Contacts of the helix formed by residues 289 - 299 (chain C) in PDB entry 5MR5
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 289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C ASN 4.6 2.8 - - - +
285C CYS* 4.1 8.7 - - - +
286C PRO 3.0 16.1 + - - +
287C ALA* 4.0 10.2 - - + +
288C ASP* 1.3 73.4 - - - +
290C TYR* 1.3 62.0 + - - +
291C GLN* 3.3 9.5 + - - +
292C ALA* 3.0 35.5 + - + +
293C CYS* 3.6 15.2 + - - +
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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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283C THR* 3.3 40.5 - - + +
285C CYS* 3.8 11.0 - - - -
288C ASP 3.3 7.3 + - - -
289C ASN* 1.3 73.1 - - - +
291C GLN* 1.3 65.3 + - + +
293C CYS* 3.1 6.3 + - - +
294C LEU* 3.0 28.6 + - + +
350C ASN* 3.4 25.7 + - + +
351C ALA* 3.3 40.7 - - + +
354C ALA* 3.4 26.7 - - + +
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Residues in contact with GLN 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C SER* 4.8 4.9 + - - -
217C TYR* 3.7 32.6 + - - -
289C ASN* 3.3 7.5 + - - +
290C TYR* 1.3 79.6 - - + +
292C ALA* 1.3 57.1 + - - +
294C LEU* 3.2 11.2 + - - +
295C GLY* 2.9 26.5 + - - -
355C PHE* 4.1 17.4 - - - -
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Residues in contact with ALA 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ASN* 3.6 22.1 + - + +
289C ASN* 3.0 32.9 + - + +
291C GLN* 1.3 73.5 - - - +
293C CYS* 1.3 64.1 + - - +
295C GLY* 3.7 1.5 + - - +
296C SER* 2.9 28.9 + - - -
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Residues in contact with CYS 293 (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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274C ASN* 3.5 18.0 - - - +
275C CYS* 2.0 57.7 - - - -
289C ASN 3.6 7.5 + - - +
290C TYR 3.1 10.1 + - - +
292C ALA* 1.3 76.8 - - - +
294C LEU* 1.3 60.2 + - - +
296C SER 3.1 1.6 + - - -
297C TYR* 2.8 26.5 + - - +
347C CYS* 4.0 15.5 - - - -
348C LEU* 3.9 22.4 - - - -
351C ALA* 4.5 5.6 - - + -
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Residues in contact with LEU 294 (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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217C TYR* 4.4 9.0 - - + -
221C PHE* 3.8 25.8 - - + -
290C TYR* 3.0 20.1 + - + +
291C GLN* 3.7 17.0 - - - +
293C CYS* 1.3 77.9 - - - +
295C GLY* 1.3 57.4 + - - +
297C TYR* 3.2 4.7 + - - +
298C ALA* 2.9 30.3 + - - +
348C LEU* 4.9 4.7 - - + -
351C ALA* 3.6 40.8 - - + +
352C ILE* 3.9 18.8 - - + +
355C PHE* 3.7 32.8 - - + -
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Residues in contact with GLY 295 (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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217C TYR* 2.9 26.9 + - - -
291C GLN 2.9 14.7 + - - -
292C ALA* 4.0 2.5 - - - -
294C LEU* 1.3 78.0 - - - +
296C SER* 1.3 55.9 + - - +
298C ALA* 3.4 2.4 + - - +
299C GLY* 2.8 25.6 + - - -
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Residues in contact with SER 296 (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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267C ARG* 4.5 3.3 - - - +
270C ASP* 3.5 11.3 + - - +
271C PHE* 3.6 29.9 - - - +
274C ASN* 2.7 32.1 + - - -
292C ALA 2.9 10.5 + - - -
293C CYS* 3.1 5.6 + - - -
295C GLY* 1.3 73.0 - - - +
297C TYR* 1.3 66.9 + - - +
299C GLY* 3.4 9.0 + - - +
300C MET* 3.6 17.2 + - - +
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Residues in contact with TYR 297 (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 LEU* 4.4 12.6 - - + -
221C PHE* 3.7 27.1 - + + -
271C PHE* 4.1 17.6 - + + -
293C CYS 2.8 12.7 + - - +
294C LEU* 3.5 8.7 - - - +
296C SER* 1.3 77.2 - - - +
298C ALA* 1.3 66.9 + - - +
300C MET* 3.1 21.4 + - + +
301C ILE* 4.1 7.1 + - + +
307C PRO* 3.5 49.6 + - + +
308C ASN* 3.6 5.4 + - - -
309C TYR* 4.2 5.3 + + - -
319C VAL* 3.5 42.7 - - + +
342C PHE* 5.0 1.8 - + - -
348C LEU* 4.0 29.4 - - + -
352C ILE* 5.3 1.3 - - + -
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Residues in contact with ALA 298 (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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208C PHE* 4.3 21.9 - - + +
217C TYR* 4.1 21.3 - - + -
220C LEU* 4.0 18.6 - - + -
221C PHE* 4.7 0.2 - - + -
294C LEU 2.9 16.7 + - - +
295C GLY* 3.8 4.5 - - - +
297C TYR* 1.3 77.8 - - - +
299C GLY* 1.3 61.1 + - - +
300C MET 3.1 1.8 + - - -
301C ILE* 3.2 31.4 + - - +
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Residues in contact with GLY 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C PHE* 6.2 0.9 - - - -
267C ARG* 2.8 46.4 + - - +
295C GLY 2.8 17.0 + - - -
296C SER* 3.8 5.8 - - - -
297C TYR 3.1 1.0 - - - -
298C ALA* 1.3 76.0 - - - +
300C MET* 1.3 57.6 + - - +
301C ILE 3.5 1.1 - - - -
303C PHE* 3.3 10.8 - - - -
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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
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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