Contacts of the strand formed by residues 392 - 398 (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 LYS 392 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391D ALA* 1.3 73.8 - - - +
393D VAL* 1.3 61.7 + - - +
394D ILE* 3.8 16.6 - - + -
422D THR* 4.2 18.6 - - + -
423D VAL 4.1 3.6 - - - +
424D THR* 4.8 5.2 - - + +
461D ARG* 5.2 2.2 - - - +
463D TYR* 2.7 39.9 + - - -
515D THR 3.6 1.4 - - - +
516D ALA* 3.1 3.8 - - - +
517D PHE* 2.5 63.5 + - + +
525D PHE* 3.9 27.0 + - + +
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Residues in contact with VAL 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D LEU* 5.3 5.4 - - + -
382D VAL* 5.5 3.6 - - + -
384D ILE* 4.2 16.6 - - + -
391D ALA* 5.4 0.2 - - + -
392D LYS* 1.3 77.2 - - - +
394D ILE* 1.3 71.1 + - - +
395D VAL* 5.1 0.5 - - - +
421D CYS 3.7 1.4 - - - +
422D THR* 3.7 2.4 - - - +
423D VAL* 3.2 40.9 + - + +
425D ALA* 4.5 6.5 - - + +
432D VAL* 3.9 25.8 - - + -
434D PHE* 4.0 23.6 - - + -
514D PHE* 4.4 14.4 - - + -
515D THR 3.3 7.4 - - - +
516D ALA* 4.7 8.3 - - + -
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Residues in contact with ILE 394 (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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392D LYS* 3.8 17.3 - - + -
393D VAL* 1.3 76.9 - - - +
395D VAL* 1.3 65.5 + - - +
396D GLN* 3.8 18.6 - - + +
420D VAL* 4.1 7.4 - - + -
421D CYS 3.3 3.6 - - - -
422D THR* 3.8 11.2 - - - +
463D TYR* 3.5 55.0 - - + +
464D ASN* 4.3 0.4 - - - +
513D MET 3.6 0.3 - - - +
514D PHE* 3.3 6.9 - - - +
515D THR* 2.8 57.4 + - + +
517D PHE* 3.6 15.5 - - + -
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Residues in contact with VAL 395 (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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393D VAL* 4.8 0.2 - - + -
394D ILE* 1.3 77.8 - - - +
396D GLN* 1.3 66.4 + - - +
411D LEU* 3.4 25.9 - - + +
419D GLY 4.1 0.3 - - - +
420D VAL* 3.4 9.3 - - - +
421D CYS* 2.8 40.1 + - + +
434D PHE* 3.3 42.6 - - + -
437D LEU* 5.1 3.4 - - + -
512D LEU* 4.5 15.9 - - + -
513D MET 3.7 4.0 - - - +
514D PHE* 3.5 22.0 - - + -
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Residues in contact with GLN 396 (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* 3.8 22.1 - - + +
395D VAL* 1.3 78.3 - - - +
397D LEU* 1.3 66.5 + - - +
398D VAL* 3.7 6.2 + - + -
406D LEU* 3.8 18.6 - - + +
419D GLY 4.9 3.8 - - - -
420D VAL* 4.4 15.6 - - + +
458D ALA* 4.7 4.3 - - - +
463D TYR* 3.9 16.2 + - - +
464D ASN* 3.1 26.3 + - - -
468D LEU* 3.4 25.6 - - - +
511D ARG 3.4 3.5 - - - +
512D LEU* 3.6 2.9 - - - -
513D MET* 3.0 38.8 + - + +
515D THR* 3.8 5.7 + - - -
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Residues in contact with LEU 397 (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* 1.3 71.8 - - - +
398D VAL* 1.3 57.1 + - - +
406D LEU* 3.6 11.7 - - - +
407D HIS* 2.7 35.4 + - + +
409D HIS* 3.3 39.9 - - + +
410D SER 3.3 24.7 - - - +
411D LEU* 3.4 35.0 - - + +
419D GLY 5.0 3.5 + - - +
439D ILE* 3.8 12.8 - - + -
510D VAL* 4.2 14.8 - - + -
511D ARG 3.4 3.1 - - - +
512D LEU* 3.7 20.9 - - + -
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Residues in contact with VAL 398 (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* 4.2 3.4 - - + +
397D LEU* 1.3 79.4 - - - +
399D THR* 1.3 62.1 + - - +
404D ILE* 4.0 7.9 - - + -
405D HIS 3.0 14.8 - - - +
406D LEU* 4.7 0.4 - - - -
407D HIS* 3.9 5.8 - - - +
468D LEU* 3.7 28.3 - - + -
510D VAL* 3.6 4.5 - - - +
511D ARG* 2.7 61.3 + - + +
512D LEU 4.3 1.3 - - - +
513D MET* 3.9 27.6 - - + -
533D VAL* 4.4 9.6 - - + -
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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