Contacts of the helix formed by residues 286 - 292 (chain C) in PDB entry 5MLE
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 286 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C THR* 1.3 91.9 + - - +
287C GLY* 1.3 60.9 + - - +
288C SER* 2.6 45.1 + - - -
289C HIS* 3.6 12.3 - - - -
301C PHE* 4.0 6.1 - - - -
307C LEU* 3.9 13.0 - - - +
308C SER 3.7 10.5 - - - +
309C PRO 5.0 1.6 - - - -
310C ASP 4.3 2.5 - - - +
311C PRO* 3.7 35.6 - - + +
314C PRO* 4.7 4.9 - - + +
607C EDO 4.1 6.5 - - - +
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Residues in contact with GLY 287 (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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286C ASP* 1.3 71.8 - - - +
288C SER* 1.3 63.8 + - - +
289C HIS 3.1 3.0 + - - -
290C TYR* 3.3 25.0 + - - -
291C TRP* 3.6 12.6 - - - -
301C PHE* 5.6 0.7 - - - -
307C LEU* 3.8 19.9 - - - +
308C SER 2.8 21.7 + - - -
309C PRO* 4.0 7.1 - - - +
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Residues in contact with SER 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ASP* 2.6 26.4 + - - -
287C GLY* 1.3 78.8 - - - +
289C HIS* 1.3 73.5 + - - +
291C TRP* 3.4 27.0 + - - +
309C PRO* 4.3 10.3 - - - +
311C PRO* 5.9 3.6 - - - -
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Residues in contact with HIS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C THR* 3.7 14.3 + - - -
286C ASP* 3.6 21.7 + - - -
287C GLY 3.1 1.2 - - - -
288C SER* 1.3 86.9 + - - +
290C TYR* 1.3 63.5 + - - +
291C TRP 3.1 1.8 - - - -
292C SER* 3.0 24.3 + - - +
297C LYS* 3.2 26.5 + - - +
298C ALA* 3.7 10.0 - - - -
301C PHE* 3.5 39.9 - + + -
433C ILE 5.4 1.0 + - - -
437C MET* 5.1 7.6 - - + +
605C EDO 5.6 1.1 - - - -
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Residues in contact with TYR 290 (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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220C PRO 3.9 13.2 - - - -
221C GLU* 3.9 23.2 + - - +
223C HIS* 4.5 3.5 - + - -
224C VAL* 3.7 30.3 - - + -
287C GLY* 3.3 24.1 + - - +
288C SER 3.3 0.4 - - - -
289C HIS* 1.3 74.9 - - - +
291C TRP* 1.3 64.9 + - + +
292C SER 3.2 4.2 + - - +
298C ALA* 3.4 28.7 - - - +
301C PHE* 2.7 45.7 + - + -
302C VAL* 3.8 12.6 - - + -
303C THR 3.9 4.5 + - - -
306C PRO* 3.7 11.2 - - + +
307C LEU* 3.3 45.9 + - + +
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Residues in contact with TRP 291 (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 GLU* 3.7 22.8 - - + +
224C VAL* 3.7 24.0 - - + -
225C LEU* 4.2 30.6 - - + +
287C GLY 3.6 22.9 - - - -
288C SER* 3.4 15.7 + - - +
289C HIS 3.1 1.4 - - - -
290C TYR* 1.3 78.4 - - + +
292C SER* 1.3 63.5 + - - +
293C LYS* 3.7 6.1 + - - +
309C PRO* 4.0 24.2 - - + -
603C EDO 3.8 28.2 + - - -
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Residues in contact with SER 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C HIS* 3.0 21.9 + - - +
290C TYR 3.2 2.3 - - - +
291C TRP* 1.3 80.0 - - - +
293C LYS* 1.3 63.5 + - - +
294C ASN* 3.1 26.2 + - - +
295C TRP* 4.5 1.2 + - - -
297C LYS* 3.6 30.0 - - - +
298C ALA* 4.2 10.3 - - - +
603C EDO 4.7 4.6 + - - -
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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
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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