + -
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Residues in contact with MET 513 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394F ILE 3.5 3.8 - - - +
395F VAL* 3.6 1.3 - - - -
396F GLN* 2.9 42.7 + - + +
398F VAL* 3.9 18.8 - - + -
404F ILE* 5.0 1.3 - - - -
464F ASN* 3.4 32.8 - - + +
467F LEU* 5.5 3.8 - - + -
468F LEU* 3.6 33.0 - - + -
512F LEU* 1.3 76.8 - - - +
514F PHE* 1.3 68.7 + - - +
515F THR* 3.8 6.5 + - - +
531F PRO* 4.1 11.4 - - + -
532F VAL 3.2 14.6 - - - +
533F VAL* 3.6 21.5 - - + -
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Residues in contact with PHE 514 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342F LEU* 3.8 9.5 - - + +
344F ILE* 3.7 30.1 - - + -
348F PRO* 5.9 1.3 - - + -
380F PRO* 4.7 10.3 - - + -
381F GLN 5.6 0.2 - - - -
382F VAL* 3.7 22.4 - - + -
393F VAL* 4.4 6.7 - - + -
394F ILE 3.3 5.8 - - - +
395F VAL* 3.8 26.2 - - + -
434F PHE* 3.6 31.6 - + - -
512F LEU* 4.0 33.4 - - + -
513F MET* 1.3 72.1 - - - +
515F THR* 1.3 63.4 + - - +
531F PRO* 3.1 3.6 - - - +
532F VAL* 2.7 52.5 + - + +
534F SER* 4.3 5.4 - - - -
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Residues in contact with THR 515 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342F LEU* 4.1 2.7 - - - -
392F LYS 3.8 0.3 - - - +
393F VAL* 3.3 3.8 - - - -
394F ILE* 2.9 46.3 + - - +
396F GLN* 4.4 1.9 + - - -
464F ASN* 3.0 22.2 + - - +
513F MET* 3.8 6.1 + - - +
514F PHE* 1.3 75.7 + - - +
516F ALA* 1.3 62.7 + - - +
517F PHE* 3.7 25.2 - - + -
528F ARG* 3.9 18.8 - - + -
529F LEU 4.3 1.3 - - - +
531F PRO* 2.8 28.2 - - + +
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Residues in contact with ALA 516 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342F LEU* 3.7 29.6 - - + +
384F ILE* 4.6 7.0 - - + -
392F LYS 3.2 8.1 - - - +
393F VAL* 4.0 10.1 - - + -
515F THR* 1.3 75.4 - - - +
517F PHE* 1.3 63.9 + - - +
518F LEU* 5.5 2.0 - - + -
527F ARG 3.6 0.7 - - - +
528F ARG* 3.5 2.8 - - - -
529F LEU* 3.0 50.5 + - + +
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Residues in contact with PHE 517 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391F ALA* 3.7 2.4 - - - -
392F LYS* 2.7 56.9 + - + +
394F ILE* 3.6 28.0 - - + -
462F GLY 4.9 2.7 - - - -
463F TYR* 3.9 28.3 - + - -
464F ASN* 5.2 0.2 - - - -
478F ALA* 4.8 10.1 - - + -
515F THR* 3.7 17.3 - - + -
516F ALA* 1.3 74.3 - - - +
518F LEU* 1.3 63.9 + - - +
525F PHE* 3.6 30.6 - - + +
526F THR* 4.1 9.9 - - - -
527F ARG 3.0 5.8 - - - +
528F ARG* 3.4 45.3 - - + -
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Residues in contact with LEU 518 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340F PRO* 4.7 6.1 - - + -
384F ILE* 4.7 7.6 - - + -
387F TYR* 3.3 49.8 - - + -
391F ALA* 3.9 16.4 - - + -
516F ALA* 5.5 1.3 - - + -
517F PHE* 1.3 75.6 - - - +
519F PRO* 1.4 70.1 - - + +
525F PHE* 4.0 2.0 - - - -
526F THR 3.4 2.8 + - - -
527F ARG* 2.6 74.1 + - + +
529F LEU* 3.8 36.1 - - + -
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Residues in contact with PRO 519 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387F TYR* 3.6 15.7 - - + +
390F PRO* 3.5 28.3 - - + +
518F LEU* 1.4 83.8 - - + +
520F ASP* 1.3 64.0 + - - +
523F GLY* 3.4 23.1 - - - +
524F SER 3.8 7.6 - - - +
525F PHE* 3.8 19.9 - - + -
527F ARG* 3.3 19.4 + - - +
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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