Contacts of the helix formed by residues 378 - 382 (chain B) in PDB entry 1M54
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 VAL 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A VAL* 6.4 0.7 - - + -
379A ARG* 5.2 7.0 - - - -
339B ILE* 3.7 15.5 - - + -
345B LEU* 2.9 39.7 + - + +
346B CYS 2.7 27.4 - - - +
377B SER* 1.3 77.5 + - - +
379B ARG* 1.3 58.1 + - - +
381B TYR* 2.7 34.4 + - - +
382B MET* 3.1 18.1 + - - +
385B PHE* 3.4 20.6 - - + -
386B LEU* 4.4 7.0 - - + -
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Residues in contact with ARG 379 (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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345A LEU* 5.0 10.4 - - - +
378A VAL* 3.9 19.1 - - - -
379A ARG* 4.7 12.3 - - + +
382A MET* 3.3 37.2 - - + -
115B GLY 3.4 25.0 + - - -
116B GLY* 4.5 8.9 + - - -
149B ASN* 5.3 1.0 + - - -
152B ILE* 4.1 22.4 - - - +
176B GLU* 4.2 7.4 - - - +
180B VAL* 4.0 23.8 - - + +
377B SER* 2.9 16.4 + - - +
378B VAL* 1.3 78.3 - - - +
380B ASN* 1.3 74.3 + - - +
381B TYR 2.9 4.3 + - - -
382B MET* 3.0 28.3 + - - +
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Residues in contact with ASN 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLY 4.9 2.1 - - - +
149B ASN* 3.6 15.1 + - - +
152B ILE* 4.8 6.3 - - + +
174B SER* 4.5 4.2 + - - -
176B GLU* 4.9 9.6 - - - +
177B LYS* 3.5 46.2 + - + +
180B VAL* 6.1 0.2 - - + -
304B GLU* 4.3 0.2 - - - +
376B ASP* 2.9 28.4 + - - +
377B SER* 4.0 5.5 + - - +
379B ARG* 1.3 96.7 + - - +
381B TYR* 1.3 84.3 + - - +
382B MET 3.8 0.8 + - - -
383B THR* 5.4 1.6 + - - -
384B LYS* 5.1 2.8 - - - +
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Residues in contact with TYR 381 (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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149B ASN* 4.6 0.9 + - - -
304B GLU* 3.2 57.6 + - + +
332B PHE* 6.4 2.0 - + - -
347B GLY* 3.4 24.2 - - - -
348B GLY* 3.9 9.4 - - - -
349B SER 4.9 0.6 + - - -
376B ASP* 2.9 39.3 + - - -
377B SER 3.1 18.4 - - - -
378B VAL 2.7 13.0 + - - +
379B ARG 2.9 0.2 - - - -
380B ASN* 1.3 99.3 + - - +
382B MET* 1.3 57.1 + - - -
383B THR 3.3 3.4 - - - +
384B LYS* 2.7 32.5 - - + +
385B PHE* 3.6 17.5 - + + -
386B LEU* 3.2 14.0 - - - +
1210B PLP 3.5 3.8 - - - +
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Residues in contact with MET 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLU* 3.4 47.8 - - + +
179A ASP* 4.8 0.7 - - - +
180A VAL* 4.0 10.5 - - + -
379A ARG* 3.5 34.8 - - + +
382A MET* 4.2 11.4 - - + -
176B GLU* 4.2 12.9 - - + +
378B VAL* 3.6 13.2 - - - +
379B ARG* 3.0 24.0 + - - +
380B ASN 3.8 1.0 - - - -
381B TYR* 1.3 72.2 - - - +
383B THR* 1.3 61.1 + - + +
384B LYS 3.5 0.4 - - - -
386B LEU* 4.3 17.9 - - + +
387B SER* 2.8 21.0 + - - -
389B ARG* 4.4 2.8 + - - -
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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
------------------------------------------------------------
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