Contacts of the strand formed by residues 509 - 519 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355B PHE* 4.3 4.4 - - - -
398B VAL 4.9 0.2 - - - +
400B ASN* 3.7 39.6 + - + +
407B HIS* 3.1 24.9 + - - -
506B ASP* 3.4 27.9 + - + +
507B LEU 3.4 2.2 + - - -
508B SER* 1.3 94.4 - - - +
510B VAL* 1.3 65.3 + - - +
536B ALA* 4.0 11.2 - - + -
537B ILE 3.1 13.9 - - - +
538B TYR* 3.9 20.4 - - + -
544B ASN* 6.1 2.0 - - - +
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Residues in contact with VAL 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 4.2 16.6 - - + -
397B LEU* 3.5 48.0 - - + -
398B VAL 3.6 6.5 - - - +
400B ASN* 5.4 0.9 - - - -
407B HIS* 3.6 28.5 - - + +
409B HIS* 4.8 1.8 - - - +
439B ILE* 4.8 4.9 - - + -
509B VAL* 1.3 74.2 - - - +
511B ARG* 1.3 69.0 + - - +
536B ALA* 3.4 0.5 - - - -
537B ILE* 2.6 54.7 + - + +
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Residues in contact with ARG 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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397B LEU* 3.2 7.3 - - - +
398B VAL* 3.0 41.0 + - + -
399B THR 3.6 19.5 - - - +
400B ASN* 3.2 32.4 + - + +
401B GLY 5.0 4.4 + - - -
404B ILE* 5.1 10.2 - - - +
510B VAL* 1.3 81.4 - - - +
512B LEU* 1.3 67.5 + - - +
533B VAL* 4.5 17.7 + - + +
534B SER* 2.8 34.4 + - - +
535B ASP* 4.0 8.8 + - - +
536B ALA* 3.6 17.2 - - + +
537B ILE* 4.7 1.6 - - - +
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Residues in contact with LEU 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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348B PRO* 4.5 12.1 - - + -
367B LEU* 4.3 21.8 - - + -
380B PRO* 4.6 7.0 - - + -
395B VAL* 4.3 7.6 - - + -
396B GLN 3.5 1.8 - - - -
397B LEU* 3.5 28.0 - - + -
398B VAL* 4.6 0.2 - - - -
411B LEU* 4.1 18.6 - - + -
437B LEU* 5.0 6.5 - - + -
439B ILE* 5.2 0.9 - - + -
511B ARG* 1.3 76.5 - - - +
513B MET* 1.3 62.3 + - - +
514B PHE* 3.7 31.0 - - + -
533B VAL* 3.3 4.9 - - - +
534B SER* 2.7 41.2 + - - +
537B ILE* 4.2 15.3 - - + -
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Residues in contact with MET 513 (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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394B ILE 3.4 4.3 - - - +
395B VAL* 3.4 1.5 - - - -
396B GLN* 2.7 46.8 + - + +
398B VAL* 3.9 18.8 - - + -
404B ILE* 4.9 3.1 - - - -
464B ASN* 3.6 31.9 - - + +
467B LEU* 5.2 4.3 - - + -
468B LEU* 3.7 32.5 - - + -
512B LEU* 1.3 75.4 - - - +
514B PHE* 1.3 68.9 + - - +
515B THR* 3.9 7.3 + - - +
531B PRO* 4.0 14.1 - - + -
532B VAL 3.4 11.0 - - - +
533B VAL* 3.7 20.0 - - + -
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Residues in contact with PHE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B LEU* 4.5 7.9 - - + -
344B ILE* 3.9 26.9 - - + -
348B PRO* 6.0 1.8 - - + -
380B PRO* 4.7 9.0 - - + -
381B GLN 5.6 0.4 - - - -
382B VAL* 3.6 21.3 - - + -
393B VAL* 4.5 7.4 - - + -
394B ILE 3.3 5.4 - - - +
395B VAL* 3.9 19.5 - - + -
434B PHE* 3.5 37.0 - + - -
512B LEU* 3.7 37.7 - - + -
513B MET* 1.3 74.0 - - - +
515B THR* 1.3 69.3 + - - +
531B PRO* 3.2 1.6 - - - +
532B VAL* 2.7 50.6 + - + +
534B SER* 4.3 4.9 - - - -
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Residues in contact with THR 515 (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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342B LEU* 5.3 1.6 - - - -
392B LYS 3.8 0.3 - - - +
393B VAL* 3.2 5.7 - - - +
394B ILE* 2.9 46.9 + - - +
396B GLN* 4.3 3.1 + - - -
464B ASN* 3.2 22.4 + - - +
513B MET* 3.9 6.8 + - - +
514B PHE* 1.3 75.3 + - - +
516B ALA* 1.3 63.1 + - - +
517B PHE* 4.1 15.5 - - + -
528B ARG* 4.0 23.8 - - + -
529B LEU 4.3 1.1 - - - +
531B PRO* 2.9 28.9 - - + +
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Residues in contact with ALA 516 (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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342B LEU* 3.7 28.7 - - + +
384B ILE* 4.7 6.5 - - + -
391B ALA* 5.8 0.4 - - + -
392B LYS 3.1 6.5 - - - +
393B VAL* 4.0 8.5 - - + -
515B THR* 1.3 77.4 - - - +
517B PHE* 1.3 63.9 + - - +
518B LEU* 5.5 2.0 - - + -
527B ARG 3.5 0.9 - - - +
528B ARG* 3.5 2.8 - - - -
529B LEU* 2.9 52.5 + - + +
531B PRO* 5.3 0.2 - - - +
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Residues in contact with PHE 517 (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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391B ALA* 3.5 4.0 - - - -
392B LYS* 2.6 62.9 + - + +
394B ILE* 3.5 29.4 - - + -
462B GLY 4.7 4.3 - - - -
463B TYR* 3.6 28.5 - + - -
464B ASN* 5.3 0.2 - - - -
478B ALA* 4.5 15.5 - - + -
515B THR* 4.1 13.2 - - + -
516B ALA* 1.3 73.8 - - - +
518B LEU* 1.3 62.5 + - - +
525B PHE* 3.7 28.5 - - + +
526B THR 4.1 9.0 - - - -
527B ARG 3.0 6.5 - - - +
528B ARG* 3.5 41.3 - - + -
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Residues in contact with LEU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PRO* 4.6 5.8 - - + -
384B ILE* 4.7 7.0 - - + -
387B TYR* 3.3 48.2 - - + -
391B ALA* 3.7 18.4 - - + -
516B ALA* 5.5 1.1 - - + -
517B PHE* 1.3 77.3 - - - +
519B PRO* 1.3 68.1 - - + +
525B PHE* 4.1 2.7 - - - -
526B THR 3.5 1.4 + - - -
527B ARG* 2.6 78.4 + - + +
529B LEU* 3.8 33.0 - - + -
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Residues in contact with PRO 519 (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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387B TYR* 3.5 16.2 - - + +
390B PRO* 3.4 28.5 - - + +
518B LEU* 1.3 83.1 - - + +
520B ASP* 1.3 64.4 + - - +
523B GLY* 3.8 22.2 - - - +
524B SER 3.9 6.5 - - - +
525B PHE* 3.8 21.2 - - + -
527B ARG* 3.1 19.6 + - - +
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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