Contacts of the strand formed by residues 391 - 396 (chain A) in PDB entry 1TTU
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 391 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A EDO 3.9 29.6 - - - +
389A GLY 5.1 1.8 - - - +
390A THR* 1.3 83.3 + - - +
392A VAL* 1.3 67.9 + - - +
424A ALA* 4.0 19.3 - - + -
425A PHE 3.0 8.3 - - - +
426A THR* 4.2 14.6 - - - +
460A SER* 3.8 24.9 - - - +
540A SER* 3.7 2.3 - - - -
541A THR* 3.1 39.2 + - + +
542A ASP* 5.0 3.6 + - - +
543A LYS* 4.4 29.6 - - - +
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A ILE* 4.1 25.1 - - + -
391A LYS* 1.3 80.8 - - - +
393A ALA* 1.3 66.0 + - - +
394A LEU* 5.0 3.8 - - + -
424A ALA* 3.6 2.0 - - - -
425A PHE* 2.8 40.5 + - + +
427A ILE* 4.3 7.2 - - + -
457A LEU* 4.1 22.4 - - + -
538A ILE* 4.1 20.4 - - + -
539A ILE 3.3 16.4 - - - +
540A SER* 3.9 9.2 - - - +
541A THR* 4.1 7.2 - - - +
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Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A PRO* 3.6 38.8 - - + -
392A VAL* 1.3 76.1 - - - +
394A LEU* 1.3 69.3 + - - +
395A PHE* 5.5 1.8 - - + -
407A TYR* 5.5 1.1 - - + -
422A TRP* 3.9 15.7 - - + -
423A GLY 4.0 7.6 - - - +
537A THR 4.6 0.4 - - - -
538A ILE* 3.7 0.3 - - - -
539A ILE* 2.8 34.6 + - + +
541A THR* 4.1 4.4 + - - +
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A VAL* 5.0 4.7 - - + -
393A ALA* 1.3 82.7 - - - +
395A PHE* 1.3 64.1 + - - +
407A TYR* 3.5 3.8 - - - +
408A LEU* 2.9 53.6 + - + +
422A TRP* 6.2 0.4 - - - +
425A PHE* 4.8 8.6 - - + -
457A LEU* 3.6 32.8 - - + -
496A CYS* 4.9 0.2 - - - -
498A PHE* 3.9 26.5 - - + -
508A LEU* 6.4 0.7 - - + -
536A TRP* 4.1 18.6 - - + -
537A THR 3.6 3.8 - - - +
538A ILE* 3.7 31.2 - - + -
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Residues in contact with PHE 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A EDO 3.7 1.6 - - - -
58A EDO 5.9 2.0 - - - -
237A CYS* 3.9 32.1 - - + -
238A PRO* 4.6 6.5 - - + -
394A LEU* 1.3 76.9 - - - +
396A ASN* 1.3 64.9 + - - +
397A ARG* 3.8 31.0 - - + -
405A THR* 3.9 11.9 - - + -
406A ARG 3.1 13.9 - - - +
407A TYR* 3.3 31.6 - + + -
493A LEU* 4.6 9.0 - - + -
536A TRP* 3.5 9.1 - - - -
537A THR* 2.9 69.3 + - + -
539A ILE* 4.6 6.7 - - + -
8B G 4.9 0.4 - - - -
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Residues in contact with ASN 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A EDO 2.9 2.8 + - - -
395A PHE* 1.3 75.1 - - - +
397A ARG* 1.3 70.7 + - - +
398A LEU* 3.8 24.4 - - - +
404A SER 3.6 3.6 + - - +
405A THR* 3.1 5.5 - - - +
406A ARG 2.7 34.5 + - - +
510A LEU* 3.1 37.3 - - + +
532A ASP 2.9 16.4 + - - +
533A GLY* 3.9 9.2 - - - +
535A ALA 2.8 24.4 - - - +
536A TRP* 3.7 13.8 - - + -
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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