Contacts of the helix formed by residues 421 - 435 (chain C) in PDB entry 5TXV
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 ASP 421 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369C THR* 3.4 20.2 - - + -
372C GLY* 4.0 2.7 - - - -
419C THR* 4.1 14.2 - - + +
420C ILE* 1.3 74.3 - - - +
422C ALA* 1.3 65.1 + - - +
423C ASP* 3.1 14.5 + - - +
424C TYR* 2.5 41.3 + - - +
425C VAL* 3.1 25.8 + - - +
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Residues in contact with ALA 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C THR* 3.8 5.9 + - - -
371C SER* 4.0 22.0 - - - +
372C GLY* 4.2 6.3 - - - -
375C ARG* 3.2 38.5 + - - +
421C ASP* 1.3 75.4 - - - +
423C ASP* 1.3 64.7 + - - +
425C VAL* 3.4 3.1 + - - +
426C SER* 3.1 28.2 + - - -
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Residues in contact with ASP 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C ARG* 4.5 7.5 + - - +
421C ASP* 3.1 11.7 + - - +
422C ALA* 1.3 81.1 - - - +
424C TYR* 1.3 59.7 + - - +
426C SER* 3.7 4.4 + - - -
427C LYS* 3.1 24.3 + - - +
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Residues in contact with TYR 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C LEU* 3.6 31.7 + - + -
405C GLU* 4.4 4.9 - - - +
406C ILE* 3.4 31.3 - - + +
418C ILE* 5.6 4.5 - - + -
419C THR 4.7 4.5 - - - +
420C ILE* 3.9 26.0 - - + -
421C ASP* 2.5 32.6 + - - +
423C ASP* 1.3 70.5 - - - +
425C VAL* 1.3 66.8 + - - +
427C LYS* 3.3 11.1 + - + -
428C HIS* 3.1 61.8 + + - -
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Residues in contact with VAL 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C GLY* 3.6 20.6 - - - +
375C ARG* 3.9 24.2 - - + +
376C ILE* 3.9 12.3 - - + -
379C ALA* 5.4 0.2 - - + -
402C LEU* 3.9 24.2 - - + -
420C ILE* 4.0 9.6 - - + -
421C ASP 3.1 17.1 + - - +
422C ALA 3.8 4.5 - - - +
423C ASP 3.4 0.2 - - - -
424C TYR* 1.3 76.9 - - - +
426C SER* 1.3 62.5 + - - +
427C LYS 3.3 0.2 + - - -
428C HIS 3.5 0.2 + - - -
429C LEU* 3.1 52.7 + - + +
430C ASP* 5.5 1.3 - - - +
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Residues in contact with SER 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C ARG* 3.0 34.0 + - - +
422C ALA 3.1 8.3 + - - -
423C ASP* 4.1 4.7 - - - -
425C VAL* 1.3 77.1 - - - +
427C LYS* 1.3 63.4 + - - +
430C ASP* 3.2 51.6 + - - +
431C ALA 4.4 1.2 + - - -
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Residues in contact with LYS 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423C ASP 3.1 18.9 + - - +
424C TYR* 3.6 10.9 - - + +
425C VAL 3.2 0.4 - - - -
426C SER* 1.3 80.1 - - - +
428C HIS* 1.3 78.3 + - + +
429C LEU 3.7 0.2 + - - -
430C ASP 5.0 0.2 + - - -
431C ALA* 5.1 8.8 - - - +
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Residues in contact with HIS 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C ARG* 4.8 6.3 + - - +
402C LEU* 3.7 34.5 + - + +
405C GLU* 3.1 41.0 + - + +
424C TYR* 3.1 65.4 + + - -
427C LYS* 1.3 98.2 + - + +
429C LEU* 1.3 65.1 + - - +
432C LEU* 3.4 23.0 - - - +
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Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C ILE* 4.9 2.0 - - + -
379C ALA* 4.1 10.1 - - + -
398C VAL* 3.7 37.0 - - + +
401C ARG* 4.2 21.8 - - + -
402C LEU* 4.3 22.9 - - + +
425C VAL* 3.1 36.8 + - + +
427C LYS 3.4 0.8 - - - -
428C HIS* 1.3 88.8 - - - +
430C ASP* 1.3 62.5 + - - +
431C ALA 3.1 2.2 - - - -
432C LEU* 2.5 34.5 + - + +
433C VAL* 2.9 21.7 + - + +
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Residues in contact with ASP 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C ALA* 5.9 1.6 - - - +
425C VAL* 4.3 1.9 - - - +
426C SER* 3.2 42.9 + - - +
429C LEU* 1.3 77.4 - - - +
431C ALA* 1.3 58.2 + - - +
433C VAL* 3.9 10.0 - - - +
434C ALA* 3.0 31.2 + - - +
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Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426C SER 4.4 1.8 + - - -
427C LYS 5.1 8.3 + - - +
429C LEU 2.9 1.0 + - - +
430C ASP* 1.3 78.6 - - - +
432C LEU* 1.3 69.9 + - + +
434C ALA* 3.8 9.8 + - - +
435C ASP* 4.0 11.6 + - - +
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Residues in contact with LEU 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C ARG* 3.6 42.2 - - + +
428C HIS 3.4 22.0 - - - +
429C LEU* 2.5 15.7 + - + +
431C ALA* 1.3 80.2 - - + +
433C VAL* 1.3 61.7 + - + +
434C ALA 3.3 0.2 + - - -
435C ASP* 3.0 26.9 + - - +
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Residues in contact with VAL 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C ALA* 4.5 22.9 - - + +
382C GLN* 3.6 37.0 - - + +
383C VAL* 4.3 21.8 - - + -
386C SER* 5.3 2.8 + - - +
398C VAL* 6.3 1.1 - - + -
429C LEU* 2.9 21.4 + - + +
430C ASP* 4.3 7.9 - - - +
432C LEU* 1.3 78.5 - - + +
434C ALA* 1.3 61.9 + - - +
435C ASP 3.3 5.2 + - - -
436C GLU* 4.5 6.9 + - - +
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Residues in contact with ALA 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430C ASP 3.0 19.5 + - - +
431C ALA* 4.0 7.4 - - - +
432C LEU 3.2 0.6 - - - -
433C VAL* 1.3 78.1 - - - +
435C ASP* 1.3 57.4 + - - +
436C GLU* 3.8 6.1 + - - +
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Residues in contact with ASP 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C ALA 4.0 8.6 + - - +
432C LEU* 3.0 19.0 + - - +
433C VAL 3.2 1.8 - - - +
434C ALA* 1.3 77.6 - - + +
436C GLU* 1.3 70.5 + - - +
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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