Contacts of the helix formed by residues 325 - 342 (chain C) in PDB entry 1TAD
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 325 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C GLN* 2.9 28.1 + - - +
51C ILE* 4.1 16.2 - - + +
52C ILE* 3.6 26.4 - - + +
167C GLU* 4.9 3.8 + - - +
171C LEU* 3.8 11.3 - - - +
323C THR 3.5 1.2 + - - -
324C ASP* 1.3 72.7 + - - +
326C GLN* 1.3 69.0 + - - +
329C LYS* 2.8 32.8 + - + +
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Residues in contact with GLN 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ASP* 3.2 9.6 + - - +
325C THR* 1.3 86.5 - - - +
327C ASN* 1.3 57.0 + - - +
329C LYS* 3.3 28.7 + - - +
330C PHE* 2.9 29.9 + - - +
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Residues in contact with ASN 327 (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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267C LYS* 3.8 21.0 - - - +
319C MET 4.1 3.0 + - - -
320C THR* 3.3 11.4 - - - +
321C CYS 2.9 30.3 + - - +
324C ASP* 3.1 31.3 + - + +
326C GLN* 1.3 77.9 - - - +
328C VAL* 1.3 57.8 + - - +
330C PHE* 3.2 9.6 + - - +
331C VAL* 2.9 42.2 + - - +
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Residues in contact with VAL 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 3.9 18.2 - - + -
48C GLN* 3.6 27.1 - - + -
49C MET* 3.8 18.2 - - + -
52C ILE* 4.3 1.1 - - + -
263C PHE* 5.9 2.5 - - + -
320C THR* 5.7 2.7 - - - -
321C CYS 3.6 10.5 - - - +
322C ALA* 3.4 30.3 - - - +
324C ASP 2.9 20.3 + - - +
325C THR 3.9 3.6 - - - +
327C ASN* 1.3 77.0 - - - +
329C LYS* 1.3 54.8 + - - +
331C VAL* 4.0 4.7 - - - +
332C PHE* 2.8 35.1 + - + +
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Residues in contact with LYS 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ILE* 3.6 42.4 + - + +
53C HIS* 5.8 2.1 - - + +
325C THR* 2.8 23.7 + - + +
326C GLN* 3.4 31.4 - - - +
328C VAL* 1.3 71.5 - - - +
330C PHE* 1.3 62.5 + - - +
332C PHE* 4.1 3.0 - - - +
333C ASP* 3.2 24.9 + - + +
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Residues in contact with PHE 330 (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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318C HIS* 5.4 5.8 - + - -
326C GLN 2.9 14.2 + - - +
327C ASN* 3.5 12.6 - - - +
329C LYS* 1.3 78.0 - - - +
331C VAL* 1.3 77.6 + - + +
333C ASP* 3.2 9.9 + - + +
334C ALA* 3.2 27.3 + - + +
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Residues in contact with VAL 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C PHE* 3.5 35.4 - - + -
318C HIS* 3.5 30.5 - - + +
319C MET 4.5 2.2 - - - +
320C THR* 3.9 17.7 - - + -
327C ASN* 2.9 39.2 + - - +
328C VAL* 4.0 4.0 - - - +
330C PHE* 1.3 84.4 - - + +
332C PHE* 1.3 56.3 + - - +
334C ALA* 3.2 8.2 + - - +
335C VAL* 3.0 24.8 + - - +
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Residues in contact with PHE 332 (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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32C LEU* 4.0 11.4 - - + -
45C ILE* 5.6 2.0 - - + -
49C MET* 3.9 18.8 - - + -
53C HIS* 3.6 20.6 - + + -
185C PHE* 3.6 36.8 - + - -
187C PHE* 4.0 4.5 - + - -
192C PHE* 3.8 17.5 - + - -
194C MET* 3.6 22.4 - - + -
218C ILE* 4.3 13.5 - - + -
263C PHE* 5.2 6.5 - + + -
328C VAL* 2.8 23.8 + - + +
329C LYS* 4.2 2.7 - - - +
331C VAL* 1.3 72.2 - - - +
333C ASP* 1.3 59.4 + - - +
335C VAL* 3.2 10.1 + - + +
336C THR* 2.9 53.6 + - + +
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Residues in contact with ASP 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C PHE* 3.6 15.4 - - + -
188C LYS* 3.0 29.1 + - - -
329C LYS* 3.2 14.9 + - + +
330C PHE* 3.2 14.0 + - + +
332C PHE* 1.3 76.8 - - - +
334C ALA* 1.3 61.1 + - - +
336C THR* 2.7 22.6 + - - -
337C ASP* 3.1 18.7 + - - +
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Residues in contact with ALA 334 (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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318C HIS* 3.8 24.0 - - + -
330C PHE* 3.2 17.6 + - + +
331C VAL* 3.2 9.4 + - - +
333C ASP* 1.3 80.7 + - - +
335C VAL* 1.3 62.8 + - - +
337C ASP* 3.5 10.8 + - - +
338C ILE* 3.2 26.6 + - - +
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Residues in contact with VAL 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 5.0 0.4 - - + -
216C CYS* 4.2 16.8 - - - -
218C ILE* 4.4 12.8 - - + -
261C VAL* 3.9 19.7 - - + -
263C PHE* 3.8 30.7 - - + -
318C HIS* 4.6 4.5 - - - +
331C VAL* 3.0 19.5 + - + +
332C PHE* 3.2 17.2 + - + +
334C ALA* 1.3 75.3 - - - +
336C THR* 1.3 65.5 + - - +
338C ILE* 3.1 9.9 + - - +
339C ILE* 3.0 36.4 + - + +
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Residues in contact with THR 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C PHE* 3.4 32.2 - - + -
188C LYS* 3.4 19.5 + - - +
190C LEU* 5.1 1.8 - - - -
192C PHE* 3.4 17.0 - - + -
332C PHE* 2.9 34.5 + - + +
333C ASP 2.7 20.3 + - - -
335C VAL* 1.3 75.3 - - - +
337C ASP* 1.3 56.9 + - - +
339C ILE* 3.3 10.7 + - + +
340C ILE* 2.9 37.8 + - - +
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Residues in contact with ASP 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C LYS* 2.7 29.9 + - - +
333C ASP* 3.1 18.8 + - - +
334C ALA* 3.6 13.1 - - - +
336C THR* 1.3 83.4 + - - +
338C ILE* 1.3 59.0 + - + +
340C ILE* 3.4 9.2 + - - +
341C LYS* 2.8 30.4 + - - +
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Residues in contact with ILE 338 (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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259C SER* 4.5 9.6 - - - +
261C VAL* 5.2 6.5 - - + -
316C TYR* 3.4 63.0 - - + +
318C HIS* 6.0 2.5 - - - +
334C ALA 3.2 15.8 + - - +
335C VAL* 3.1 10.9 + - - +
337C ASP* 1.3 76.1 - - + +
339C ILE* 1.3 60.6 + - + +
341C LYS* 3.3 17.3 + - + +
342C GLU* 2.8 37.5 + - - +
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Residues in contact with ILE 339 (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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28C ARG* 3.4 25.1 + - - +
30C VAL* 4.1 10.1 - - + -
32C LEU* 3.7 29.2 - - + -
190C LEU* 4.3 4.5 - - + -
192C PHE* 3.9 15.7 - - + -
215C THR* 4.1 19.7 - - + -
216C CYS* 4.1 22.0 - - + -
259C SER* 4.8 6.1 - - - -
335C VAL* 3.0 29.8 + - + +
336C THR* 3.5 10.5 - - - +
338C ILE* 1.3 78.4 - - + +
340C ILE* 1.3 65.3 + - - +
342C GLU* 3.4 7.7 + - - +
343C ASN* 3.4 10.7 + - - +
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Residues in contact with ILE 340 (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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28C ARG* 4.1 7.4 - - - +
188C LYS* 4.1 39.9 - - + +
190C LEU* 3.8 23.3 - - + -
336C THR 2.9 22.2 + - - +
337C ASP* 3.6 9.2 - - - +
339C ILE* 1.3 74.8 - - - +
341C LYS* 1.3 62.2 + - - +
343C ASN* 3.0 15.1 + - - +
344C LEU* 3.1 22.0 - - + +
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Residues in contact with LYS 341 (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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314C GLU* 5.4 1.8 + - - -
316C TYR* 3.3 22.3 + - - -
337C ASP 2.8 20.6 + - - +
338C ILE* 3.3 21.1 + - + +
340C ILE* 1.3 68.9 - - - +
342C GLU* 1.3 78.6 + - - +
343C ASN 2.9 4.7 - - - -
344C LEU* 2.8 47.9 + - + +
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Residues in contact with GLU 342 (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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259C SER* 3.2 28.6 + - - +
313C LYS* 6.1 1.0 - - - +
314C GLU 5.3 0.7 - - - +
316C TYR* 3.0 26.9 + - - -
338C ILE* 2.8 21.8 + - - +
339C ILE 3.7 6.5 - - - +
340C ILE 3.3 0.2 - - - -
341C LYS* 1.3 99.3 - - - +
343C ASN* 1.3 56.0 + - - +
344C LEU 3.2 5.7 + - - -
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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