Contacts of the strand formed by residues 509 - 519 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355H PHE* 4.8 0.7 - - - -
399H THR* 5.7 0.3 - - - -
400H ASN* 3.8 35.3 + - + +
407H HIS* 3.0 11.9 + - - -
506H ASP* 2.9 36.4 + - + +
507H LEU 3.5 0.4 - - - -
508H SER* 1.3 86.0 - - - +
510H VAL* 1.3 64.6 + - - +
536H ALA* 4.0 10.1 - - + -
537H ILE 3.6 10.3 - - - +
538H TYR* 2.9 44.4 - - + -
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Residues in contact with VAL 510 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355H PHE* 3.9 23.6 - - + -
397H LEU* 4.2 25.8 - - + -
398H VAL 3.5 7.2 - - - +
400H ASN* 5.2 1.3 - - - +
407H HIS* 2.9 45.3 - - + +
409H HIS* 4.9 1.3 - - - +
439H ILE* 4.7 9.2 - - + -
509H VAL* 1.3 75.8 - - - +
511H ARG* 1.3 71.7 + - - +
512H LEU* 5.4 0.2 - - + -
536H ALA* 3.8 0.3 - - - -
537H ILE* 2.9 41.3 + - + +
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Residues in contact with ARG 511 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397H LEU* 3.5 4.4 - - - -
398H VAL* 2.8 52.1 + - + +
399H THR 3.7 15.3 - - - -
400H ASN* 3.5 35.5 + - + +
401H GLY 5.1 3.0 + - - -
404H ILE* 4.3 16.4 - - - +
510H VAL* 1.3 81.9 - - - +
512H LEU* 1.3 66.4 + - - +
533H VAL* 4.0 21.9 + - + +
534H SER 2.7 33.2 + - - +
535H ASP* 3.7 15.7 + - - +
536H ALA* 4.1 2.7 - - - -
537H ILE* 5.5 0.7 - - - -
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Residues in contact with LEU 512 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H PRO* 3.6 32.8 - - + -
367H LEU* 4.5 15.7 - - + -
395H VAL* 4.5 3.8 - - + -
396H GLN 3.4 3.4 - - - +
397H LEU* 3.6 25.8 - - + -
411H LEU* 4.2 13.5 - - + -
437H LEU* 5.3 7.6 - - + -
439H ILE* 5.1 0.9 - - + -
510H VAL* 5.4 1.8 - - + -
511H ARG* 1.3 75.1 - - - +
513H MET* 1.3 59.0 + - - +
514H PHE* 4.3 22.0 - - + -
532H VAL 4.4 0.2 - - - +
533H VAL* 3.4 3.3 - - - +
534H SER* 2.7 44.8 + - - +
537H ILE* 3.9 17.5 - - + -
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Residues in contact with MET 513 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394H ILE 3.6 0.7 - - - +
395H VAL* 3.4 4.0 - - - +
396H GLN* 2.9 52.8 + - + +
398H VAL* 3.9 22.7 - - + -
404H ILE* 4.7 2.5 - - - -
464H ASN* 3.8 20.6 - - + +
467H LEU* 5.2 5.8 - - + -
468H LEU* 3.7 34.8 - - + -
512H LEU* 1.3 75.3 - - - +
514H PHE* 1.3 64.5 + - - +
515H THR* 3.8 5.5 + - - +
531H PRO* 4.0 20.9 - - + -
532H VAL 3.8 5.4 - - - +
533H VAL* 3.5 27.8 - - + +
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Residues in contact with PHE 514 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342H LEU* 3.3 19.7 - - + +
344H ILE* 4.0 25.4 - - + -
348H PRO* 6.0 2.2 - - + -
380H PRO* 6.4 1.8 - - + -
382H VAL* 3.4 24.2 - - + -
393H VAL* 4.5 5.2 - - + -
394H ILE 3.3 6.1 - - - +
395H VAL* 3.5 26.9 - - + -
434H PHE* 3.3 32.8 - + - -
437H LEU* 6.3 0.4 - - + -
512H LEU* 4.3 31.0 - - + -
513H MET* 1.3 71.9 - - - +
515H THR* 1.3 61.1 + - - +
531H PRO* 3.1 3.5 - - - +
532H VAL* 2.9 47.3 + - + +
534H SER* 4.4 5.6 - - - -
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Residues in contact with THR 515 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342H LEU* 4.2 0.9 - - - -
392H LYS 3.6 1.0 - - - +
393H VAL* 3.6 1.3 - - - -
394H ILE* 2.9 46.9 + - - +
396H GLN* 3.9 2.6 + - - -
464H ASN* 2.9 26.6 + - - +
513H MET* 3.8 6.1 + - - +
514H PHE* 1.3 74.7 - - - +
516H ALA* 1.3 62.2 + - - +
517H PHE* 3.8 17.0 - - + -
528H ARG* 3.7 29.6 - - + -
529H LEU 4.5 0.4 - - - +
531H PRO* 3.0 21.6 - - + +
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Residues in contact with ALA 516 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342H LEU* 3.7 26.7 - - + +
384H ILE* 4.4 10.8 - - + -
391H ALA* 5.6 0.9 - - + -
392H LYS 3.0 8.5 - - - +
393H VAL* 4.4 6.1 - - + +
515H THR* 1.3 74.8 - - - +
517H PHE* 1.3 64.2 + - - +
518H LEU* 5.5 2.0 - - + -
527H ARG 3.6 0.7 - - - +
528H ARG* 3.6 3.5 - - - -
529H LEU* 3.1 52.0 + - + +
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Residues in contact with PHE 517 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391H ALA* 3.3 4.7 - - - -
392H LYS* 2.5 67.2 + - + -
394H ILE* 3.7 25.6 - - + -
462H GLY 4.3 7.4 - - - -
463H TYR* 3.9 25.6 - + - -
477H GLN* 5.6 0.9 - - - -
478H ALA* 4.4 14.1 - - + -
515H THR* 3.8 18.6 - - + -
516H ALA* 1.3 75.8 - - - +
518H LEU* 1.3 62.9 + - - +
525H PHE* 3.6 26.9 - - - +
526H THR* 4.2 5.6 - - - -
527H ARG 3.2 5.4 - - - -
528H ARG* 3.5 42.8 - - + -
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Residues in contact with LEU 518 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340H PRO* 4.7 4.9 - - + -
384H ILE* 4.9 1.8 - - + -
387H TYR* 3.0 53.2 - - + +
391H ALA* 3.5 17.3 - - + -
516H ALA* 5.5 0.4 - - + -
517H PHE* 1.3 76.2 - - - +
519H PRO* 1.4 64.0 - - + +
525H PHE* 3.7 2.9 - - - -
526H THR 3.2 6.8 + - - -
527H ARG* 2.8 81.8 + - + +
529H LEU* 4.0 29.4 - - + -
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Residues in contact with PRO 519 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387H TYR* 3.1 15.5 - - + +
390H PRO* 3.0 32.5 - - + +
518H LEU* 1.4 83.5 - - + +
520H ASP* 1.3 64.7 + - - +
523H GLY* 3.7 22.2 - - - +
524H SER 3.5 7.6 - - - +
525H PHE* 3.4 18.4 - - + -
527H ARG* 3.5 13.9 + - - +
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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