Contacts of the strand formed by residues 509 - 519 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355D PHE* 4.7 1.6 - - - -
400D ASN* 4.2 22.6 + - + +
407D HIS* 3.1 10.6 + - - -
506D ASP* 3.0 38.1 + - + +
507D LEU 3.5 0.4 - - - -
508D SER* 1.3 85.2 - - - +
510D VAL* 1.3 65.1 + - - +
536D ALA* 3.9 17.0 - - + -
537D ILE 3.6 10.1 - - - +
538D TYR* 3.0 46.7 - - + -
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Residues in contact with VAL 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D PHE* 4.0 24.9 - - + -
397D LEU* 4.2 26.0 - - + -
398D VAL 3.6 7.2 - - - +
399D THR* 5.2 0.9 - - - +
400D ASN* 5.3 0.4 - - - -
407D HIS* 3.1 45.1 - - + +
409D HIS* 4.7 2.5 - - - +
439D ILE* 4.7 9.2 - - + -
509D VAL* 1.3 76.6 - - - +
511D ARG* 1.3 70.3 + - - +
512D LEU* 5.6 0.4 - - + -
536D ALA* 3.8 0.2 - - - -
537D ILE* 2.9 39.7 + - + +
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Residues in contact with ARG 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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396D GLN 3.4 2.1 - - - +
397D LEU* 3.4 3.1 - - - -
398D VAL* 2.7 52.0 + - + +
399D THR 3.4 24.0 + - - +
400D ASN* 3.4 27.8 + - + +
401D GLY 5.2 3.2 + - - -
404D ILE* 4.6 13.6 - - - +
510D VAL* 1.3 80.5 - - - +
512D LEU* 1.3 67.6 + - - +
533D VAL* 3.6 25.8 + - - +
534D SER 2.7 32.0 + - - +
535D ASP* 3.8 17.9 + - - +
536D ALA* 4.2 2.5 - - - -
537D ILE* 5.6 0.4 - - - -
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Residues in contact with LEU 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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348D PRO* 3.4 35.0 - - + -
367D LEU* 4.6 10.8 - - + -
395D VAL* 4.5 3.8 - - + -
396D GLN 3.6 2.7 - - - -
397D LEU* 3.7 24.9 - - + -
398D VAL* 4.4 0.2 - - - -
411D LEU* 4.3 20.2 - - + -
437D LEU* 5.4 5.2 - - + -
439D ILE* 5.2 0.4 - - + -
510D VAL* 5.6 0.9 - - + -
511D ARG* 1.3 76.9 - - - +
513D MET* 1.3 58.3 + - - +
514D PHE* 4.3 21.8 - - + -
533D VAL* 3.4 4.7 - - - +
534D SER* 2.8 43.2 + - - +
537D ILE* 3.8 17.3 - - + -
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Residues in contact with MET 513 (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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394D ILE 3.6 2.9 - - - +
395D VAL* 4.5 1.3 - - - +
396D GLN* 3.0 43.3 + - + +
398D VAL* 3.9 11.2 - - + -
404D ILE* 4.6 3.1 - - - -
464D ASN* 3.6 35.0 - - + +
467D LEU* 5.2 4.5 - - + -
468D LEU* 3.7 36.3 - - + -
512D LEU* 1.3 75.5 - - - +
514D PHE* 1.3 62.0 + - - +
515D THR* 4.0 3.4 + - - +
531D PRO* 3.9 26.0 - - + -
532D VAL 3.8 7.9 - - - +
533D VAL* 3.5 26.9 - - + -
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Residues in contact with PHE 514 (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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342D LEU* 3.6 18.9 - - + +
344D ILE* 3.9 25.4 - - + -
346D GLU 6.1 0.7 - - - -
348D PRO* 5.9 3.1 - - + -
380D PRO* 6.3 2.7 - - + -
382D VAL* 3.4 24.9 - - + -
393D VAL* 4.4 6.7 - - + -
394D ILE 3.3 6.1 - - - +
395D VAL* 3.5 25.6 - - + -
434D PHE* 3.1 35.0 - + - -
437D LEU* 6.4 0.4 - - + -
512D LEU* 4.3 30.3 - - + -
513D MET* 1.3 71.9 - - - +
515D THR* 1.3 60.0 + - - +
531D PRO* 3.4 4.9 - - - +
532D VAL* 3.2 39.1 + - + +
534D SER* 4.6 3.8 - - - -
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Residues in contact with THR 515 (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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342D LEU* 4.2 2.0 - - - -
392D LYS 3.6 1.2 - - - +
393D VAL* 3.3 2.9 - - - -
394D ILE* 2.8 49.1 + - - +
396D GLN* 3.8 7.8 + - - -
464D ASN* 2.9 28.6 + - - +
513D MET* 4.0 3.1 + - - +
514D PHE* 1.3 78.0 + - - +
516D ALA* 1.3 60.6 + - - +
517D PHE* 3.6 26.8 - - + -
528D ARG* 3.8 19.1 - - + -
529D LEU 4.6 0.7 - - - +
531D PRO* 3.6 14.9 - - + +
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Residues in contact with ALA 516 (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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342D LEU* 3.7 27.6 - - + +
384D ILE* 4.5 10.5 - - + -
391D ALA* 5.8 1.1 - - + -
392D LYS 3.1 7.4 - - - +
393D VAL* 4.3 5.6 - - + +
515D THR* 1.3 75.2 - - - +
517D PHE* 1.3 64.0 + - - +
518D LEU* 4.3 2.9 - - + -
527D ARG 3.6 0.6 - - - +
528D ARG* 3.6 3.6 - - - -
529D LEU* 3.1 54.7 + - + -
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Residues in contact with PHE 517 (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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391D ALA* 3.6 1.0 - - - -
392D LYS* 2.5 66.6 + - + +
394D ILE* 3.6 26.7 - - + -
462D GLY 4.6 6.3 - - - -
463D TYR* 3.8 24.2 - + - -
477D GLN* 5.8 0.4 - - - -
478D ALA* 4.6 13.0 - - + -
515D THR* 3.6 19.5 - - + -
516D ALA* 1.3 74.0 - - - +
518D LEU* 1.3 62.6 + - - +
525D PHE* 3.5 29.0 - - - +
526D THR* 4.3 4.9 - - - -
527D ARG 3.1 5.8 - - - +
528D ARG* 3.5 44.0 - - + -
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Residues in contact with LEU 518 (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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340D PRO* 4.9 5.8 - - + -
384D ILE* 4.8 7.2 - - + -
387D TYR* 3.0 61.2 - - + +
391D ALA* 3.7 15.9 - - + -
516D ALA* 5.6 1.1 - - + -
517D PHE* 1.3 75.6 - - - +
519D PRO* 1.4 63.8 - - + +
525D PHE* 3.8 2.2 - - - -
526D THR 3.3 5.4 + - - -
527D ARG* 2.7 70.6 + - + +
529D LEU* 4.4 27.1 - - + -
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Residues in contact with PRO 519 (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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387D TYR* 2.9 16.2 - - + +
390D PRO* 2.9 38.8 - - + +
518D LEU* 1.4 79.5 - - + +
520D ASP* 1.3 66.9 + - - +
523D GLY* 3.8 19.7 - - - +
524D SER 3.8 6.1 - - - +
525D PHE* 3.5 18.1 - - + -
527D ARG* 3.1 14.4 + - - -
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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