Contacts of the strand formed by residues 385 - 389 (chain F) 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 SER 385 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355F VAL 3.2 5.6 - - - -
356F GLU* 3.6 32.1 + - - +
357F LEU 4.3 1.0 + - - -
372F ALA* 4.9 0.2 - - - +
383F LEU* 3.8 29.0 - - - +
384F LYS* 1.3 91.4 + - - +
386F CYS* 1.3 63.1 + - - +
387F MET* 4.1 18.1 + - - +
397F PHE* 4.0 2.4 - - - -
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Residues in contact with CYS 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F LYS* 3.4 2.3 - - - +
355F VAL* 2.9 35.7 + - + +
372F ALA* 4.2 11.9 - - - -
373F THR 4.2 1.1 - - - -
374F CYS* 2.0 59.2 - - + -
375F LEU* 4.7 1.1 - - + -
385F SER* 1.3 74.6 - - - +
387F MET* 1.3 62.3 + - - +
389F LEU* 3.5 6.2 - - + +
395F VAL* 3.4 34.1 - - + -
397F PHE* 4.4 2.8 - - + -
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Residues in contact with MET 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354F LYS* 3.6 26.7 - - + -
356F GLU* 4.7 12.1 - - + +
374F CYS* 4.8 1.6 - - - +
375F LEU* 3.3 16.7 - - - +
383F LEU* 6.0 2.2 - - + -
385F SER* 4.1 22.0 + - - +
386F CYS* 1.3 79.9 - - - +
388F GLY* 1.3 60.6 + - - +
389F LEU* 3.6 5.2 - - - -
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Residues in contact with GLY 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F ARG* 3.9 23.5 - - - +
353F SER 3.4 5.1 + - - -
354F LYS* 5.3 0.2 - - - +
375F LEU* 3.1 20.8 - - - +
387F MET* 1.3 76.4 - - - +
389F LEU* 1.3 65.4 + - - +
390F LYS* 4.0 9.4 + - - +
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Residues in contact with LEU 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F GLN* 4.7 5.2 - - + +
110F TYR* 3.2 11.0 + - - -
351F ILE 3.9 0.5 - - - +
352F ARG* 3.3 11.8 - - - +
353F SER* 3.1 42.0 + - - +
354F LYS* 4.1 0.2 - - - -
355F VAL* 4.1 22.7 - - + -
375F LEU* 4.1 10.5 - - + -
386F CYS* 3.5 33.2 - - + +
387F MET 4.0 2.7 - - - -
388F GLY* 1.3 80.4 - - - +
390F LYS* 1.3 63.4 + - - +
393F ASP* 3.5 28.9 - - + +
395F VAL* 3.7 23.8 - - + -
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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