Contacts of the helix formed by residues 476 - 486 (chain L) 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 THR 476 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109I LYS* 3.2 6.2 + - - -
110I GLN* 2.8 31.7 + - - -
111I LYS* 3.1 17.6 + - + +
463L SER* 3.6 5.7 + - - -
466L ALA* 3.6 26.0 - - + -
473L PRO 3.6 4.5 + - - -
474L ILE 2.8 1.6 + - - -
475L SER* 1.3 79.8 - - - +
477L VAL* 1.3 71.3 + - - +
479L GLU* 3.6 2.3 - - - +
480L LEU* 3.3 41.8 + - + +
483L ARG* 4.7 2.4 + - - +
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Residues in contact with VAL 477 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E ARG 4.6 7.0 - - - +
127E GLY* 6.1 0.9 - - - -
463L SER* 2.3 44.4 + - - +
473L PRO* 5.1 2.0 - - + +
474L ILE* 3.1 35.1 + - + +
475L SER 3.4 0.2 - - - -
476L THR* 1.3 82.8 - - - +
478L THR* 1.3 70.8 + - - +
479L GLU* 3.1 0.7 + - - -
480L LEU 3.2 4.3 + - - -
481L ARG* 3.2 26.2 + - - +
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Residues in contact with THR 478 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E GLY 6.1 0.7 - - - +
128E ILE* 3.8 17.8 - - + +
129E HIS* 6.1 3.8 - - + -
132E ARG* 2.7 44.5 + - - +
446E TYR* 3.8 3.5 - - - -
474L ILE* 4.7 4.2 + - + +
477L VAL* 1.3 79.7 - - - +
479L GLU* 1.3 69.8 + - - +
481L ARG* 2.9 14.5 - - - +
482L ASN* 2.6 47.6 + - - +
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Residues in contact with GLU 479 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454G GLY 5.5 2.8 - - - +
474L ILE 4.0 1.4 - - - +
475L SER* 2.9 28.1 - - - +
476L THR 4.0 1.6 - - - +
477L VAL 3.5 2.9 + - - -
478L THR* 1.3 95.0 + - + +
480L LEU* 1.3 52.4 + - - +
482L ASN* 2.4 14.3 + - - +
483L ARG* 2.3 68.4 + - + +
486L GLN* 5.9 0.7 - - - +
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Residues in contact with LEU 480 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I LYS* 4.8 10.3 - - - +
430L ILE* 3.8 13.5 - - - +
462L PRO* 3.1 54.1 - - + +
463L SER* 3.2 14.8 - - - +
476L THR* 3.3 28.6 + - + +
477L VAL 3.2 2.0 + - - -
479L GLU* 1.3 76.5 - - - +
481L ARG* 1.3 62.7 + - - +
483L ARG* 3.3 37.3 + - + +
484L HIS 4.2 1.6 + - - -
493L ILE* 3.4 19.7 - - + +
494L ASN 5.6 0.2 - - - +
495L VAL* 4.6 7.4 - - + -
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Residues in contact with ARG 481 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E ARG* 2.9 66.1 + - - +
128E ILE* 3.2 30.8 - - - +
446E TYR* 3.0 30.2 + - - +
430L ILE* 3.8 15.6 - - - +
434L LEU* 4.8 0.2 - - - +
459L GLU* 3.9 30.6 + - + +
460L VAL* 6.3 0.2 - - - +
463L SER* 3.9 2.4 + - - +
477L VAL* 3.2 24.6 + - - +
478L THR* 2.9 15.7 - - - +
479L GLU 3.0 0.2 - - - -
480L LEU* 1.3 81.2 - - - +
482L ASN* 1.3 63.1 + - - +
484L HIS 3.7 1.2 + - - -
485L ALA* 3.5 14.0 + - - +
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Residues in contact with ASN 482 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ARG* 2.8 29.4 + - - +
442E THR* 3.1 34.7 + - - +
445E GLN* 2.9 26.5 - - - +
446E TYR* 3.5 4.9 - - - -
478L THR* 2.6 29.2 + - - +
479L GLU* 2.4 15.2 + - - +
481L ARG* 1.3 71.2 - - - +
483L ARG* 1.3 54.3 + - - +
485L ALA* 2.6 11.8 + - - -
486L GLN* 2.2 44.5 + - - +
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Residues in contact with ARG 483 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I LYS* 3.9 15.8 + - - +
112I ILE* 3.4 34.3 + - - +
475L SER 4.6 7.3 + - - -
476L THR 4.7 1.8 + - - -
479L GLU* 2.3 55.7 + - + +
480L LEU* 3.3 42.2 - - + +
481L ARG 3.2 0.8 - - - -
482L ASN* 1.3 66.7 - - - +
484L HIS* 1.3 57.6 + - - +
486L GLN* 3.2 37.6 + - - +
487L GLY* 3.4 1.6 + - - -
491L ALA 3.2 12.0 - - - +
492L GLY* 3.4 7.1 - - - -
493L ILE* 3.4 48.7 - - + +
500L ILE* 4.5 7.2 - - + +
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Residues in contact with HIS 484 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430L ILE* 3.5 21.2 + - + -
431L GLU* 3.2 55.8 - - + +
434L LEU* 3.4 23.8 - - + +
480L LEU 4.2 2.0 + - - +
481L ARG 3.7 1.8 + - - -
482L ASN 3.1 0.4 - - - -
483L ARG* 1.3 78.3 - - - +
485L ALA* 1.3 55.3 + - - +
487L GLY 2.7 15.2 + - - -
488L GLU 2.7 41.1 + - - +
489L LYS* 3.2 20.8 + - + -
490L THR 4.1 0.2 - - - -
491L ALA* 3.3 31.4 - - - +
492L GLY* 4.1 4.3 - - - +
503L ILE* 4.2 4.7 - - + -
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Residues in contact with ALA 485 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E PRO* 3.1 20.7 - - + +
445E GLN* 3.2 40.8 - - - +
434L LEU* 3.5 23.6 - - + +
481L ARG 3.5 5.8 + - - +
482L ASN* 2.6 17.5 + - - +
484L HIS* 1.3 74.4 + - - +
486L GLN* 1.3 56.7 + - - +
488L GLU* 2.9 20.4 + - - +
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Residues in contact with GLN 486 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E PRO* 3.7 10.8 - - + +
442E THR* 5.3 8.0 - - + +
479L GLU* 5.9 0.7 - - - +
482L ASN* 2.2 42.9 + - + +
483L ARG* 3.2 36.7 + - - +
485L ALA* 1.3 69.5 - - - +
487L GLY* 1.3 57.8 + - - +
488L GLU* 3.1 14.3 + - - +
500L ILE* 4.0 19.2 - - - +
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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