Contacts of the helix formed by residues 410 - 418 (chain B) in PDB entry 3RFU
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 410 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B ALA 4.8 8.7 - - - -
209B ARG* 5.5 6.5 - - + +
329B ARG* 4.0 21.0 - - - +
408B ILE* 3.0 21.5 + - - +
409B LYS* 1.3 81.6 + - - +
411B ALA* 1.3 66.0 + - - +
412B GLU* 3.3 21.1 + - - +
413B ALA* 3.3 26.6 + - - +
653B GLY* 3.4 16.5 - - - -
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Residues in contact with ALA 411 (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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208B ALA 4.8 2.4 + - - -
209B ARG* 3.5 47.7 - - + +
394B ILE* 3.7 28.0 - - + +
398B VAL* 5.9 0.2 - - - +
408B ILE* 4.7 1.6 - - - -
410B ASN* 1.3 70.5 - - - +
412B GLU* 1.3 58.1 + - - +
414B LEU* 2.6 31.3 + - - +
415B GLU* 3.2 16.5 + - - +
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Residues in contact with GLU 412 (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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209B ARG* 4.1 20.4 + - - +
329B ARG* 5.0 15.4 + - - +
332B ILE* 4.4 18.8 - - + -
334B ARG* 5.1 5.7 + - - -
410B ASN* 3.3 29.8 + - - +
411B ALA* 1.3 77.5 + - - +
413B ALA* 1.3 62.7 + - - +
415B GLU* 4.0 10.3 - - - +
416B ARG* 3.0 41.7 + - + +
637B ILE* 4.3 2.5 - - + -
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Residues in contact with ALA 413 (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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408B ILE* 4.9 2.5 - - + -
410B ASN* 3.3 26.3 + - - +
411B ALA 3.0 0.8 - - - -
412B GLU* 1.3 78.8 - - - +
414B LEU* 1.3 57.9 + - - +
417B MET* 2.9 33.4 + - - +
637B ILE* 3.5 18.8 - - + +
653B GLY* 3.9 6.3 - - - +
654B VAL* 3.4 31.9 - - + +
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Residues in contact with LEU 414 (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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394B ILE* 4.5 13.9 - - + +
398B VAL* 4.0 31.0 - - + +
408B ILE* 3.9 19.3 - - + -
410B ASN 4.0 0.4 + - - -
411B ALA* 2.6 20.4 + - - +
413B ALA* 1.3 73.7 - - - +
415B GLU* 1.3 60.9 + - + +
417B MET* 3.9 1.9 + - + -
667B ALA* 4.7 4.3 - - + +
670B LEU* 3.2 35.9 - - + -
671B SER* 2.4 54.5 + - - +
674B THR* 4.1 17.7 - - + +
675B MET* 4.3 2.8 - - - +
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Residues in contact with GLU 415 (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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209B ARG* 3.3 26.0 + - - -
332B ILE* 3.8 26.3 - - + +
333B GLN 5.7 0.3 - - - +
334B ARG* 5.0 10.5 + - - +
390B THR* 4.5 7.3 - - - +
394B ILE* 4.3 17.1 - - + +
411B ALA* 3.2 13.5 + - - +
412B GLU* 4.1 9.0 - - - +
414B LEU* 1.3 78.4 - - - +
416B ARG* 1.3 65.3 + - + +
418B GLU* 3.9 20.3 - - - +
419B LYS* 4.4 7.4 - - - +
675B MET* 3.9 27.7 - - - +
678B ILE* 5.0 2.6 - - + +
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Residues in contact with ARG 416 (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 ALA 5.9 1.8 - - - -
332B ILE* 3.1 44.0 - - + +
412B GLU* 3.0 26.5 + - - +
415B GLU* 1.3 78.4 - - + +
417B MET* 1.3 63.9 + - - +
418B GLU 3.2 2.7 - - - -
419B LYS* 3.0 39.2 + - - +
420B VAL* 4.0 1.9 - - - +
618B ILE* 3.3 31.5 - - + +
636B ASP* 3.3 28.7 + - - +
637B ILE* 3.4 21.5 - - + -
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Residues in contact with MET 417 (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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413B ALA 2.9 23.3 + - - +
414B LEU* 4.6 1.8 - - + -
415B GLU 3.5 0.4 - - - -
416B ARG* 1.3 76.8 - - - +
418B GLU* 1.3 63.6 + - - +
419B LYS 3.1 1.0 + - - -
420B VAL* 3.2 36.5 - - - +
620B ALA* 4.9 3.6 - - + -
637B ILE* 3.4 32.8 - - + +
639B ILE* 3.8 23.8 - - + -
654B VAL* 4.8 7.6 - - + -
664B ILE* 5.1 5.6 - - + +
667B ALA* 4.0 14.6 - - + +
668B ARG* 3.6 37.0 - - - +
671B SER* 4.0 7.4 - - - -
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Residues in contact with GLU 418 (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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415B GLU 3.9 5.9 - - - +
417B MET* 1.3 73.9 - - - +
419B LYS* 1.3 79.6 + - - +
420B VAL 3.7 2.1 + - - -
668B ARG* 4.3 12.0 + - - -
671B SER* 2.8 31.4 + - - +
672B GLU* 3.4 43.1 - - + +
675B MET* 3.5 28.5 - - + +
679B ARG* 4.2 16.0 + - - -
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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