Contacts of the helix formed by residues 351 - 359 (chain C) in PDB entry 1M6X
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 PRO 351 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366B PRO* 4.3 15.3 - - + -
323C LEU* 3.4 25.6 - - + -
326C VAL* 4.4 15.9 - - + -
327C VAL* 5.3 0.9 - - + -
349C ALA* 3.1 9.8 - - + +
350C ILE* 1.3 92.9 - - + +
352C ASP* 1.3 67.3 + - - +
353C HIS* 3.3 26.9 - - + -
354C TYR* 3.2 17.4 + - + +
355C PHE* 3.8 2.4 - - - -
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Residues in contact with ASP 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B PRO* 5.6 4.1 - - + +
207C GLN 4.5 4.3 - - - +
208C ASN* 3.1 34.2 + - - +
209C LYS* 3.1 40.0 + - + +
210C TYR* 4.0 13.8 - - + -
350C ILE 3.5 2.8 + - - +
351C PRO* 1.3 72.7 - - - +
353C HIS* 1.3 65.1 + - - +
354C TYR 3.1 1.4 + - - -
355C PHE* 3.4 8.6 + - - -
356C ALA 3.6 3.8 + - - -
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Residues in contact with HIS 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B PRO* 4.0 7.8 - - + +
367B ILE* 3.6 50.3 + - + +
210C TYR* 3.7 17.4 - - + +
320C LEU* 4.8 10.6 - - + +
322C GLU* 4.3 6.4 + - - -
323C LEU* 3.9 24.8 - - + +
351C PRO* 3.3 28.7 - - + +
352C ASP* 1.3 74.1 + - - +
354C TYR* 1.3 69.0 + - - +
355C PHE 3.3 0.2 - - - -
356C ALA* 3.1 4.8 + - - +
357C LEU* 3.0 20.6 + - - +
364C TYR* 5.6 0.7 - + - -
371C MET* 3.7 27.4 - - + +
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Residues in contact with TYR 354 (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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187C ILE 2.6 28.9 + - - -
188C ASN* 5.6 0.4 - - - -
233C PHE* 5.3 0.7 - + - -
311C MET* 3.3 23.6 - - - +
315C LEU* 3.9 26.7 - - + -
323C LEU* 4.2 17.5 - - + -
327C VAL* 3.5 33.2 - - + +
350C ILE* 3.5 23.6 - - + -
351C PRO* 3.2 16.6 + - + +
352C ASP 3.1 1.2 + - - -
353C HIS* 1.3 84.2 + - - +
355C PHE* 1.3 82.5 + + - +
357C LEU* 3.2 5.8 + - + +
358C VAL* 3.1 43.3 + - + +
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Residues in contact with PHE 355 (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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187C ILE* 5.7 0.2 - - + -
188C ASN* 5.5 0.4 - - - -
208C ASN* 3.7 21.5 - - - +
211C LEU* 3.9 19.5 - - + -
214C ILE* 3.8 13.2 - - + -
231C TYR* 3.3 55.0 - + + -
233C PHE* 3.5 27.0 - + + -
350C ILE* 3.4 36.3 - - + -
351C PRO 3.8 5.2 - - - -
352C ASP* 3.4 6.7 + - - +
354C TYR* 1.3 85.6 - + - +
356C ALA* 1.3 67.3 + - - +
358C VAL* 4.4 4.3 - - - +
359C SER* 2.8 28.5 + - - -
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Residues in contact with ALA 356 (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 ASN* 5.0 0.6 + - - -
210C TYR* 3.7 38.1 - - + -
211C LEU* 4.4 3.7 - - - +
352C ASP 3.6 2.4 + - - -
353C HIS* 3.1 16.4 + - - +
355C PHE* 1.3 76.2 - - - +
357C LEU* 1.3 60.5 + - - +
359C SER* 2.6 23.0 + - - -
360C ARG 3.5 2.6 + - - -
362C TYR* 3.8 19.7 + - + +
371C MET* 3.7 17.0 - - + -
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Residues in contact with LEU 357 (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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155C TRP* 5.2 0.3 + - - -
314C PHE* 3.4 36.4 - - + -
315C LEU* 5.0 5.8 - - + -
318C LYS* 4.3 19.3 - - + +
320C LEU* 3.7 30.3 - - + -
323C LEU* 6.3 0.2 - - + -
353C HIS 3.0 11.3 + - - +
354C TYR* 3.5 9.4 - - - +
356C ALA* 1.3 74.0 - - - +
358C VAL* 1.3 67.1 + - + +
360C ARG* 2.9 18.7 + - - +
362C TYR 4.0 10.8 - - - +
363C ALA* 4.2 2.2 - - - -
364C TYR* 3.9 28.3 - - + +
371C MET* 3.6 8.5 - - + +
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Residues in contact with VAL 358 (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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155C TRP* 3.1 30.1 - - + +
187C ILE* 3.7 30.1 - - + -
233C PHE* 3.8 18.9 - - + -
235C ALA* 4.6 1.0 - - - +
311C MET* 3.8 18.2 - - + -
314C PHE* 4.4 15.3 - - + -
354C TYR* 3.1 47.7 + - + +
355C PHE 4.2 0.2 - - - +
357C LEU* 1.3 76.9 - - + +
359C SER* 1.3 60.8 + - - +
360C ARG* 3.2 0.8 - - - +
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Residues in contact with SER 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C LEU* 3.3 28.7 - - - +
233C PHE* 3.7 10.7 - - - -
234C SER 3.5 18.6 - - - -
235C ALA* 3.2 5.8 - - - +
236C ARG 2.8 25.3 + - - -
355C PHE 2.8 14.1 + - - -
356C ALA 2.6 21.8 + - - -
358C VAL* 1.3 75.0 - - - +
360C ARG* 1.3 67.2 + - - +
361C TYR* 3.2 9.2 + - - +
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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