Contacts of the helix formed by residues 355 - 359 (chain B) in PDB entry 5MJ6
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 SER 355 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B PRO* 2.8 30.7 + - - +
311B PHE 4.6 1.1 - - - -
312B LYS* 3.6 18.4 - - - +
315B PHE* 4.5 0.7 - - - -
354B MET* 1.3 81.9 - - - +
356B THR* 1.3 66.1 + - - +
357B TYR* 3.6 26.7 - - - -
358B LEU* 3.0 25.6 + - - +
359B VAL* 3.8 1.9 + - - +
473B ASN 5.7 0.2 + - - -
476B THR* 3.9 9.2 + - - +
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Residues in contact with THR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 4.1 10.8 - - + +
294B PHE* 3.9 8.5 - - - -
299B ALA* 4.1 10.6 - - - +
303B PHE* 4.9 2.6 - - + -
305B CYS* 4.0 15.5 - - + -
306B PHE 3.8 18.3 + - - +
307B ASP* 2.6 34.3 + - - -
308B GLU 4.2 4.7 + - - -
309B PRO* 5.7 0.2 - - - +
311B PHE 4.7 6.5 + - - +
315B PHE* 3.8 26.9 - - + -
354B MET 4.0 1.0 + - - -
355B SER* 1.3 72.8 - - - +
357B TYR* 1.3 60.3 + - - +
358B LEU 3.0 5.5 + - - -
359B VAL* 3.1 17.9 + - - +
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Residues in contact with TYR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 3.6 23.3 - - - +
295B GLU* 3.3 44.9 + - + +
296B PRO 4.0 19.7 - - - +
299B ALA* 4.9 2.0 - - - -
307B ASP* 5.2 1.3 - - - +
309B PRO* 4.1 8.5 - - + -
355B SER* 3.1 26.7 - - - -
356B THR* 1.3 81.6 + - - +
358B LEU* 1.3 80.6 + - + +
359B VAL 3.6 0.2 - - - -
430B MET* 4.2 1.8 - - + +
431B GLU* 4.1 9.1 + - - -
432B ASN* 3.9 8.1 - - - +
472B GLY 3.4 21.7 + - - -
476B THR* 3.6 6.7 - - + +
477B MET* 3.4 31.0 - - + +
480B TRP* 4.1 10.1 - + + -
486B ASN* 3.9 4.9 + - - -
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Residues in contact with LEU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B ASN* 3.1 18.0 + - - -
354B MET* 3.7 15.5 - - + -
355B SER* 3.0 20.4 + - - +
356B THR 3.0 1.2 - - - -
357B TYR* 1.3 111.5 - - + +
359B VAL* 1.3 66.1 + - - +
430B MET* 3.9 15.5 - - + -
431B GLU* 4.0 5.8 - - + -
432B ASN* 3.3 18.8 - - - +
433B TRP* 4.5 5.6 - - + +
472B GLY 4.0 6.7 - - - +
473B ASN* 3.4 51.8 - - + +
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Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B THR* 4.2 0.3 + - - -
294B PHE* 3.0 29.1 - - + -
303B PHE* 4.4 12.3 - - + -
315B PHE* 3.4 40.2 - - + -
317B ILE* 4.0 27.1 - - + -
330B ASN* 3.2 9.0 - - - +
354B MET* 3.4 15.0 - - + +
356B THR* 3.1 14.7 + - - +
358B LEU* 1.3 79.3 - - - +
360B ALA* 1.3 66.2 + - - +
361B PHE* 4.4 13.7 - - + -
432B ASN* 4.2 2.6 - - - +
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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
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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