Contacts of the helix formed by residues 255 - 274 (chain H) in PDB entry 6MZL
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 MET 255 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H GLN* 3.7 51.8 - - + +
223H TYR* 4.9 11.0 - - + -
224H TYR* 5.2 11.1 - - + -
252H LEU* 3.7 30.1 - - + -
253H TYR 3.0 5.4 - - - +
254H GLN* 1.3 101.3 - - + +
256H LEU* 1.3 60.6 + - - +
257H PRO 3.3 0.9 - - - -
258H ARG* 3.2 18.8 + - - +
259H PHE* 2.9 36.7 + - + +
182K GLN* 5.3 0.9 - - - +
186K VAL* 5.4 12.6 - - + -
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Residues in contact with LEU 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252H LEU* 5.3 2.3 - - + +
253H TYR* 4.3 16.6 - - + +
254H GLN 3.8 0.4 - - - +
255H MET* 1.3 78.2 - - - +
257H PRO* 1.3 61.1 - - + +
259H PHE* 3.2 9.7 - - + +
260H SER* 2.9 34.8 + - - +
289H LEU* 3.8 30.3 - - + -
295H LEU* 3.7 28.5 - - + -
296H TYR 4.7 7.0 - - - +
297H LEU* 4.3 20.9 - - + -
300H TYR* 3.5 31.1 - - + -
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Residues in contact with PRO 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254H GLN* 3.5 25.1 - - + +
255H MET 3.5 0.4 - - - -
256H LEU* 1.3 91.2 - - + +
258H ARG* 1.3 57.9 + - + +
260H SER* 2.9 15.7 + - - +
261H THR* 2.5 28.7 + - - -
300H TYR* 3.8 34.5 - - + +
303H GLU* 5.2 0.6 - - - +
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Residues in contact with ARG 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220H GLN* 3.1 44.7 + - - +
221H GLN* 5.3 6.3 - - - +
224H TYR* 3.4 35.7 + - + +
254H GLN* 4.7 17.2 + - - +
255H MET* 3.2 15.2 + - - +
257H PRO* 1.3 79.3 - - + +
259H PHE* 1.3 57.1 + - - +
261H THR* 3.6 6.3 - - - -
262H PHE 2.9 24.1 + - - -
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Residues in contact with PHE 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H TYR* 5.7 1.6 - + - -
224H TYR* 4.3 18.1 - + - -
227H ILE* 4.2 22.4 - - + -
228H THR* 5.8 0.7 - - + -
246H ILE* 3.9 26.2 - - + -
252H LEU* 5.1 12.3 - - + -
255H MET* 2.9 24.8 + - + +
256H LEU* 3.2 12.8 - - + +
258H ARG* 1.3 76.5 - - - +
260H SER* 1.3 59.0 + - - +
262H PHE* 3.1 9.0 + - - +
263H ILE* 3.0 37.7 + - + +
285H MET* 3.5 31.4 - - + -
289H LEU* 3.6 38.8 - - + -
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Residues in contact with SER 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256H LEU* 2.9 14.8 + - - +
257H PRO* 2.9 12.5 + - - +
259H PHE* 1.3 80.2 - - - +
261H THR* 1.3 60.4 + - - +
263H ILE* 3.0 14.9 + - - +
264H SER* 2.9 31.5 + - - -
289H LEU* 6.2 0.4 - - - -
300H TYR* 4.8 12.1 - - - +
303H GLU* 2.6 28.1 + - - -
304H LEU* 4.2 20.5 - - - +
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Residues in contact with THR 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H PRO* 2.5 23.8 + - - +
258H ARG* 3.6 7.8 - - - -
260H SER* 1.3 77.6 + - - +
262H PHE* 1.3 64.3 + - - +
264H SER* 3.3 6.3 + - - -
265H GLU* 3.0 26.5 + - + +
303H GLU* 3.7 17.2 + - - +
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Residues in contact with PHE 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224H TYR* 3.6 17.0 - + + +
228H THR* 4.3 22.2 - - + -
231H CYS* 4.6 5.6 - - - -
232H VAL* 4.5 21.8 - - + -
258H ARG 2.9 14.0 + - - +
259H PHE* 3.3 7.9 - - - +
261H THR* 1.3 76.8 - - - +
263H ILE* 1.3 56.9 + - - +
265H GLU* 5.1 2.2 - - - -
266H GLY* 2.9 37.8 + - - -
282H LEU* 4.3 16.2 - - + -
285H MET* 3.6 33.4 - - + -
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Residues in contact with ILE 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259H PHE* 3.0 38.6 + - + +
260H SER* 3.0 13.7 + - - +
262H PHE* 1.3 78.0 - - - +
264H SER* 1.3 58.3 + - - +
266H GLY 3.8 0.2 - - - -
267H VAL* 2.9 39.9 + - + +
282H LEU* 4.3 15.7 - - + +
283H MET* 5.7 0.7 - - + -
285H MET* 3.7 26.0 - - + -
286H VAL* 4.2 21.3 - - + -
289H LEU* 3.7 19.3 - - + -
304H LEU* 4.7 7.2 - - + -
307H ALA* 4.5 14.4 - - + -
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Residues in contact with SER 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260H SER 2.9 15.8 + - - -
261H THR* 3.3 10.3 + - - -
263H ILE* 1.3 76.8 - - - +
265H GLU* 1.3 66.3 + - - +
267H VAL* 3.2 5.7 + - - +
268H ARG* 3.0 29.0 + - - +
303H GLU* 3.3 34.4 + - - +
304H LEU* 5.8 0.2 - - - +
306H PRO* 6.2 0.9 - - - -
307H ALA* 4.2 11.2 - - - +
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Residues in contact with GLU 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H THR* 3.0 18.0 + - + +
262H PHE* 4.4 2.7 - - - +
264H SER* 1.3 76.8 - - - +
266H GLY* 1.3 61.2 + - - +
268H ARG* 3.1 41.0 + - - +
269H VAL* 2.9 38.6 + - + +
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Residues in contact with GLY 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262H PHE* 2.9 28.8 + - - -
263H ILE 3.8 0.4 - - - -
265H GLU* 1.3 74.5 - - - +
267H VAL* 1.3 57.7 + - - +
269H VAL* 3.5 8.2 - - - +
270H ASN* 2.8 43.1 + - - -
282H LEU* 4.1 5.8 - - - -
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Residues in contact with VAL 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263H ILE* 2.9 26.5 + - + +
264H SER* 3.3 7.9 - - - +
266H GLY* 1.3 76.3 - - - +
268H ARG* 1.3 61.1 + - + +
270H ASN* 3.3 2.8 + - - +
271H VAL* 2.8 43.3 + - + +
279H LEU* 5.0 2.9 - - + +
282H LEU* 3.9 18.1 - - + +
283H MET* 4.6 4.7 - - + -
307H ALA* 4.0 37.2 - - + +
310H THR* 4.7 10.1 - - + -
311H CYS* 4.1 18.6 - - - -
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Residues in contact with ARG 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264H SER* 3.0 21.8 + - - +
265H GLU* 3.1 42.4 + - - +
267H VAL* 1.3 76.5 - - + +
269H VAL* 1.3 63.4 + - + +
271H VAL* 3.3 9.6 + - - +
272H VAL* 3.0 28.5 + - + +
310H THR* 6.2 2.9 - - + -
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Residues in contact with VAL 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265H GLU* 2.9 27.0 + - + +
266H GLY* 3.5 10.5 - - - +
268H ARG* 1.3 75.7 - - + +
270H ASN* 1.3 63.4 + - - +
272H VAL* 2.8 11.3 + - - +
273H GLN* 2.7 47.3 + - + +
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Residues in contact with ASN 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H GLY* 2.8 26.4 + - - +
269H VAL* 1.3 85.1 - - - +
271H VAL* 1.3 58.6 + - - +
273H GLN* 3.6 12.8 - - - +
274H ASN* 2.6 29.5 + - - -
275H ASN* 3.7 6.1 + - - +
278H LEU* 3.3 40.0 - - - +
279H LEU* 3.7 28.2 - - + +
282H LEU* 3.8 11.1 - - - +
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Residues in contact with VAL 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H VAL* 2.8 23.4 + - + +
268H ARG* 3.3 13.9 - - - +
270H ASN* 1.3 76.5 - - - +
272H VAL* 1.3 66.2 + - + +
274H ASN* 3.0 23.5 + - - +
279H LEU* 5.7 4.5 - - + -
310H THR* 3.9 33.4 - - + +
311H CYS* 5.5 2.7 - - - +
314H SER* 4.8 18.6 - - - -
317H LEU* 5.6 2.3 - - - +
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Residues in contact with VAL 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268H ARG 3.0 14.5 + - - +
269H VAL* 2.8 11.7 + - - +
271H VAL* 1.3 81.6 - - + +
273H GLN* 1.3 72.9 + - - +
274H ASN* 3.9 8.5 + - - -
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Residues in contact with GLN 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H VAL* 2.7 34.9 + - + +
270H ASN* 4.0 12.3 - - - +
272H VAL* 1.3 95.5 - - - +
274H ASN* 1.3 71.3 + - - +
275H ASN* 3.4 8.0 + - + +
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Residues in contact with ASN 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H ASN 2.6 19.1 + - - +
271H VAL* 3.0 20.5 + - - +
272H VAL 3.9 8.9 + - - -
273H GLN* 1.3 74.8 - - - +
275H ASN* 1.3 57.4 + - - +
276H LEU* 3.7 7.0 + - - +
279H LEU* 5.0 3.1 - - - +
314H SER* 4.2 11.1 + - - -
317H LEU* 2.6 49.4 + - - +
318H CYS* 3.6 28.6 - - - +
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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
------------------------------------------------------------
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