Contacts of the strand formed by residues 419 - 424 (chain A) in PDB entry 3TXO
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 LEU 419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A LYS 4.6 5.8 - - - +
407A LEU* 3.8 47.8 + - + +
408A SER 4.7 0.2 - - - +
411A ARG* 5.7 6.3 - - - +
417A THR 3.8 2.8 + - - -
418A GLN* 1.3 74.1 + - - +
420A PHE* 1.3 58.3 + - - +
421A CYS 3.2 27.1 - - - +
422A CYS* 3.8 20.0 - - - -
431A PHE* 4.3 9.2 - - + -
432A VAL 3.3 17.9 - - - +
433A MET* 4.3 3.8 - - + +
676A TYR* 3.5 45.0 + - + +
678A SER* 4.2 7.6 + - - -
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Residues in contact with PHE 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 6.1 2.5 - + - -
374A VAL* 6.1 1.1 - - + -
381A TYR* 3.2 53.8 - + + -
418A GLN 3.9 2.2 + - - -
419A LEU* 1.3 72.8 - - - +
421A CYS* 1.3 70.7 + - + +
432A VAL* 2.7 23.0 + - + +
433A MET* 5.1 2.0 - - - -
434A GLU 5.1 0.7 - - - +
677A VAL* 4.0 5.1 - - + +
678A SER* 3.0 53.1 + - - -
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Residues in contact with CYS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 4.8 7.4 - - - -
419A LEU* 3.2 10.6 - - - +
420A PHE* 1.3 91.0 - - + +
422A CYS* 1.3 60.7 + - - +
423A PHE* 4.4 11.9 - - - -
432A VAL* 2.7 64.2 + - - +
676A TYR* 3.4 15.9 - - - +
677A VAL* 4.4 12.6 - - + -
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Residues in contact with CYS 422 (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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404A LYS* 3.9 13.9 - - - -
419A LEU* 3.8 20.6 - - - -
421A CYS* 1.3 76.5 - - - +
423A PHE* 1.3 64.1 + - - +
430A PHE 3.2 4.0 - - - -
431A PHE* 3.6 36.6 - - - -
674A PHE* 3.6 28.0 - - + +
675A GLU* 3.6 6.3 - - - +
676A TYR* 3.0 27.9 + - + +
677A VAL* 5.3 1.0 - - - +
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Residues in contact with PHE 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASP* 3.6 37.2 - - + -
355A PHE* 3.7 33.7 - + - -
383A VAL* 5.8 0.2 - - + -
421A CYS* 4.4 9.2 - - - -
422A CYS* 1.3 76.1 - - - +
424A GLN* 1.3 73.1 + - - +
425A THR* 4.8 1.3 - - + -
430A PHE* 2.9 72.2 + + + +
432A VAL* 3.7 15.5 - - + -
674A PHE* 3.6 7.9 - - - -
675A GLU* 3.8 16.6 - - + +
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Residues in contact with GLN 424 (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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388A LYS* 3.1 21.1 + - - +
423A PHE* 1.3 88.4 - - - +
425A THR* 1.3 67.3 + - - +
428A ARG 3.4 11.9 - - - +
429A LEU* 3.8 10.8 - - + -
430A PHE* 4.5 0.4 - - - -
668A GLN* 4.9 3.0 - - - +
671A PHE* 3.2 37.9 + - - +
672A ARG* 4.6 4.8 + - - +
674A PHE* 3.8 10.9 - - + +
675A GLU* 3.2 30.0 + - - +
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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