Contacts of the helix formed by residues 324 - 341 (chain C) in PDB entry 4IYM
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 324 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C PHE* 5.4 13.9 - - + -
24C PRO* 5.8 0.2 - - - -
175C ARG* 3.6 33.7 - - - +
322C VAL* 4.0 6.0 - - - +
323C VAL* 1.3 88.0 - - + +
325C LYS* 1.3 63.7 + - - +
326C GLU* 3.4 19.1 + - - +
327C ALA* 3.0 24.5 + - - +
328C GLU* 3.1 22.0 + - - +
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Residues in contact with LYS 325 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C GLY* 6.4 2.2 - - - -
324C THR* 1.3 70.9 - - - +
326C GLU* 1.3 70.9 + - - +
328C GLU* 3.1 34.2 + - - +
329C GLN* 2.9 53.2 + - - +
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Residues in contact with GLU 326 (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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22C PHE* 6.0 2.1 - - - -
324C THR* 3.4 21.1 - - - +
325C LYS* 1.3 85.1 + - - +
327C ALA* 1.3 63.4 + - - +
329C GLN* 3.2 14.8 + - - +
330C ARG* 3.0 24.7 + - - +
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Residues in contact with ALA 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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147C PHE* 6.2 0.4 - - + -
277C GLU* 5.1 1.8 - - - +
322C VAL* 4.5 9.0 - - + -
323C VAL* 4.1 12.6 - - + +
324C THR* 3.0 29.2 + - - +
326C GLU* 1.3 75.8 - - - +
328C GLU* 1.3 63.3 + - - +
330C ARG* 3.5 8.5 + - - +
331C ILE* 3.1 34.1 + - + +
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Residues in contact with GLU 328 (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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322C VAL* 3.9 19.4 - - + +
324C THR 3.1 13.9 + - - +
325C LYS* 3.1 40.9 + - - +
327C ALA* 1.3 75.5 - - - +
329C GLN* 1.3 59.2 + - + +
331C ILE* 3.4 5.9 + - - +
332C ARG* 2.9 68.7 + - + +
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Residues in contact with GLN 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C LYS* 2.9 39.4 + - + +
326C GLU* 3.6 14.2 - - - +
328C GLU* 1.3 75.8 - - + +
330C ARG* 1.3 58.0 + - - +
332C ARG* 3.2 9.4 + - - +
333C SER* 2.9 32.4 + - - +
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Residues in contact with ARG 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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326C GLU 3.0 16.4 + - - +
327C ALA* 3.9 7.2 - - - +
329C GLN* 1.3 74.7 - - - +
331C ILE* 1.3 72.1 + - - +
333C SER* 3.3 6.9 + - - -
334C LEU* 3.1 48.0 + - + +
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Residues in contact with ILE 331 (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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275C ALA 5.7 1.8 - - - +
277C GLU* 5.7 2.9 - - + +
322C VAL* 3.8 32.1 - - + -
327C ALA* 3.1 25.7 + - + +
328C GLU* 3.8 4.0 - - - +
330C ARG* 1.3 83.3 - - + +
332C ARG* 1.3 63.8 + - + +
334C LEU* 3.3 9.7 + - + +
335C ILE* 3.0 40.9 + - + +
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Residues in contact with ARG 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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328C GLU* 2.9 53.5 + - + +
329C GLN* 3.2 7.6 + - - +
331C ILE* 1.3 77.9 - - + +
333C SER* 1.3 61.9 + - - +
335C ILE* 3.4 13.9 + - + +
336C ASP* 3.1 29.6 + - - +
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Residues in contact with SER 333 (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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329C GLN* 2.9 18.8 + - - +
330C ARG* 3.3 8.9 + - - -
332C ARG* 1.3 75.8 - - - +
334C LEU* 1.3 59.7 + - - +
336C ASP* 3.3 9.8 + - - +
337C SER* 3.0 27.3 + - - -
340C GLU* 5.0 0.3 - - - +
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Residues in contact with LEU 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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330C ARG* 3.1 55.7 + - + +
331C ILE* 3.8 7.9 - - + +
333C SER* 1.3 75.9 - - - +
335C ILE* 1.3 66.8 + - + +
337C SER* 2.8 30.2 + - - +
338C GLY* 3.1 6.9 + - - -
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Residues in contact with ILE 335 (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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331C ILE* 3.0 41.2 + - + +
332C ARG* 3.7 13.0 - - + +
333C SER 3.3 0.2 - - - -
334C LEU* 1.3 76.3 - - + +
336C ASP* 1.3 64.2 + - - +
338C GLY* 3.2 10.5 + - - +
339C ILE* 3.3 26.3 + - + +
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Residues in contact with ASP 336 (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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332C ARG* 3.1 19.1 + - - +
333C SER* 3.6 11.0 - - - +
335C ILE* 1.3 77.9 - - - +
337C SER* 1.3 63.2 + - - +
339C ILE* 3.2 19.3 + - - +
340C GLU* 3.0 33.5 + - - +
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Residues in contact with SER 337 (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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333C SER 3.0 14.0 + - - -
334C LEU* 2.8 29.3 + - - +
336C ASP* 1.3 76.1 - - - +
338C GLY* 1.3 56.7 + - - +
340C GLU* 3.2 16.1 + - - +
341C GLN* 2.9 55.0 + - - +
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Residues in contact with GLY 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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334C LEU 3.1 7.5 + - - -
335C ILE* 3.2 5.3 + - - -
337C SER* 1.3 83.0 + - - +
339C ILE* 1.3 59.3 + - - +
341C GLN* 3.4 6.0 + - - +
342C GLY 3.3 5.0 + - - -
343C ALA* 2.9 40.0 + - - +
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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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335C ILE* 3.3 23.9 + - + +
336C ASP* 3.2 20.3 + - - +
338C GLY* 1.3 74.6 - - - +
340C GLU* 1.3 63.1 + - + +
342C GLY* 3.3 13.0 + - - -
343C ALA 4.2 11.3 - - - +
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Residues in contact with GLU 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C SER 5.0 0.5 - - - +
336C ASP* 3.0 24.8 + - - +
337C SER* 3.4 27.8 + - - +
339C ILE* 1.3 77.8 - - + +
341C GLN* 1.3 63.0 + - + +
342C GLY 3.4 0.6 + - - -
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Residues in contact with GLN 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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337C SER* 2.9 38.3 + - - +
338C GLY* 3.4 4.9 + - - +
339C ILE 3.2 0.2 - - - -
340C GLU* 1.3 84.3 - - + +
342C GLY* 1.3 57.6 + - - +
343C ALA 3.7 2.1 + - - -
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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