Contacts of the helix formed by residues 260 - 274 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482G PRO* 5.4 5.6 - - + +
483G SER* 4.4 25.7 - - - +
258H ASP 3.8 1.6 + - - -
259H ALA* 1.3 71.7 - - - +
261H MET* 1.3 63.0 + - - +
262H ASP* 4.0 14.4 + - - +
263H ASN* 3.2 30.1 + - + +
264H ALA* 3.0 21.8 + - - +
415H PHE* 5.8 0.2 - - - -
417H ARG* 4.9 6.0 - - + +
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Residues in contact with MET 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H VAL* 3.8 30.7 - - + -
256H MET 5.1 2.7 - - - +
257H PRO 5.7 2.2 - - - +
259H ALA* 3.1 11.9 + - - +
260H ASP* 1.3 72.9 + - - +
262H ASP* 1.3 58.1 + - - +
264H ALA* 3.7 4.9 - - - +
265H VAL* 3.0 38.1 + - + +
293H ALA* 3.9 30.5 - - + +
296H ALA* 4.1 17.7 - - + +
297H LEU* 4.1 23.8 - - - -
300H LYS* 4.1 27.6 - - + +
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Residues in contact with ASP 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260H ASP* 3.3 12.8 + - - +
261H MET* 1.3 74.0 - - - +
263H ASN* 1.3 64.1 + - - +
265H VAL* 4.5 2.8 - - - +
266H ASN* 3.3 23.4 + - - +
300H LYS* 2.6 37.6 + - - +
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Residues in contact with ASN 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480G ARG* 3.7 19.7 + - - +
482G PRO* 3.7 27.6 - - + +
260H ASP* 3.2 31.0 + - + +
262H ASP* 1.3 76.3 - - - +
264H ALA* 1.3 67.9 + - - +
266H ASN* 3.4 7.3 + - - +
267H GLN* 3.0 51.8 + - - +
415H PHE* 4.8 2.4 - - - -
437H ASN* 4.8 4.5 - - - +
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Residues in contact with ALA 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H VAL* 4.8 10.8 - - + -
259H ALA* 5.5 0.7 - - + -
260H ASP 3.0 12.4 + - - +
261H MET* 3.4 13.4 + - - +
263H ASN* 1.3 77.2 - - - +
265H VAL* 1.3 51.7 + - + +
267H GLN* 3.1 3.8 + - - +
268H LEU* 2.7 44.6 + - + +
297H LEU* 5.5 0.2 - - + -
415H PHE* 3.8 43.4 - - + -
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Residues in contact with VAL 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H MET* 3.0 26.6 + - + +
262H ASP* 4.5 3.6 - - - +
264H ALA* 1.3 72.8 - - - +
266H ASN* 1.3 67.8 + - - +
268H LEU* 3.4 7.9 + - - +
269H LEU* 3.1 22.3 + - - +
297H LEU* 3.9 25.8 - - + +
300H LYS* 3.7 42.4 - - + +
301H MET* 3.8 23.8 - - + +
304H ALA* 4.3 9.6 - - + -
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Residues in contact with ASN 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H ASP 3.3 21.3 + - - +
263H ASN* 3.6 8.5 + - - +
265H VAL* 1.3 78.6 - - - +
267H GLN* 1.3 67.7 + - - +
269H LEU* 3.2 34.2 - - - +
270H GLY 3.9 1.7 + - - -
304H ALA* 6.1 0.4 - - - -
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Residues in contact with GLN 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480G ARG* 3.4 22.9 + - - +
263H ASN* 3.0 40.9 + - - +
264H ALA 3.7 2.7 - - - +
266H ASN* 1.3 81.5 - - + +
268H LEU* 1.3 63.7 + - - +
269H LEU 3.3 0.2 + - - -
270H GLY* 3.5 3.6 + - - -
271H ALA* 3.3 20.4 + - - +
415H PHE* 3.9 12.9 - - + -
437H ASN 3.3 21.2 + - - +
438H ILE* 4.9 3.1 - - - +
439H PRO* 3.7 26.7 - - + +
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Residues in contact with LEU 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H ALA* 4.4 1.8 - - + -
255H VAL* 4.8 3.8 - - + -
264H ALA* 2.7 31.3 + - + +
265H VAL* 3.8 5.6 - - - +
267H GLN* 1.3 69.4 - - - +
269H LEU* 1.3 58.3 + - - +
271H ALA* 3.7 3.4 - - - -
272H ALA* 2.8 35.7 + - - +
273H PHE* 4.6 0.2 - - - -
283H LEU* 3.8 45.5 - - + +
286H ALA* 4.7 13.5 - - + -
297H LEU* 4.1 24.0 - - + -
301H MET* 4.5 11.2 - - - -
388H LEU* 4.8 10.5 - - + -
415H PHE* 4.1 22.2 - - + -
439H PRO* 4.5 0.4 - - + -
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Residues in contact with LEU 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265H VAL 3.1 10.9 + - - +
266H ASN* 3.2 26.0 - - - +
267H GLN 3.2 0.2 - - - -
268H LEU* 1.3 76.7 - - - +
270H GLY* 1.3 61.3 + - - +
273H PHE* 3.1 35.8 + - + +
274H GLY 3.9 0.3 + - - -
301H MET* 3.3 29.6 - - + +
304H ALA* 3.9 31.6 - - + +
305H MET* 4.3 0.2 - - - -
308H LEU* 3.9 36.8 - - + +
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Residues in contact with GLY 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H ASN 3.9 2.6 + - - -
267H GLN 3.5 5.8 + - - -
268H LEU 3.4 0.2 - - - -
269H LEU* 1.3 79.6 - - - +
271H ALA* 1.3 56.7 + - - +
274H GLY* 2.8 27.6 + - - -
279H ARG* 3.0 14.3 + - - -
440H LEU* 5.0 2.7 - - - -
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Residues in contact with ALA 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H GLN 3.3 17.1 + - - +
268H LEU* 3.8 5.4 - - - +
269H LEU 3.3 0.2 - - - -
270H GLY* 1.3 77.7 - - - +
272H ALA* 1.3 60.7 + - - +
274H GLY 5.0 0.3 - - - +
279H ARG* 3.9 5.9 + - - +
282H ALA* 3.5 10.7 - - - +
283H LEU* 3.0 31.6 + - + -
439H PRO* 3.7 27.4 - - + -
440H LEU* 4.0 18.9 - - + +
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Residues in contact with ALA 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268H LEU* 2.8 22.4 + - + +
271H ALA* 1.3 75.7 - - - +
273H PHE* 1.3 75.1 + - + +
274H GLY 3.6 0.7 - - - -
277H GLY* 3.4 21.2 - - - -
282H ALA* 4.8 2.3 - - - +
283H LEU* 3.4 24.5 - - + +
284H SER* 5.4 0.4 - - - +
385H GLY 4.1 5.0 - - - +
386H PRO* 4.2 0.2 - - - +
387H VAL 4.4 5.8 - - - +
388H LEU* 3.7 24.0 - - + -
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Residues in contact with PHE 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H LEU* 3.1 27.2 + - + +
272H ALA* 1.3 83.4 - - + +
274H GLY* 1.3 65.9 + - - +
276H SER* 3.2 9.4 + - - -
277H GLY 3.9 4.0 - - - +
301H MET* 4.3 10.8 - - + -
305H MET* 3.7 41.7 - - + -
308H LEU* 4.0 16.4 - - + -
320H PHE* 3.1 38.5 - + + -
366H GLY* 4.1 4.0 - - - -
367H THR 3.7 16.4 - - - -
386H PRO* 3.3 39.3 - - + -
387H VAL 4.0 7.0 - - - -
388H LEU* 4.0 14.1 - - + -
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Residues in contact with GLY 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H ASP* 4.6 5.2 - - - -
269H LEU 3.9 0.8 + - - -
270H GLY* 2.8 25.5 + - - -
271H ALA 5.0 0.5 - - - +
272H ALA 3.6 0.7 - - - +
273H PHE* 1.3 74.0 - - - +
275H SER* 1.3 73.6 + - - -
277H GLY* 3.1 13.3 + - - -
278H GLU 4.3 0.2 + - - -
279H ARG* 3.6 18.0 + - - -
282H ALA* 5.5 0.2 - - - +
319H ASP 5.2 3.6 - - - -
320H PHE* 5.0 1.8 - - - -
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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