Contacts of the helix formed by residues 377 - 386 (chain B) in PDB entry 3RC0
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 377 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338B ARG* 4.0 0.5 + - - -
375B CYS 3.7 2.4 - - - +
376B MET* 1.3 86.9 - - - +
378B ALA* 1.3 60.2 + - - +
379B GLU* 3.2 3.1 - - + +
380B GLU* 2.9 49.3 + - + +
381B PHE 3.1 10.9 + - - -
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Residues in contact with ALA 378 (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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334B LEU* 4.1 22.4 - - + +
338B ARG* 3.5 18.3 - - - +
377B PRO* 1.3 72.6 - - - +
379B GLU* 1.3 56.5 + - - +
380B GLU 3.4 0.2 - - - -
381B PHE* 3.9 4.3 - - - +
382B ARG* 3.1 27.2 + - - +
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Residues in contact with GLU 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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377B PRO* 3.2 3.0 - - + +
378B ALA* 1.3 77.1 - - - +
380B GLU* 1.3 63.1 + - - +
381B PHE 3.3 0.7 - - - -
382B ARG* 4.0 6.9 - - - +
383B GLU* 3.4 22.7 + - - +
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Residues in contact with GLU 380 (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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372B LYS* 5.6 3.5 - - - -
376B MET* 3.8 27.4 - - + +
377B PRO* 2.9 43.0 + - + +
379B GLU* 1.3 80.2 - - - +
381B PHE* 1.3 56.8 + - - +
383B GLU* 4.0 4.7 + - - +
384B LEU* 3.5 22.8 + - + +
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Residues in contact with PHE 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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334B LEU* 4.4 11.0 - - + -
337B GLU* 3.7 45.1 - - + -
338B ARG* 3.8 33.2 - - + +
341B PHE* 3.5 38.4 - + + -
373B VAL* 4.1 21.3 - - + -
376B MET* 3.5 18.2 - - - -
377B PRO 3.1 7.2 + - - +
378B ALA 4.5 2.7 - - - +
380B GLU* 1.3 76.2 - - - +
382B ARG* 1.3 63.6 + - - +
383B GLU 2.9 5.4 - - - -
384B LEU* 3.6 5.4 - - + +
385B LYS* 3.2 31.4 + - + +
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Residues in contact with ARG 382 (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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378B ALA 3.1 21.9 + - - +
379B GLU* 3.9 8.3 + - - +
381B PHE* 1.3 81.5 - - + +
383B GLU* 1.3 57.8 + - - +
384B LEU 3.5 0.2 - - - -
385B LYS* 4.5 1.7 - - - +
386B ASP* 3.4 26.2 + - - +
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Residues in contact with GLU 383 (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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379B GLU 3.4 17.4 + - - +
380B GLU* 4.3 5.8 - - - +
381B PHE 2.9 0.6 - - - -
382B ARG* 1.3 80.7 - - - +
384B LEU* 1.3 57.6 + - - +
385B LYS 3.6 0.4 - - - -
386B ASP* 5.1 1.1 - - - -
387B GLN* 3.3 24.9 - - - +
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Residues in contact with LEU 384 (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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341B PHE* 3.5 34.1 - - + -
345B LEU* 5.6 0.9 - - + -
372B LYS* 6.1 1.8 - - - -
373B VAL* 5.4 5.2 - - + -
376B MET* 3.9 26.9 - - + -
380B GLU* 3.5 16.5 + - + +
381B PHE* 3.2 11.0 + - + +
383B GLU* 1.3 79.5 - - - +
385B LYS* 1.3 62.7 + - - +
387B GLN* 4.0 13.7 + - - +
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Residues in contact with LYS 385 (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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337B GLU* 6.0 0.9 - - - +
341B PHE* 4.0 22.5 - - + -
381B PHE* 3.2 39.4 + - + +
382B ARG* 5.0 1.3 - - - +
384B LEU* 1.3 76.7 - - - +
386B ASP* 1.3 65.0 + - - +
387B GLN 3.1 7.1 + - - -
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Residues in contact with ASP 386 (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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382B ARG 3.4 21.1 + - - +
383B GLU* 5.1 1.6 - - - -
385B LYS* 1.3 78.1 - - - +
387B GLN* 1.3 58.9 + - - +
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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