Contacts of the helix formed by residues 445 - 456 (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 GLY 445 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475E THR* 3.4 15.0 + - - -
478E ARG* 3.9 0.2 - - - -
443L LEU* 3.0 19.4 + - - -
444L SER* 1.3 80.4 - - - +
446L MET* 1.3 65.0 + - - -
447L GLU 3.2 2.9 - - - -
448L SER* 2.2 30.3 + - - -
449L TYR* 3.7 4.2 - - - -
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Residues in contact with MET 446 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469E ASN* 5.0 4.9 - - - +
471E ILE* 3.7 13.9 - - + -
472E GLN* 3.5 47.3 - - + +
475E THR* 3.2 23.6 + - + +
455J GLY* 5.7 5.4 - - - +
128L ILE* 3.7 9.9 - - - +
132L ILE* 4.0 36.8 - - + -
445L GLY* 1.3 72.6 - - - -
447L GLU* 1.3 60.8 + - + +
449L TYR* 3.3 21.5 - - - +
450L CYS* 3.7 3.2 + - - -
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Residues in contact with GLU 447 (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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131L THR 3.9 0.2 - - - +
132L ILE* 2.8 49.6 - - + +
135L GLU* 3.1 44.7 - - - +
136L SER* 3.3 13.7 - - - +
139L LYS* 3.9 7.8 - - + +
443L LEU* 3.7 12.8 - - + +
445L GLY* 3.2 1.2 - - - -
446L MET* 1.3 73.4 - - + +
448L SER* 1.3 55.2 + - - +
449L TYR 3.2 1.6 - - - -
450L CYS* 3.0 8.5 + - - +
451L VAL* 2.5 38.3 + - - +
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Residues in contact with SER 448 (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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478E ARG* 2.7 19.6 + - - -
440L SER* 2.9 32.4 - - - +
443L LEU* 3.2 16.4 - - - +
444L SER 3.5 4.0 - - - -
445L GLY 2.2 41.1 + - - -
447L GLU* 1.3 77.4 - - - +
449L TYR* 1.3 52.4 + - - +
451L VAL* 3.5 4.7 - - - +
452L ARG* 2.7 33.3 + - - +
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Residues in contact with TYR 449 (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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427E ILE* 4.9 0.2 - - - +
456E GLU* 4.6 2.7 - - - -
471E ILE* 3.3 22.4 - - + -
474E MET* 3.0 40.3 + - + +
475E THR* 2.9 42.4 + - - -
478E ARG* 3.1 45.0 - - - +
123L LEU* 4.6 2.2 - - - +
126L LYS* 3.6 24.9 - - - -
128L ILE* 4.5 1.1 - - + -
445L GLY 3.7 1.3 - - - -
446L MET 3.3 17.7 - - - +
447L GLU 3.2 0.2 - - - -
448L SER* 1.3 74.0 + - - +
450L CYS* 1.3 54.9 + - - +
452L ARG* 2.9 16.6 + - - +
453L ALA* 2.8 34.8 + - - +
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Residues in contact with CYS 450 (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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119L SER* 4.1 1.0 + - - -
123L LEU* 3.5 26.5 - - + +
128L ILE* 3.5 41.7 - - - -
132L ILE 4.0 0.9 - - - -
136L SER* 3.0 37.5 - - - +
446L MET 3.7 0.2 - - - -
447L GLU* 3.0 15.3 + - - +
449L TYR* 1.3 78.7 - - - +
451L VAL* 1.3 62.3 + - - +
453L ALA* 3.3 4.3 + - - +
454L PHE* 3.0 23.1 + - - +
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Residues in contact with VAL 451 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136L SER 4.3 3.1 - - - +
139L LYS* 3.9 19.5 - - + -
140L ALA* 4.0 22.0 - - + +
143L LYS* 3.5 26.2 - - - +
436L LEU* 3.4 30.7 - - + +
440L SER* 3.1 15.7 - - - +
447L GLU* 2.5 23.4 + - + +
448L SER* 3.5 6.5 - - - +
450L CYS* 1.3 71.2 - - - +
452L ARG* 1.3 51.0 + - - +
454L PHE* 3.0 2.4 + - - +
455L ALA* 2.4 38.6 + - - +
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Residues in contact with ARG 452 (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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434E SER* 6.0 0.2 - - - +
449E ARG* 2.6 45.5 + - - +
452E ALA* 4.7 3.0 - - - +
453E ASP* 3.2 37.1 + - - +
456E GLU* 4.5 9.3 + - - -
478E ARG* 5.1 2.9 - - - +
437L THR* 4.8 6.8 - - + +
440L SER* 3.0 16.5 + - - +
441L ARG* 2.9 37.0 - - - +
448L SER 2.7 18.7 + - - +
449L TYR* 2.9 20.0 + - - +
451L VAL* 1.3 71.3 - - - +
453L ALA* 1.3 64.7 + - - +
455L ALA* 3.7 3.3 - - - +
456L ASP* 3.1 34.8 + - - +
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Residues in contact with ALA 453 (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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118L ASP* 5.6 0.2 - - - +
119L SER* 3.0 23.8 + - - +
122L LYS* 4.9 13.7 - - + -
123L LEU* 4.5 11.4 - - + -
126L LYS* 6.2 0.4 - - + -
449L TYR 2.8 15.5 + - - +
450L CYS 3.3 7.4 + - - +
452L ARG* 1.3 74.1 - - - +
454L PHE* 1.3 61.2 + - - +
456L ASP* 3.6 5.5 + - - +
457L ALA* 3.4 15.9 + - - +
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Residues in contact with PHE 454 (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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112L ILE* 5.1 2.7 - - + -
115L SER* 3.1 44.0 - - - -
116L LEU* 3.4 34.5 - - + -
119L SER* 2.8 15.8 + - - +
137L PHE* 6.1 1.6 - - + -
140L ALA* 3.8 30.5 - - + -
436L LEU* 4.0 6.7 - - + -
450L CYS 3.0 11.2 + - - +
451L VAL* 3.0 4.2 + - - +
453L ALA* 1.3 71.6 - - - +
455L ALA* 1.3 60.7 + - - +
456L ASP 3.0 2.2 - - - -
457L ALA* 2.7 20.5 + - + -
458L MET* 3.3 43.9 + - + +
519L LEU* 4.4 16.6 - - + -
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Residues in contact with ALA 455 (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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433L ALA* 2.9 36.3 - - - +
436L LEU* 3.5 24.5 - - + +
437L THR* 3.2 37.0 - - - +
440L SER* 3.8 1.1 - - - +
451L VAL 2.4 32.1 + - - +
452L ARG 3.7 3.6 - - - +
454L PHE* 1.3 68.5 - - - +
456L ASP* 1.3 59.2 + - - +
458L MET* 4.1 2.0 - - - -
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Residues in contact with ASP 456 (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* 4.5 17.5 + - - +
449E ARG* 2.9 46.3 + - - +
437L THR* 3.0 23.9 + - - +
452L ARG* 3.1 23.1 + - - +
453L ALA* 3.9 5.2 - - - +
454L PHE 3.0 0.8 - - - -
455L ALA* 1.3 75.7 - - - +
457L ALA* 1.3 60.8 + - - +
458L MET 3.3 3.3 + - - -
459L GLU* 3.8 27.1 + - - +
460L VAL* 4.6 3.6 - - - +
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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