Contacts of the helix formed by residues 275 - 291 (chain I) 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 ASN 275 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270I ASN* 3.5 7.7 + - + +
273I GLN* 4.4 10.9 - - + +
274I ASN* 1.3 75.2 - - - +
276I LEU* 1.3 68.2 + - - +
277I ALA* 3.3 15.3 + - - +
278I LEU* 3.4 37.7 + - + +
279I LEU* 3.2 25.3 + - - +
318I CYS* 3.8 4.3 - - - -
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Residues in contact with LEU 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I ASN* 1.3 72.2 + - - +
277I ALA* 1.3 80.0 + - + +
279I LEU* 3.2 14.1 + - - +
280I ILE* 2.9 34.0 + - + +
318I CYS* 3.3 19.6 - - + -
322I ASP* 4.4 6.7 - - + +
325I ASN* 4.4 26.7 - - + +
326I HIS* 3.5 37.0 - - + +
329I LEU* 3.9 11.7 - - + +
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Residues in contact with ALA 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I ASN* 3.3 13.5 + - - +
276I LEU* 1.3 88.1 - - + +
278I LEU* 1.3 66.6 + - + +
280I ILE* 3.2 10.7 - - - +
281I TYR* 3.0 48.7 + - + +
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Residues in contact with LEU 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231I CYS 5.7 0.2 - - - +
232I VAL* 5.7 11.4 - - + -
270I ASN* 3.5 44.4 - - + +
273I GLN* 5.9 0.2 - - + -
275I ASN* 3.4 34.2 + - + +
276I LEU 3.4 0.2 - - - -
277I ALA* 1.3 78.3 - - + +
279I LEU* 1.3 57.3 + - - +
281I TYR* 3.5 16.4 + - + +
282I LEU* 2.9 39.7 + - + +
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Residues in contact with LEU 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I VAL* 5.3 7.2 - - + +
270I ASN* 5.3 9.4 - - + +
271I VAL* 4.9 15.5 - - + +
274I ASN* 5.4 1.8 - - - +
275I ASN 3.2 22.2 - - - +
276I LEU* 3.2 18.6 + - + +
277I ALA 3.1 0.4 - - - -
278I LEU* 1.3 78.6 - - - +
280I ILE* 1.3 58.6 + - - +
282I LEU* 3.2 6.5 + - + +
283I MET* 2.9 37.1 + - + +
311I CYS* 3.9 26.0 - - - -
316I GLN* 4.1 34.8 - - + +
326I HIS* 4.8 1.6 - - + +
329I LEU* 4.4 12.3 - - + -
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Residues in contact with ILE 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276I LEU* 2.9 22.5 + - + +
277I ALA* 3.2 20.4 - - - +
279I LEU* 1.3 73.1 - - - +
281I TYR* 1.3 75.8 + - + +
283I MET* 4.6 2.5 - - - -
284I ARG* 3.0 64.6 + - + +
329I LEU* 3.7 23.3 - - + +
332I PHE* 5.9 2.9 - - + -
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Residues in contact with TYR 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231I CYS* 3.2 24.7 - - - +
232I VAL 3.6 10.0 + - - -
233I GLY 4.1 4.2 + - - -
234I SER* 4.9 6.4 + - - -
236I GLU* 5.4 3.8 - - - -
239I ARG* 3.2 52.0 + - + +
243I LEU* 5.6 0.9 - - - +
277I ALA* 3.0 39.1 + - + +
278I LEU* 3.7 18.2 - - + +
280I ILE* 1.3 88.9 - - + +
282I LEU* 1.3 58.1 + - - +
284I ARG* 3.9 4.1 - - - +
285I MET* 2.9 29.0 + - - +
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Residues in contact with LEU 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231I CYS* 4.3 9.2 - - - -
263I ILE* 3.7 33.0 - - + +
266I GLY* 4.6 5.4 - - - +
267I VAL* 3.7 31.2 - - + +
270I ASN* 4.9 7.9 - - + +
278I LEU* 2.9 26.9 + - + +
279I LEU* 3.8 6.5 - - + +
281I TYR* 1.3 76.3 - - - +
283I MET* 1.3 72.8 + - + +
285I MET* 3.2 20.5 + - - +
286I VAL* 2.8 31.5 + - - +
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Residues in contact with MET 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I VAL* 4.5 11.2 - - + -
279I LEU* 2.9 23.5 + - + +
280I ILE* 4.1 4.0 - - - +
281I TYR 3.3 0.2 - - - -
282I LEU* 1.3 93.6 - - + +
284I ARG* 1.3 61.9 + - - +
286I VAL* 3.2 13.9 + - + +
287I LYS 2.9 22.7 + - - -
307I ALA* 4.9 4.7 - - + +
308I VAL* 4.7 17.0 - - + -
311I CYS* 3.6 38.8 - - + -
329I LEU* 5.6 6.1 - - + +
332I PHE* 3.5 23.3 - - + -
333I ALA* 5.3 7.4 - - + -
336I LEU* 3.4 21.8 - - + +
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Residues in contact with ARG 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236I GLU* 4.9 12.5 + - - -
239I ARG* 6.2 5.1 - - - +
243I LEU* 3.7 26.5 - - + +
280I ILE* 3.0 50.4 + - + +
281I TYR* 4.2 4.3 - - - +
283I MET* 1.3 76.3 - - - +
285I MET* 1.3 56.4 + - - +
287I LYS* 3.2 4.3 + - + +
288I ALA* 3.0 29.1 + - - +
332I PHE* 3.6 31.0 - - + -
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Residues in contact with MET 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I ILE* 4.0 17.0 - - + +
228I THR* 5.4 4.0 - - + -
231I CYS* 3.6 34.8 - - + -
243I LEU* 4.4 2.9 - - + +
246I ILE* 3.7 24.1 - - + +
259I PHE* 3.5 32.1 - - + -
263I ILE* 3.7 19.3 - - + -
281I TYR 2.9 19.2 + - - +
282I LEU* 3.2 16.2 - - - +
283I MET 3.1 0.2 - - - -
284I ARG* 1.3 77.3 - - - +
286I VAL* 1.3 57.8 + - + +
288I ALA* 3.3 3.1 + - - +
289I LEU* 2.8 39.2 + - + +
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Residues in contact with VAL 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263I ILE* 5.3 12.1 - - + -
282I LEU 2.8 20.8 + - - +
283I MET* 3.2 19.3 + - + +
285I MET* 1.3 74.6 - - + +
287I LYS* 1.3 61.3 + - - +
289I LEU* 3.2 18.8 + - + +
290I MET* 2.8 41.8 + - + +
304I LEU* 6.2 5.6 - - + -
308I VAL* 4.7 18.6 - - + -
336I LEU* 4.8 12.6 - - + -
340I ILE* 5.9 1.8 - - + -
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Residues in contact with LYS 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I MET 2.9 12.5 + - - +
284I ARG* 3.3 10.8 - - + +
286I VAL* 1.3 76.5 - - - +
288I ALA* 1.3 61.4 + - + +
290I MET* 2.8 22.2 + - - +
291I ASP* 3.1 35.1 + - - +
332I PHE* 4.0 17.5 - - + -
336I LEU* 3.6 27.1 - - + +
339I GLN* 3.5 26.3 + - - +
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Residues in contact with ALA 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243I LEU* 3.6 33.0 - - + +
246I ILE* 3.4 19.9 - - + +
247I ALA* 3.4 28.0 - - + +
284I ARG 3.0 16.3 + - - +
285I MET 3.7 2.7 - - - +
287I LYS* 1.3 81.4 - - + +
289I LEU* 1.3 61.1 + - - +
290I MET 3.5 0.2 + - - -
291I ASP* 3.6 2.1 + - - +
292I ASN* 3.6 7.8 + - - +
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Residues in contact with LEU 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I ILE* 3.8 15.5 - - + -
256I LEU* 5.2 9.2 - - + -
259I PHE* 3.5 37.5 - - + -
260I SER* 5.2 7.6 - - - -
263I ILE* 5.0 5.6 - - + -
285I MET* 2.8 24.2 + - + +
286I VAL* 3.3 24.9 - - + +
288I ALA* 1.3 76.7 - - - +
290I MET* 1.3 63.9 + - + +
292I ASN* 3.7 13.7 + - - +
295I LEU* 5.2 17.9 - - + +
297I LEU* 5.4 10.7 - - + +
304I LEU* 6.3 3.1 - - + -
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Residues in contact with MET 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286I VAL* 2.8 26.7 + - + +
287I LYS* 2.8 12.5 + - - +
289I LEU* 1.3 79.9 - - + +
291I ASP* 1.3 64.9 + - - +
292I ASN 3.4 2.6 + - - +
293I PRO* 5.5 1.6 - - - +
297I LEU* 3.7 35.0 - - + -
305I ILE* 5.6 1.1 - - + -
336I LEU* 5.3 4.5 - - + +
339I GLN* 4.5 29.2 - - + +
340I ILE* 3.7 32.5 - - + -
343I HIS* 5.7 4.3 - - + +
344I PHE* 5.0 7.4 - - - -
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Residues in contact with ASP 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247I ALA* 3.7 14.8 - - + +
287I LYS* 3.1 40.8 + - + +
288I ALA* 3.6 5.8 + - - +
289I LEU 3.3 0.4 - - - -
290I MET* 1.3 84.6 - - - +
292I ASN* 1.3 59.4 + - - +
293I PRO* 3.3 14.3 - - - +
339I GLN* 4.8 4.3 - - - +
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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