Contacts of the helix formed by residues 410 - 428 (chain A) in PDB entry 1TF5
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 THR 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A TYR* 4.0 0.9 - - - +
409A ARG* 1.3 109.8 - - - +
411A MET* 1.3 64.2 + - - +
412A GLU* 3.5 15.8 + - - +
413A GLY 3.2 8.8 + - - -
414A LYS* 3.0 18.5 + - - +
540A SER* 3.6 10.6 - - - -
542A GLU* 3.4 20.2 - - - +
565A ASP* 2.5 31.4 + - - +
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Residues in contact with MET 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A THR* 1.3 69.4 - - - +
412A GLU* 1.3 73.9 + - - +
414A LYS* 3.2 18.9 + - - +
415A PHE* 2.9 48.9 + - + -
511A GLU* 5.6 4.3 - - - +
540A SER* 3.7 3.9 + - - +
542A GLU* 3.1 38.2 + - + +
543A ASP* 3.3 28.0 - - - +
544A GLU* 5.8 5.2 - - + +
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Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A THR* 3.5 15.2 - - - +
411A MET* 1.3 88.1 + - - +
413A GLY* 1.3 57.1 + - - +
415A PHE* 3.8 5.7 - - - +
416A LYS* 2.9 30.9 + - - +
542A GLU* 3.7 7.3 - - - +
565A ASP* 5.4 0.2 - - - +
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Residues in contact with GLY 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TYR* 3.9 9.0 - - - -
410A THR* 3.2 7.9 + - - -
412A GLU* 1.3 75.6 - - - +
414A LYS* 1.3 65.7 + - - +
416A LYS* 3.3 9.7 + - - +
417A ALA* 2.9 24.3 + - - +
565A ASP* 3.7 28.4 + - - -
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Residues in contact with LYS 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TYR* 3.9 13.7 - - + +
410A THR 3.0 13.6 + - - +
411A MET* 3.4 19.0 - - - +
413A GLY* 1.3 74.7 - - - +
415A PHE* 1.3 84.1 + - + +
417A ALA* 3.1 6.4 + - - +
418A VAL* 2.9 29.2 + - + +
510A THR 2.9 20.2 + - - +
511A GLU* 4.0 8.1 + - - +
538A TYR* 3.3 36.3 - - + +
539A LEU 3.4 26.5 - - - +
540A SER* 3.7 2.2 - - - +
543A ASP* 2.9 28.3 + - - -
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Residues in contact with PHE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A MET* 2.9 46.0 + - + +
412A GLU* 3.9 4.3 - - - +
414A LYS* 1.3 97.8 - - - +
416A LYS* 1.3 65.7 + - - +
418A VAL* 3.0 12.1 + - + +
419A ALA* 2.9 23.2 + - - +
441A THR* 3.7 28.3 - - + -
444A LEU* 3.6 23.3 - - + -
445A ILE* 3.1 30.4 - - + +
448A LEU* 3.7 14.9 - - + +
510A THR* 4.1 11.4 - - - -
511A GLU* 6.4 1.3 - - - -
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Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A GLU 2.9 18.3 + - - +
413A GLY* 3.6 8.7 - - - +
414A LYS 3.3 0.2 - - - -
415A PHE* 1.3 76.0 - - - +
417A ALA* 1.3 58.8 + - - +
419A ALA* 3.3 4.9 + - - +
420A GLU* 2.9 36.9 + - + +
448A LEU* 4.3 9.5 - - + +
452A LYS* 4.3 6.2 + - - +
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Residues in contact with ALA 417 (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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408A TYR* 3.3 39.5 - - + +
413A GLY 2.9 9.9 + - - +
414A LYS 3.1 10.1 + - - +
416A LYS* 1.3 77.1 - - - +
418A VAL* 1.3 62.8 + - - +
420A GLU* 3.4 7.7 + - - +
421A ASP* 3.0 23.7 + - - +
538A TYR* 3.9 12.0 - - + -
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Residues in contact with VAL 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LYS* 2.9 18.9 + - + +
415A PHE* 3.0 15.7 + - + +
417A ALA* 1.3 75.9 - - - +
419A ALA* 1.3 63.4 + - - +
421A ASP* 3.1 8.5 + - - +
422A VAL* 3.0 33.5 + - + +
434A VAL* 4.3 9.4 - - + -
445A ILE* 4.2 23.6 - - + -
508A VAL* 4.0 18.1 - - + +
510A THR* 4.2 15.7 - - + -
538A TYR* 3.8 32.3 - - + -
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Residues in contact with ALA 419 (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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415A PHE 2.9 11.5 + - - +
416A LYS* 3.6 7.4 - - - +
418A VAL* 1.3 79.5 - - - +
420A GLU* 1.3 57.9 + - - +
422A VAL* 3.5 2.1 + - - +
423A ALA* 3.0 29.3 + - - +
445A ILE* 5.4 1.3 - - + +
448A LEU* 4.0 28.3 - - + -
449A LEU* 4.0 22.1 - - + +
452A LYS* 3.5 18.9 + - + +
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Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LYS* 2.9 27.0 + - + +
417A ALA* 3.6 8.7 - - - +
418A VAL 3.2 0.2 - - - -
419A ALA* 1.3 73.8 - - - +
421A ASP* 1.3 65.6 + - - +
423A ALA* 3.4 8.1 + - - +
424A GLN* 3.0 55.6 + - + +
452A LYS* 3.2 20.9 + - - +
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Residues in contact with ASP 421 (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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417A ALA 3.0 13.3 + - - +
418A VAL* 3.3 9.4 - - - +
420A GLU* 1.3 77.4 - - - +
422A VAL* 1.3 63.0 + - - +
424A GLN* 3.2 9.6 + - - +
425A ARG* 3.0 50.7 + - - +
508A VAL* 3.7 16.8 - - + +
536A GLN* 4.8 4.7 - - - +
538A TYR* 2.6 34.6 + - + +
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A VAL* 3.0 21.3 + - + +
419A ALA* 3.7 7.6 - - - +
421A ASP* 1.3 75.1 - - - +
423A ALA* 1.3 58.9 + - - +
425A ARG* 3.3 8.4 + - - +
426A TYR* 2.8 29.1 + - - +
432A VAL* 4.4 13.4 - - + +
434A VAL* 3.7 26.9 - - + -
445A ILE* 5.7 0.4 - - + -
449A LEU* 4.1 19.5 - - + -
454A ILE* 4.9 4.0 - - + -
480A VAL* 3.6 36.8 - - + -
508A VAL* 4.9 3.8 - - + -
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Residues in contact with ALA 423 (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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419A ALA 3.0 18.4 + - - +
420A GLU* 3.6 13.7 - - - +
421A ASP 3.2 0.2 - - - -
422A VAL* 1.3 78.4 - - - +
424A GLN* 1.3 63.3 + - - +
426A TYR* 3.8 4.6 - - - +
427A MET* 3.0 33.8 + - - +
449A LEU* 5.3 0.2 - - - +
452A LYS* 4.3 18.2 - - + -
454A ILE* 4.8 15.7 - - + -
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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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420A GLU* 3.0 38.5 + - + +
421A ASP* 3.6 8.5 - - - +
423A ALA* 1.3 74.7 - - - +
425A ARG* 1.3 67.6 + - + +
427A MET* 3.3 17.0 + - - +
428A THR* 3.2 22.8 + - - +
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Residues in contact with ARG 425 (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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421A ASP* 3.0 40.0 + - - +
422A VAL* 3.6 1.6 - - - +
424A GLN* 1.3 78.3 - - + +
426A TYR* 1.3 62.5 + - - +
428A THR* 2.7 27.1 + - - -
429A GLY 3.0 5.4 + - - -
430A GLN* 3.2 38.4 + - - +
432A VAL* 3.2 29.4 - - + -
506A ALA* 4.0 12.5 - - + +
508A VAL* 6.0 0.6 - - + +
534A ILE* 3.7 39.8 - - - +
536A GLN* 6.0 2.4 - - - +
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Residues in contact with TYR 426 (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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422A VAL 2.8 21.6 + - - +
423A ALA* 3.8 3.8 - - - +
425A ARG* 1.3 72.8 - - - +
427A MET* 1.3 77.6 + - + +
429A GLY* 3.0 17.9 + - - +
430A GLN 4.6 5.6 - - - -
432A VAL* 4.5 0.4 - - - +
453A GLY 5.2 0.4 - - - -
454A ILE* 3.3 37.9 - - + -
455A PRO* 3.2 33.9 - - + +
478A GLY* 3.2 36.6 - - - -
480A VAL* 3.8 17.9 - - + -
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Residues in contact with MET 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ALA* 3.0 27.0 + - - +
424A GLN* 3.5 15.5 - - - +
425A ARG 3.2 0.4 - - - -
426A TYR* 1.3 100.9 - - + +
428A THR* 1.3 61.3 + - + +
454A ILE* 4.7 8.3 - - + -
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Residues in contact with THR 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLN* 3.2 17.0 - - + +
425A ARG* 2.7 15.5 + - - -
427A MET* 1.3 79.5 - - + +
429A GLY* 1.3 58.9 + - - +
430A GLN* 3.2 19.2 + - - +
477A LYS* 5.1 1.4 - - - +
502A LEU* 3.6 23.0 + - - +
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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
------------------------------------------------------------
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