Contacts of the helix formed by residues 410 - 418 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ALA 4.9 9.4 - - - -
209A ARG* 5.5 6.7 - - + +
329A ARG* 4.0 20.8 - - - +
408A ILE* 3.0 20.6 - - - +
409A LYS* 1.3 82.6 + - - +
411A ALA* 1.3 64.6 + - - +
412A GLU* 3.3 21.3 + - - +
413A ALA* 3.3 26.7 + - - +
653A GLY* 3.3 16.5 - - - -
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Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ALA 4.8 2.8 + - - +
209A ARG* 3.5 48.4 - - + +
394A ILE* 3.7 27.8 - - + +
398A VAL* 5.9 0.2 - - - +
408A ILE* 4.8 1.1 - - - -
410A ASN* 1.3 73.1 - - - +
412A GLU* 1.3 55.7 + - - +
414A LEU* 2.7 31.4 + - - +
415A GLU* 3.2 16.5 + - - +
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Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ARG* 4.1 21.3 + - - +
329A ARG* 5.0 16.3 + - - +
332A ILE* 4.4 18.8 - - + -
334A ARG* 5.1 5.4 + - - -
410A ASN* 3.3 29.5 + - - +
411A ALA* 1.3 76.4 + - - +
413A ALA* 1.3 62.3 + - - +
415A GLU* 4.2 10.3 - - - +
416A ARG* 3.0 40.4 + - + +
637A ILE* 4.3 2.7 - - + -
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Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ILE* 4.9 2.7 - - + -
410A ASN* 3.3 26.3 + - - +
411A ALA 3.0 0.6 + - - -
412A GLU* 1.3 77.6 - - - +
414A LEU* 1.3 58.5 + - - +
417A MET* 2.9 32.9 + - - +
637A ILE* 3.5 19.9 - - + +
653A GLY* 3.9 6.3 - - - +
654A VAL* 3.4 30.6 - - + +
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A ILE* 4.5 12.6 - - + +
397A GLY* 4.4 0.9 - - - -
398A VAL* 4.0 31.0 - - + +
408A ILE* 3.9 20.0 - - + -
410A ASN 4.0 0.4 + - - -
411A ALA* 2.7 20.2 + - - +
413A ALA* 1.3 74.4 - - - +
415A GLU* 1.3 61.2 + - + +
417A MET* 3.8 2.0 + - + -
667A ALA* 4.7 4.0 - - + +
670A LEU* 3.2 35.2 - - + -
671A SER* 2.4 57.2 + - - +
674A THR* 4.1 17.9 - - + +
675A MET* 4.3 2.1 - - - +
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ARG* 3.3 25.9 + - - -
332A ILE* 3.8 25.9 - - + +
333A GLN 5.7 0.7 - - - +
334A ARG* 5.0 10.5 + - - +
390A THR* 4.4 6.9 - - - +
394A ILE* 4.3 17.0 - - + +
411A ALA* 3.2 14.1 + - - +
412A GLU* 4.1 8.0 - - - +
414A LEU* 1.3 76.1 - - - +
416A ARG* 1.3 64.2 + - + +
418A GLU* 3.9 19.9 - - - +
419A LYS* 4.4 7.3 - - - +
675A MET* 3.9 28.5 - - - +
678A ILE* 5.0 2.3 - - + +
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Residues in contact with ARG 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A ALA 5.9 1.8 - - - -
332A ILE* 3.1 44.6 - - + +
412A GLU* 3.0 25.4 + - + +
415A GLU* 1.3 79.9 - - + +
417A MET* 1.3 65.5 + - - +
418A GLU 3.2 2.2 - - - -
419A LYS* 3.0 39.7 + - - +
420A VAL* 4.0 2.1 - - - +
618A ILE* 3.3 30.3 - - + +
636A ASP* 3.3 28.9 + - + +
637A ILE* 3.4 20.9 - - + -
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Residues in contact with MET 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ALA 2.9 23.5 + - - +
414A LEU* 4.6 2.2 - - + -
415A GLU 3.5 0.4 - - - -
416A ARG* 1.3 76.9 - - - +
418A GLU* 1.3 64.5 + - - +
419A LYS 3.1 0.9 + - - -
420A VAL* 3.2 37.3 - - - +
620A ALA* 4.9 3.1 - - + -
637A ILE* 3.4 32.3 - - + +
639A ILE* 3.8 24.7 - - + -
654A VAL* 4.8 7.9 - - + -
664A ILE* 5.1 5.6 - - + +
667A ALA* 4.0 15.7 - - + +
668A ARG* 3.6 36.1 - - - +
671A SER* 4.0 7.0 - - - -
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A GLU 3.9 5.6 - - - +
416A ARG 3.2 0.2 - - - -
417A MET* 1.3 75.1 - - - +
419A LYS* 1.3 80.2 + - - +
420A VAL 3.7 2.8 + - - +
668A ARG* 4.3 11.9 + - - -
671A SER* 2.7 30.6 + - - +
672A GLU* 3.4 42.8 - - + +
675A MET* 3.5 29.2 - - + +
679A ARG* 4.2 15.8 + - - -
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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
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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