Contacts of the strand formed by residues 532 - 539 (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 532 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342D LEU* 3.9 44.9 - - + +
343D GLN* 4.6 2.2 - - - +
344D ILE* 4.4 23.7 - - + +
382D VAL* 5.4 0.2 - - + -
513D MET* 4.5 0.7 - - - -
514D PHE* 3.2 31.7 + - + +
530D GLU 4.6 1.8 - - - +
531D PRO* 1.3 73.4 - - - +
533D VAL* 1.3 72.9 + - - +
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Residues in contact with VAL 533 (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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344D ILE* 3.9 5.6 - - - +
347D GLN* 4.7 2.8 + - - -
398D VAL* 4.4 9.4 - - + -
404D ILE* 4.7 17.7 - - + -
511D ARG* 3.6 30.1 + - - +
512D LEU 3.4 7.2 - - - +
513D MET* 3.5 37.0 - - + +
531D PRO 4.4 0.6 + - - +
532D VAL* 1.3 85.2 - - - +
534D SER* 1.3 61.4 + - - +
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Residues in contact with SER 534 (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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344D ILE* 4.1 9.9 - - - -
347D GLN* 3.4 16.6 - - - +
348D PRO* 3.9 11.7 - - - +
511D ARG* 2.7 34.4 + - - -
512D LEU* 2.8 55.4 + - - +
514D PHE* 4.6 1.8 - - - -
533D VAL* 1.3 74.1 - - - +
535D ASP* 1.3 69.7 + - - +
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Residues in contact with ASP 535 (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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347D GLN* 3.2 43.1 + - + +
348D PRO* 4.7 5.3 - - + +
350D GLN* 3.6 31.8 + - + +
511D ARG* 3.8 12.5 + - - +
534D SER* 1.3 98.3 + - - +
536D ALA* 1.3 65.3 + - - +
537D ILE* 4.1 3.3 + - - +
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Residues in contact with ALA 536 (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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350D GLN* 2.9 34.5 + - - +
400D ASN* 3.7 23.1 - - - +
509D VAL* 3.9 17.7 - - + -
510D VAL 3.8 5.2 - - - +
511D ARG* 4.2 3.3 - - + +
535D ASP* 1.3 77.4 - - - +
537D ILE* 1.3 62.0 + - - +
538D TYR* 4.0 19.7 - - + +
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Residues in contact with ILE 537 (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* 3.3 36.1 - - + -
349D LYS 3.5 16.6 - - - +
350D GLN 3.1 12.6 - - - +
353D PHE* 4.6 16.2 - - + -
355D PHE* 3.6 22.3 - - + -
367D LEU* 4.2 20.0 - - + -
439D ILE* 5.8 1.3 - - + -
509D VAL* 3.6 1.2 - - - +
510D VAL* 2.9 40.9 + - + +
512D LEU* 3.8 21.8 - - + -
535D ASP 4.6 1.3 - - - +
536D ALA* 1.3 77.0 - - - +
538D TYR* 1.3 60.5 - - - +
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Residues in contact with TYR 538 (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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350D GLN* 2.5 30.8 + - + +
351D ARG* 3.1 70.0 + - + +
352D GLY 4.3 0.2 + - - -
353D PHE 3.6 5.9 + - - +
355D PHE* 4.1 2.7 - - - -
400D ASN* 4.4 9.2 + - - -
508D SER 3.8 2.7 - - - +
509D VAL* 3.0 43.3 - - + -
536D ALA* 4.0 23.8 - - + +
537D ILE* 1.3 71.7 - - - +
539D ASP* 1.3 67.5 + - - +
540D SER* 3.3 3.6 + - - -
545D ALA* 4.2 11.6 - - + +
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Residues in contact with ASP 539 (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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355D PHE* 3.4 44.9 + - + +
441D HIS* 3.5 26.2 + - - -
507D LEU 4.7 0.2 - - - +
508D SER* 3.1 28.0 + - - +
538D TYR* 1.3 71.9 - - - +
540D SER* 1.3 65.5 + - - +
541D LYS* 2.4 44.6 + - - +
542D ALA* 3.4 22.6 - - + +
545D ALA* 3.5 8.1 - - - +
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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