Contacts of the helix formed by residues 410 - 423 (chain G) in PDB entry 6NRB
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 GLY 410 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408G GLY 3.3 0.8 - - - -
409G GLY* 1.3 74.2 - - - +
411G ALA* 1.3 67.6 + - - +
412G ILE 3.6 0.9 - - - -
413G GLU* 3.5 33.0 + - - -
414G MET* 3.1 31.6 - - - +
446G PRO* 4.1 8.4 - - - +
475G TYR 3.1 8.5 - - - +
476G GLY* 3.2 3.1 - - - -
477G VAL 4.6 0.4 - - - -
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Residues in contact with ALA 411 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407G ALA* 3.1 20.6 - - + +
408G GLY 2.7 25.9 + - - +
409G GLY 3.1 1.6 + - - -
410G GLY* 1.3 74.2 - - - +
412G ILE* 1.3 61.4 + - - +
413G GLU* 4.1 0.6 - - - +
415G GLU* 2.9 29.3 + - - +
474G TRP* 3.1 32.5 - - + +
475G TYR 3.0 1.7 - - - +
487G ASN* 3.3 10.8 - - + +
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Residues in contact with ILE 412 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G LYS* 4.2 4.5 - - + +
136G ILE* 4.1 15.3 - - + -
139G ILE* 4.2 14.4 - - + -
406G VAL* 3.7 27.4 - - + -
407G ALA 4.1 3.1 + - - +
411G ALA* 1.3 78.3 - - - +
413G GLU* 1.3 64.0 + - + +
414G MET 3.2 0.7 - - - -
415G GLU* 2.7 19.7 + - - +
416G LEU* 2.2 64.5 + - + +
474G TRP* 4.2 12.8 - - + -
499G ARG* 3.6 36.1 - - + +
503G LEU* 5.4 0.2 - - + -
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Residues in contact with GLU 413 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G SER* 5.5 0.5 + - - -
408G GLY* 5.5 2.2 - - - -
409G GLY* 5.0 3.8 + - - -
410G GLY* 3.5 21.8 + - - +
411G ALA 3.4 0.4 - - - +
412G ILE* 1.3 85.2 - - + +
414G MET* 1.3 60.5 + - - +
416G LEU* 4.6 3.4 - - + -
417G SER 3.4 6.1 + - - -
442G LEU* 3.0 52.1 - - + +
443G GLU* 3.4 9.2 - - - +
445G ILE* 3.4 31.2 - - + +
446G PRO* 3.1 24.1 - - + +
499G ARG* 5.2 13.9 + - - +
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Residues in contact with MET 414 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410G GLY* 3.1 21.8 + - - +
413G GLU* 1.3 77.2 - - - +
415G GLU* 1.3 58.2 + - - +
418G LYS* 3.0 27.2 + - - +
443G GLU* 3.3 43.9 - - - +
446G PRO* 3.7 7.9 - - - -
461G LEU* 3.1 63.0 - - + +
464G LEU* 3.5 20.2 - - + -
465G ARG* 3.8 4.8 - - - -
468G HIS* 3.0 24.7 + - + +
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Residues in contact with GLU 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G LYS* 3.2 33.9 + - - +
139G ILE* 3.5 6.6 - - - +
411G ALA 2.9 22.5 - - - +
412G ILE* 2.7 13.8 + - - +
414G MET* 1.3 70.7 - - - +
416G LEU* 1.3 63.1 + - - +
418G LYS* 3.2 16.1 - - - +
419G TYR* 3.4 4.9 + - - +
468G HIS* 3.2 25.2 + - + +
472G GLY* 2.9 21.8 - - - +
473G THR 2.7 35.2 - - - +
474G TRP 3.2 0.3 - - - -
475G TYR 3.0 13.7 + - - -
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Residues in contact with LEU 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G ALA* 3.6 39.9 - - + +
135G LYS* 3.5 32.5 - - + +
136G ILE* 5.1 0.7 - - + +
412G ILE* 2.2 63.9 + - + +
413G GLU* 4.5 0.9 - - + +
415G GLU* 1.3 64.7 - - - +
417G SER* 1.3 55.5 + - - +
418G LYS 3.0 1.1 - - - -
419G TYR* 2.8 7.5 + - - +
420G LEU* 2.5 43.1 + - + +
442G LEU* 3.4 32.3 - - + -
503G LEU* 4.4 6.1 - - + -
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Residues in contact with SER 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413G GLU 3.4 5.4 + - - -
416G LEU* 1.3 77.0 - - - +
418G LYS* 1.3 53.1 + - - +
420G LEU* 3.4 12.3 - - - -
421G ARG* 2.4 35.2 + - - +
439G ALA* 3.0 39.3 - - - +
440G LYS* 3.4 1.9 + - - +
442G LEU* 3.4 1.8 - - - +
443G GLU* 3.1 37.0 + - - -
465G ARG* 3.7 3.7 + - - -
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Residues in contact with LYS 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414G MET 3.0 22.2 + - - +
415G GLU* 3.2 12.6 - - - +
416G LEU 2.9 0.6 + - - -
417G SER* 1.3 76.0 - - - +
419G TYR* 1.3 58.7 + - - +
422G ASP* 2.8 48.4 + - - +
443G GLU* 3.8 0.6 + - - -
465G ARG* 3.2 56.6 + - - +
468G HIS* 3.4 27.8 + - + +
469G ALA* 3.4 11.3 - - - +
425I ASN* 4.8 5.4 + - - +
428I THR* 3.6 12.7 - - - +
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Residues in contact with TYR 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G LEU* 4.2 22.8 - - + +
135G LYS* 5.1 13.9 - - + -
415G GLU 3.4 6.6 + - - +
416G LEU* 2.8 8.5 + - - +
418G LYS* 1.3 78.9 - - - +
420G LEU* 1.3 69.5 + - + +
422G ASP* 2.7 18.1 + - + -
423G TYR* 2.3 77.5 + + + +
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Residues in contact with LEU 420 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G ALA 4.9 0.2 - - - +
131G LEU* 4.2 17.0 - - + -
132G ALA* 4.9 2.9 - - + +
416G LEU* 2.5 43.4 + - + +
417G SER* 3.2 8.5 - - - -
419G TYR* 1.3 93.5 - - + +
421G ARG* 1.3 60.6 + - - +
423G TYR* 3.8 12.6 - - + -
424G SER* 4.4 0.3 - - - -
435G ILE* 3.2 26.7 - - - +
436G GLY 4.7 0.2 + - - -
438G TYR* 3.3 38.8 - - + +
439G ALA* 3.4 18.4 - - + +
442G LEU* 3.5 14.6 - - + -
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Residues in contact with ARG 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417G SER 2.4 30.6 + - - +
420G LEU* 1.3 69.7 - - - +
422G ASP* 1.3 67.9 + - - +
423G TYR 3.1 0.4 - - - -
424G SER* 3.2 21.3 - - - -
425G ARG 4.8 0.6 - - - +
436G GLY* 5.9 4.3 - - - -
439G ALA* 3.8 5.4 - - + +
465G ARG* 3.1 31.9 - - - +
421I ILE* 3.2 43.6 + - - +
424I GLU* 3.2 46.1 + - - +
425I ASN* 3.3 18.3 - - - +
428I THR* 5.1 3.6 - - - +
435I GLN* 6.0 0.2 - - - +
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Residues in contact with ASP 422 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418G LYS* 2.8 41.7 + - - +
419G TYR* 2.7 26.7 + - + +
421G ARG* 1.3 82.3 + - - +
423G TYR* 1.3 59.1 + - - +
424G SER 3.4 0.5 + - - -
425G ARG* 3.6 17.2 + - - +
426G THR* 4.7 4.3 + - - +
465G ARG* 4.3 1.6 + - - -
425I ASN* 3.3 30.6 + - - +
473I GLU* 4.9 14.3 - - - +
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Residues in contact with TYR 423 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G THR* 4.4 16.3 - - - +
128G ALA* 4.3 3.8 - - + -
131G LEU* 3.3 34.9 - - + +
419G TYR* 2.3 59.9 + - + +
420G LEU* 3.9 12.1 - - + -
421G ARG 3.1 0.4 - - - -
422G ASP* 1.3 68.2 - - - +
424G SER* 1.3 62.2 + - - +
425G ARG 3.3 0.2 - - - -
426G THR* 3.0 30.6 + - - -
427G ILE* 3.1 36.9 - - + +
435G ILE* 3.5 31.0 - - + -
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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