Contacts of the helix formed by residues 260 - 274 (chain C) in PDB entry 4ZZ7
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 260 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258C ASP 3.7 1.4 + - - -
259C ALA* 1.3 70.5 - - - +
261C MET* 1.3 59.2 + - - +
262C ASP* 3.4 16.6 + - - +
263C ASN* 3.4 23.4 + - + +
264C ALA* 3.0 28.6 + - - +
415C PHE* 5.6 0.7 - - - -
417C ARG* 4.9 5.1 - - + +
437C ASN* 6.0 0.4 + - - -
482D PRO* 5.4 5.7 - - + +
483D SER* 4.4 24.9 - - - +
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Residues in contact with MET 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL* 3.6 32.5 - - + -
256C MET 4.9 4.5 - - - +
257C PRO 5.6 2.5 - - - +
259C ALA* 3.3 9.5 + - - +
260C ASP* 1.3 71.5 + - - +
262C ASP* 1.3 60.9 + - - +
264C ALA* 3.5 4.6 - - - +
265C VAL* 2.9 39.1 + - + +
293C ALA* 3.9 28.3 - - + +
296C ALA* 4.4 18.6 - - + +
297C LEU* 4.0 26.0 - - - -
300C LYS* 4.2 24.9 - - + +
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Residues in contact with ASP 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ASP* 3.3 12.0 + - - +
261C MET* 1.3 78.8 - - - +
263C ASN* 1.3 57.4 + - - +
265C VAL* 3.6 5.0 - - - +
266C ASN* 2.9 31.2 + - - +
300C LYS* 2.7 37.7 + - - +
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Residues in contact with ASN 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ASP* 3.4 26.3 + - + +
262C ASP* 1.3 78.2 - - - +
264C ALA* 1.3 63.0 + - - +
266C ASN* 3.9 8.5 - - - +
267C GLN* 3.1 49.4 + - - +
415C PHE* 4.8 3.6 - - - -
480D ARG* 3.8 21.0 - - - +
482D PRO* 3.5 26.4 - - + +
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Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL* 4.9 5.6 - - + -
259C ALA* 5.3 0.2 - - + -
260C ASP 3.0 17.9 + - - +
261C MET* 3.5 17.0 - - - +
262C ASP 3.2 0.2 - - - -
263C ASN* 1.3 77.4 + - - +
265C VAL* 1.3 57.6 + - - +
267C GLN* 3.4 1.9 + - - +
268C LEU* 2.9 40.2 + - + +
297C LEU* 5.5 0.2 - - + -
415C PHE* 3.9 39.9 - - + -
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Residues in contact with VAL 265 (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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261C MET* 2.9 25.9 + - + +
262C ASP* 3.6 4.3 - - - +
264C ALA* 1.3 74.6 - - - +
266C ASN* 1.3 64.6 + - - +
268C LEU* 3.5 6.8 + - - +
269C LEU* 3.3 22.2 + - - +
297C LEU* 3.9 25.4 - - + +
300C LYS* 3.9 29.4 - - + +
301C MET* 3.9 30.6 - - + +
304C ALA* 4.1 14.8 - - + -
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Residues in contact with ASN 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ASP 2.9 17.2 + - - +
263C ASN* 3.9 9.8 - - - +
265C VAL* 1.3 78.7 - - - +
267C GLN* 1.3 63.0 + - + +
269C LEU* 3.5 30.4 - - - +
270C GLY 4.0 2.1 + - - -
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Residues in contact with GLN 267 (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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263C ASN* 3.1 41.4 + - - +
264C ALA 4.0 2.7 - - - +
266C ASN* 1.3 77.2 - - + +
268C LEU* 1.3 60.8 + - - +
269C LEU 3.2 1.1 + - - -
270C GLY* 3.5 3.1 + - - -
271C ALA* 3.1 26.5 + - - +
415C PHE* 3.7 14.5 - - + -
437C ASN 3.3 21.5 + - - +
438C ILE* 4.6 5.9 - - - +
439C PRO* 3.7 27.1 - - + +
480D ARG* 3.4 18.0 + - - +
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Residues in contact with LEU 268 (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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253C ALA* 4.4 2.5 - - + -
255C VAL* 4.7 7.0 - - + -
264C ALA* 2.9 27.5 + - + +
265C VAL* 4.0 6.1 - - - +
266C ASN 3.4 0.4 - - - -
267C GLN* 1.3 74.6 - - - +
269C LEU* 1.3 59.0 + - - +
271C ALA* 3.8 4.3 - - - -
272C ALA* 3.0 33.1 + - - +
273C PHE* 4.4 1.2 - - - -
283C LEU* 3.7 44.0 - - + +
286C ALA* 4.8 10.1 - - + -
297C LEU* 4.0 27.4 - - + -
301C MET* 4.8 5.4 - - - -
388C LEU* 4.6 15.9 - - + +
415C PHE* 4.1 21.8 - - + -
439C PRO* 4.5 0.2 - - + -
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Residues in contact with LEU 269 (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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265C VAL 3.3 15.2 + - - +
266C ASN* 3.5 28.3 - - - +
267C GLN 3.2 0.4 - - - -
268C LEU* 1.3 74.1 - - - +
270C GLY* 1.3 62.0 + - - +
273C PHE* 3.0 42.5 + - + +
274C GLY 3.8 0.3 + - - -
301C MET* 3.2 26.0 - - + +
304C ALA* 3.9 29.8 - - + +
308C LEU* 3.8 32.8 - - + +
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Residues in contact with GLY 270 (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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266C ASN 4.0 3.0 + - - -
267C GLN 3.5 5.4 + - - -
269C LEU* 1.3 78.9 - - - +
271C ALA* 1.3 58.9 + - - +
274C GLY* 2.8 28.0 + - - -
279C ARG* 2.9 14.2 + - - -
440C LEU* 5.0 2.0 - - - -
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Residues in contact with ALA 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C GLN 3.1 17.5 + - - +
268C LEU* 4.3 3.4 - - - -
270C GLY* 1.3 77.8 - - - +
272C ALA* 1.3 62.8 + - - +
274C GLY 4.4 0.7 + - - +
279C ARG* 3.7 9.3 + - - +
282C ALA* 3.7 8.7 - - - +
283C LEU* 3.4 23.6 + - + -
439C PRO* 3.6 26.7 - - + -
440C LEU* 3.7 26.3 - - + +
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Residues in contact with ALA 272 (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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268C LEU* 3.0 21.9 + - + +
271C ALA* 1.3 80.1 - - - +
273C PHE* 1.3 73.8 + - + +
277C GLY* 3.4 20.6 - - - -
282C ALA* 4.6 3.8 - - - +
283C LEU* 3.3 25.7 - - - +
284C SER* 6.0 0.2 - - - -
385C GLY 4.3 3.8 - - - +
386C PRO* 4.5 0.2 - - - +
387C VAL 4.7 5.3 - - - +
388C LEU* 4.1 22.0 - - + -
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Residues in contact with PHE 273 (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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268C LEU 4.5 0.7 - - - -
269C LEU* 3.0 28.8 + - + +
272C ALA* 1.3 81.4 - - + +
274C GLY* 1.3 61.5 + - - +
276C SER* 2.9 23.9 + - - -
277C GLY 3.8 3.4 - - - +
301C MET* 4.1 15.0 - - + -
305C MET* 3.8 37.5 - - + -
308C LEU* 4.0 16.2 - - + -
320C PHE* 3.5 28.7 - - + -
366C GLY* 4.3 4.0 - - - -
367C THR 3.8 12.8 - - - -
386C PRO* 3.3 37.9 - - + -
387C VAL 4.1 0.7 - - - -
388C LEU* 3.9 23.3 - - + -
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Residues in contact with GLY 274 (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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96C ASP* 4.5 5.2 - - - -
269C LEU 3.8 0.8 + - - -
270C GLY* 2.8 25.4 + - - -
271C ALA 4.7 0.9 - - - +
272C ALA 3.6 0.5 - - - +
273C PHE* 1.3 76.0 - - - +
275C SER* 1.3 68.4 + - - -
277C GLY* 3.2 11.8 + - - -
278C GLU 4.4 0.2 + - - -
279C ARG* 3.4 20.7 + - - +
319C ASP 5.0 3.8 - - - -
320C PHE* 4.9 3.1 - - - -
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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