Contacts of the helix formed by residues 323 - 338 (chain C) in PDB entry 2W4T
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 323 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321C ASN 4.2 0.8 - - - -
322C ILE* 1.3 71.7 - - - +
324C ASP* 1.3 61.0 + - - +
325C VAL* 3.0 19.1 - - - +
326C GLU* 2.8 44.9 + - + +
327C GLU* 2.9 29.6 + - - +
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Residues in contact with ASP 324 (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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280C ARG* 3.2 24.9 + - - -
286C TYR* 3.3 33.4 - - - +
287C GLN* 1.6 47.7 + - - +
290C SER* 3.8 8.0 + - - -
317C LEU 4.7 6.6 - - - +
318C THR* 5.0 4.3 - - - -
319C VAL* 4.5 6.2 + - - +
322C ILE* 3.5 11.0 + - - +
323C ASP* 1.3 72.2 - - - +
325C VAL* 1.3 57.8 + - + +
328C PHE* 3.0 12.5 + - - +
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Residues in contact with VAL 325 (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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290C SER* 3.5 29.8 - - - +
291C ASN 5.0 2.2 - - - +
292C ALA* 3.0 38.2 - - + +
323C ASP* 3.0 14.3 - - - +
324C ASP* 1.3 75.8 - - + +
326C GLU* 1.3 74.1 + - + +
328C PHE 3.1 7.8 + - - -
329C LYS* 3.1 4.2 + - - +
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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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323C ASP* 2.8 33.0 + - + +
325C VAL* 1.3 80.7 - - + +
327C GLU* 1.3 65.8 + - - +
329C LYS* 3.4 20.4 + - - +
330C LEU* 3.0 30.0 + - + +
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Residues in contact with GLU 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C PRO* 4.5 8.9 - - - +
228C ALA* 4.1 15.8 - - - +
283C HIS* 4.1 10.4 + - - +
287C GLN* 2.4 51.6 + - - +
322C ILE* 5.4 8.1 - - + -
323C ASP 2.9 14.5 + - - +
326C GLU* 1.3 77.7 - - - +
328C PHE* 1.3 56.1 + - - +
330C LEU* 3.7 8.4 - - + +
331C CYS* 2.8 34.2 + - - +
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Residues in contact with PHE 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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287C GLN* 2.7 39.1 + - + +
288C ILE* 4.1 14.6 - - + -
292C ALA* 3.3 10.8 - - + -
293C ILE* 1.8 55.4 - - + -
296C LEU* 3.7 7.2 - - + -
300C MET* 5.3 2.5 - - + -
324C ASP 3.0 15.2 + - - +
325C VAL 3.3 4.7 - - - +
327C GLU* 1.3 76.6 - - - +
329C LYS* 1.3 50.1 + - - +
331C CYS* 2.4 26.0 - - - -
332C ASP* 2.2 62.2 + - - +
349C PHE* 3.2 28.9 - + - -
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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
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292C ALA* 4.7 10.5 - - + +
293C ILE* 5.0 4.0 - - + -
325C VAL 3.1 9.7 + - - +
326C GLU* 3.6 24.9 - - - +
327C GLU 3.3 0.2 - - - -
328C PHE* 1.3 81.4 - - - +
330C LEU* 1.3 53.6 + - + +
332C ASP* 2.9 11.7 + - + +
333C GLU* 2.7 58.4 + - + +
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Residues in contact with LEU 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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221C GLN* 6.3 0.4 - - - +
224C PRO* 5.0 5.4 - - + +
326C GLU* 3.0 19.5 + - + +
327C GLU* 3.8 8.1 - - + +
329C LYS* 1.3 78.0 - - + +
331C CYS* 1.3 57.2 + - - +
333C GLU* 3.4 16.8 - - + +
334C ALA* 2.8 30.3 + - - +
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Residues in contact with CYS 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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224C PRO* 4.8 12.3 - - - +
225C VAL* 4.2 8.4 - - + +
228C ALA* 4.9 8.3 - - + -
229C TYR* 6.4 1.3 - - + -
284C ILE* 6.2 3.1 - - - -
287C GLN* 5.2 3.6 - - + -
327C GLU* 2.8 25.3 + - - +
328C PHE* 2.4 47.6 - - - -
330C LEU* 1.3 73.8 - - - +
332C ASP* 1.3 73.1 + - - +
334C ALA* 3.4 7.6 + - - +
335C PHE* 3.2 10.9 + - - +
345C LYS* 2.7 20.0 + - - -
349C PHE* 4.2 10.1 - - - -
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Residues in contact with ASP 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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293C ILE* 4.4 5.2 - - + -
296C LEU* 4.5 4.2 - - - +
328C PHE* 2.2 63.5 + - - +
329C LYS* 3.2 7.9 + - - +
331C CYS* 1.3 76.0 - - - +
333C GLU* 1.3 67.8 + - + +
335C PHE* 2.9 11.4 + - - +
336C ASP* 2.8 17.4 - - - +
345C LYS* 3.0 18.1 - - - +
349C PHE* 2.8 30.3 - - - -
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Residues in contact with GLU 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 LYS* 2.7 51.7 + - + +
330C LEU* 3.4 20.9 - - + +
332C ASP* 1.3 75.0 - - - +
334C ALA* 1.3 56.5 + - - +
336C ASP* 3.4 20.7 - - - +
337C ILE* 2.9 24.0 - - + +
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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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221C GLN* 3.5 32.8 - - - +
224C PRO* 4.2 8.7 - - + -
225C VAL* 3.9 10.8 - - + -
330C LEU 2.8 18.2 + - - +
331C CYS 3.6 6.3 - - - +
332C ASP 3.1 0.6 - - - -
333C GLU* 1.3 73.3 - - - +
335C PHE* 1.3 62.1 + - - +
336C ASP 3.2 0.7 - - - -
337C ILE* 3.1 27.4 - - - +
338C LEU* 3.1 14.0 + - - +
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Residues in contact with PHE 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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225C VAL* 4.5 6.9 - - + +
331C CYS 3.2 4.0 + - - +
332C ASP 2.9 1.4 + - - -
334C ALA* 1.3 74.9 - - - +
336C ASP* 1.3 64.6 + - - +
340C PHE* 2.2 107.4 + + + +
341C THR 3.1 9.9 - - - -
342C LYS* 5.6 0.9 - - + -
344C GLU* 3.5 5.8 - - + -
345C LYS* 2.1 98.9 - - + +
348C MET* 4.5 6.7 - - + -
441C ARG* 3.9 9.9 - - - -
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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 ASP* 2.8 24.6 - - - +
333C GLU* 3.4 18.2 - - - +
335C PHE* 1.3 81.1 - - - +
337C ILE* 1.3 55.2 + - + +
339C GLY* 2.6 28.6 + - - -
340C PHE 3.8 8.9 + - - +
342C LYS* 3.1 31.7 + - - +
345C LYS* 5.0 1.7 - - - +
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Residues in contact with ILE 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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217C ASP* 3.6 11.5 - - + +
218C GLN* 3.3 26.6 - - + +
221C GLN* 2.9 51.6 - - + +
333C GLU* 2.9 22.2 - - + +
334C ALA* 3.1 14.6 - - - +
336C ASP* 1.3 74.4 - - + +
338C LEU* 1.3 67.9 + - + +
339C GLY* 3.0 1.4 + - - -
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Residues in contact with LEU 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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218C GLN* 3.6 36.6 - - + +
221C GLN 4.2 6.1 - - - +
222C ALA* 4.3 6.1 - - + +
225C VAL* 4.0 21.8 - - + -
334C ALA 3.1 13.2 + - - +
336C ASP 3.1 1.0 - - - -
337C ILE* 1.3 83.5 - - + +
339C GLY* 1.3 57.6 + - - +
340C PHE* 2.3 56.8 - - + -
442C VAL* 3.8 17.0 - - + +
445C THR* 2.9 47.9 - - - +
446C LEU* 6.4 0.4 - - + -
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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