Contacts of the helix formed by residues 413 - 423 (chain G) in PDB entry 4BQA
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 413 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397G ASP* 6.1 0.4 - - - +
400G ALA* 3.4 13.0 - - - +
411G LYS* 3.3 7.9 + - - +
412G MET* 1.3 80.9 - - - +
414G TYR* 1.3 64.2 + - - +
415G GLU* 3.2 27.2 + - + +
416G LYS* 3.1 31.3 + - - +
417G LEU 3.3 13.7 + - - -
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Residues in contact with TYR 414 (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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393G LEU* 3.7 19.7 - - + -
396G PRO* 3.3 40.2 - - + +
397G ASP* 4.7 10.2 + - - +
400G ALA* 3.6 5.0 - - + +
413G ASN* 1.3 74.3 - - - +
415G GLU* 1.3 64.4 + - + +
416G LYS 3.2 0.7 - - - -
417G LEU* 3.9 15.7 - - + -
418G SER* 2.8 51.5 + - - -
438G TYR* 3.6 22.2 - + - -
440G TYR* 3.2 24.2 + + - -
1H A 4.7 7.2 - - - -
2H C 2.6 28.7 + - - -
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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
----------------------------------------------------------
413G ASN* 3.2 23.2 + - + +
414G TYR* 1.3 84.1 - - + +
416G LYS* 1.3 60.9 + - + +
418G SER* 3.2 13.9 + - - -
419G ARG* 3.7 10.7 + - - +
422G ARG* 4.2 5.4 + - - -
5I T 5.2 0.5 - - - +
6I C 5.4 2.9 + - - -
7I C 5.4 6.9 + - - +
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Residues in contact with LYS 416 (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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411G LYS 5.5 1.3 - - - +
412G MET* 3.5 23.8 - - + -
413G ASN* 3.1 18.7 + - - +
415G GLU* 1.3 80.3 - - + +
417G LEU* 1.3 60.0 + - - +
418G SER 3.3 0.2 - - - -
419G ARG* 3.1 4.2 + - - +
420G GLY* 2.8 26.0 + - - -
4I T 4.7 7.4 + - + +
5I T 4.1 48.3 - - + +
6I C 5.6 3.4 - - + -
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Residues in contact with LEU 417 (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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365G LEU* 3.5 23.4 - - + +
369G LEU* 5.2 2.0 - - + -
393G LEU* 4.4 15.0 - - + -
399G VAL* 4.9 7.2 - - + -
400G ALA* 4.5 12.8 - - + +
403G TRP* 3.3 40.4 - - + +
412G MET* 3.9 4.1 - - - -
413G ASN 3.3 16.0 + - - +
414G TYR* 3.5 14.6 - - + +
416G LYS* 1.3 76.5 - - - +
418G SER* 1.3 52.5 + - - +
420G GLY* 2.9 5.8 + - - -
421G LEU* 2.8 56.9 + - + -
4I T 5.0 2.2 - - - -
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Residues in contact with SER 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414G TYR* 2.8 42.8 + - - -
415G GLU* 3.2 11.6 + - - -
417G LEU* 1.3 76.5 - - - +
419G ARG* 1.3 51.9 + - - +
421G LEU* 2.9 11.7 + - - +
422G ARG* 2.6 59.1 + - - +
440G TYR* 3.9 16.4 + - - -
2H C 5.6 0.6 - - - -
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Residues in contact with ARG 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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415G GLU 3.8 7.2 - - - +
416G LYS 3.1 10.4 + - - +
418G SER* 1.3 77.6 + - - +
420G GLY* 1.3 59.3 + - - +
422G ARG* 2.7 44.8 + - - +
423G TYR* 2.8 77.1 + - - +
4H G 3.1 34.2 + - - +
5H G 2.3 47.8 + - - -
4I T 4.8 0.9 - - + -
5I T 3.9 12.8 - - + +
6I C 3.6 20.4 - - - +
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Residues in contact with GLY 420 (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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365G LEU* 3.9 12.3 - - - -
416G LYS 2.8 14.6 + - - -
417G LEU* 2.9 5.4 + - - -
419G ARG* 1.3 76.1 - - - +
421G LEU* 1.3 59.8 + - - +
423G TYR* 3.5 14.3 + - - +
424G TYR* 3.8 16.5 + - - -
3I C 4.3 19.5 - - - +
4I T 4.4 12.6 - - - +
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Residues in contact with LEU 421 (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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365G LEU* 3.8 9.9 - - + -
369G LEU* 3.6 19.3 - - + -
391G PHE* 5.2 0.2 - - + -
393G LEU* 5.0 4.5 - - + -
414G TYR* 5.3 0.2 - - + -
417G LEU* 2.8 33.5 + - + +
418G SER* 2.9 11.4 + - - +
420G GLY* 1.3 75.5 - - - +
422G ARG* 1.3 61.5 + - - +
424G TYR* 3.2 27.3 + - + +
425G TYR* 3.3 13.5 - - - -
430G ILE* 3.6 36.8 - - + +
440G TYR* 3.7 43.7 - - + +
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Residues in contact with ARG 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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415G GLU 4.2 4.2 + - - -
418G SER* 2.6 43.7 + - - +
419G ARG* 2.7 40.3 + - - +
421G LEU* 1.3 68.6 - - - +
423G TYR* 1.3 60.3 + - - +
424G TYR 3.1 5.6 + - - -
425G TYR* 3.2 48.6 + - + +
426G ASP 4.8 0.3 + - - -
440G TYR* 5.2 0.6 + - - +
2H C 4.6 6.7 - - - +
3H C 3.4 58.3 + - - +
4H G 2.8 49.7 + - + +
7I C 4.7 0.8 - - - +
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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
----------------------------------------------------------
419G ARG* 2.8 42.4 + - - -
420G GLY* 3.8 10.1 - - - +
421G LEU 3.2 0.4 - - - -
422G ARG* 1.3 77.8 - - - +
424G TYR* 1.3 60.9 + - + +
425G TYR 3.3 0.8 + - - -
426G ASP* 4.3 5.1 + - - +
427G LYS* 3.7 18.5 + - - +
5H G 4.3 3.5 + - - -
6H A 2.7 31.9 + - - -
7H A 3.7 4.9 + - - -
3I C 3.8 24.3 + + + +
4I T 3.2 41.5 - - + -
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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