Contacts of the helix formed by residues 5540 - 5552 (chain E) in PDB entry 2H7C
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 LYS5540 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5350E ILE* 4.0 19.5 - - + -
5352E LYS 5.3 6.5 + - - -
5419E ASP* 6.2 1.0 - - - +
5423E ASP* 2.9 30.9 + - - +
5427E GLY* 4.4 17.7 - - - +
5428E VAL 5.1 0.2 - - - +
5431E VAL* 3.9 14.6 - - + -
5448E GLU* 4.3 14.4 + - - -
5538E LYS 3.4 2.2 + - - -
5539E LEU* 1.3 86.8 - - + +
5541E ASP* 1.3 63.4 + - - +
5543E GLU* 3.2 33.1 + - + +
5544E VAL* 3.0 27.6 + - + +
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Residues in contact with ASP5541 (chain E).
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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5435E ARG* 3.1 28.9 + - - +
5524E GLU* 4.0 4.2 - - - +
5538E LYS* 3.4 38.0 + - + +
5539E LEU 2.9 5.8 + - - -
5540E LYS* 1.3 77.6 - - - +
5542E LYS* 1.3 71.8 + - + +
5543E GLU* 3.9 0.2 + - - -
5544E VAL* 3.5 3.1 + - - +
5545E ALA* 3.4 20.6 + - - +
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Residues in contact with LYS5542 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5402E LYS* 5.9 0.7 - - - -
5540E LYS 3.4 0.4 - - - -
5541E ASP* 1.3 85.1 - - + +
5543E GLU* 1.3 72.4 + - - +
5545E ALA* 3.5 7.5 + - - +
5546E PHE* 3.1 22.3 + - - +
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Residues in contact with GLU5543 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5403E TYR* 3.4 27.3 - - + +
5423E ASP* 3.6 12.7 - - - +
5428E VAL* 4.0 12.8 - - + -
5540E LYS* 3.2 41.3 + - + +
5541E ASP 3.9 0.2 + - - -
5542E LYS* 1.3 81.8 + - - +
5544E VAL* 1.3 65.4 + - - +
5546E PHE* 3.3 3.9 + - - -
5547E TRP* 3.0 33.4 + - - -
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Residues in contact with VAL5544 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5428E VAL* 4.1 23.1 - - + +
5431E VAL* 3.8 32.3 - - + -
5432E ILE* 4.0 18.4 - - + -
5435E ARG* 3.5 22.7 - - - +
5540E LYS* 3.0 21.3 + - + +
5541E ASP 3.8 4.9 - - - +
5543E GLU* 1.3 75.8 - - - +
5545E ALA* 1.3 57.0 + - - +
5548E THR* 2.6 47.5 + - - +
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Residues in contact with ALA5545 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5541E ASP* 3.4 11.7 + - - +
5542E LYS* 3.8 9.9 - - - +
5543E GLU 3.2 0.6 - - - -
5544E VAL* 1.3 80.0 - - - +
5546E PHE* 1.3 63.9 + - - +
5548E THR* 4.0 3.4 - - - -
5549E ASN* 3.1 26.0 + - - +
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Residues in contact with PHE5546 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5398E GLU* 4.1 5.8 - - + -
5399E ALA* 3.9 8.5 - - - -
5402E LYS* 3.4 56.5 - - + -
5403E TYR* 4.4 3.8 - + - -
5542E LYS 3.1 15.1 + - - +
5543E GLU* 3.6 5.6 - - - +
5545E ALA* 1.3 80.2 - - - +
5547E TRP* 1.3 90.3 + + - +
5549E ASN* 3.5 9.2 + - - +
5550E LEU* 2.9 61.7 + - + +
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Residues in contact with TRP5547 (chain E).
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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5391E ILE* 3.7 21.1 - - + -
5399E ALA* 3.7 16.4 - - + -
5403E TYR* 3.0 43.2 + + - -
5420E LEU* 3.6 20.0 - - + -
5423E ASP* 4.2 2.4 - - - +
5424E VAL* 3.4 29.3 - - + +
5428E VAL* 3.6 30.1 - - + -
5543E GLU* 3.0 29.9 + - + +
5544E VAL 4.3 1.3 - - - +
5546E PHE* 1.3 84.2 - + - +
5548E THR* 1.3 66.2 + - - +
5550E LEU* 3.6 26.0 - - + -
5551E PHE* 2.9 55.9 + + + -
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Residues in contact with THR5548 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5428E VAL* 5.1 0.5 - - - +
5432E ILE* 4.2 14.0 - - + +
5544E VAL* 2.6 35.4 + - - +
5545E ALA* 4.0 4.3 - - - -
5547E TRP* 1.3 76.9 - - - +
5549E ASN* 1.3 62.5 + - - +
5551E PHE* 4.1 4.5 - - - +
5552E ALA* 3.3 23.4 + - + +
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Residues in contact with ASN5549 (chain E).
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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5545E ALA 3.1 18.3 + - - +
5546E PHE* 3.5 9.1 + - - +
5547E TRP 3.1 0.2 - - - -
5548E THR* 1.3 77.2 - - - +
5550E LEU* 1.3 65.8 + - - +
5552E ALA* 3.3 17.9 + - - +
5553E LYS* 3.6 25.7 - - - +
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Residues in contact with LEU5550 (chain E).
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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5391E ILE* 5.1 2.5 - - + -
5395E LEU* 3.8 30.3 - - + +
5398E GLU* 3.3 35.4 - - + +
5399E ALA* 3.8 20.2 - - + +
5546E PHE* 2.9 34.0 + - + +
5547E TRP* 3.6 36.1 - - + +
5549E ASN* 1.3 78.5 - - - +
5551E PHE* 1.3 64.0 + - + +
5552E ALA 3.1 0.2 - - - -
5553E LYS* 3.1 28.6 + - + +
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Residues in contact with PHE5551 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5389E VAL 3.7 17.9 - - - -
5390E CYS* 3.6 23.3 - - + -
5391E ILE* 4.1 15.5 - - + -
5392E ALA 5.9 0.2 - - - -
5395E LEU* 5.2 9.2 - - + -
5424E VAL* 3.9 17.5 - - + -
5428E VAL* 6.4 0.4 - - + -
5547E TRP* 2.9 55.7 + + + +
5548E THR* 4.1 4.5 - - - +
5550E LEU* 1.3 75.2 - - + +
5552E ALA* 1.3 60.3 + - - +
5553E LYS 3.2 4.2 - - - -
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Residues in contact with ALA5552 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5548E THR* 3.3 19.7 + - + +
5549E ASN* 3.4 12.8 - - - +
5550E LEU 3.1 1.2 - - - -
5551E PHE* 1.3 77.0 - - - +
5553E LYS* 1.3 64.1 + - - +
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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