Contacts of the strand formed by residues 388 - 392 (chain E) in PDB entry 1TYE
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 GLN 388 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E THR* 5.5 2.6 + - - -
376E VAL 3.9 1.0 - - - +
378E ALA* 2.9 36.7 + - + +
381E GLY* 4.0 3.1 - - - -
382E GLY* 3.0 39.9 - - - +
383E PRO* 4.0 5.1 - - - +
387E GLY* 1.3 74.1 - - - +
389E VAL* 1.3 64.8 + - - +
390E LEU* 3.4 20.5 - - + +
406E VAL* 3.4 24.1 - - + +
407E LEU 3.2 16.8 - - - +
408E ASP* 3.0 18.0 + - - +
417E PHE* 3.9 6.8 - - - +
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Residues in contact with VAL 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375E ALA* 4.0 25.4 - - + -
376E VAL 3.4 10.8 - - - +
377E ALA* 4.8 1.8 - - - -
388E GLN* 1.3 76.7 - - - +
390E LEU* 1.3 64.5 - - - +
391E VAL* 5.4 1.6 - - + -
406E VAL* 3.6 2.1 - - - -
407E LEU* 2.7 50.2 + - + +
417E PHE* 3.5 26.0 - - + -
418E GLY* 4.4 6.3 - - - -
421E LEU* 4.0 18.6 - - + -
435E LEU* 4.4 9.2 - - + -
437E VAL* 4.0 18.8 - - + -
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Residues in contact with LEU 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E THR* 6.4 1.8 - - + -
356E PHE* 3.7 30.5 - - + -
375E ALA* 3.3 1.6 - - - -
376E VAL 2.8 42.4 + - - +
378E ALA* 4.9 2.5 - - + -
388E GLN* 3.4 36.6 - - + +
389E VAL* 1.3 78.6 - - - +
391E VAL* 1.3 63.1 + - - +
392E PHE* 3.4 30.2 - - + -
403E PRO* 4.3 12.8 - - + -
405E GLN 3.7 3.4 - - - -
406E VAL* 3.9 15.5 - - + -
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Residues in contact with VAL 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E LEU 5.3 0.4 - - - +
3E LEU* 4.3 16.6 - - + -
363E LEU* 4.1 7.9 - - + -
366E LEU* 3.8 24.5 - - + -
373E ASP* 5.1 0.2 - - + -
374E ILE 3.6 9.9 - - - +
375E ALA* 4.4 5.8 - - + +
389E VAL* 5.2 2.0 - - + +
390E LEU* 1.3 73.5 - - - +
392E PHE* 1.3 62.2 + - - +
393E LEU* 4.0 8.5 - - + -
403E PRO* 3.2 6.8 - - - +
404E SER* 2.9 43.3 + - - +
405E GLN* 3.0 19.4 + - + +
407E LEU* 4.2 24.7 - - + -
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Residues in contact with PHE 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347E LEU* 3.8 32.1 - - + -
356E PHE* 4.3 10.1 - + - -
373E ASP* 3.6 0.2 - - - +
374E ILE* 2.9 46.9 + - + -
376E VAL* 4.1 22.9 - - + -
390E LEU* 3.4 51.8 - - + -
391E VAL* 1.3 72.3 - - - +
393E LEU* 1.3 66.5 + - - +
399E LEU* 3.5 12.8 - - + +
400E ARG 3.5 19.7 - - - +
401E SER 4.1 2.7 - - - -
402E ARG 4.0 2.5 - - - -
403E PRO* 3.6 29.6 - - + -
404E SER 4.8 1.3 - - - +
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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