Contacts of the helix formed by residues 5409 - 5426 (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 ASP5409 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5372E GLN* 5.1 0.2 + - - -
5407E THR* 3.3 4.3 + - - +
5408E ASP* 1.3 75.8 - - - +
5410E THR* 1.3 61.3 + - - +
5411E VAL* 2.7 48.1 + - - +
5412E LYS* 3.0 46.2 + - + +
5413E LYS* 3.0 13.4 + - - +
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Residues in contact with THR5410 (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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3463C THR* 5.5 2.4 - - + +
5372E GLN* 2.8 34.3 + - - +
5373E LEU 2.6 54.2 + - - +
5374E ASP* 3.9 13.5 - - + +
5408E ASP 2.8 15.3 + - - +
5409E ASP* 1.3 71.8 + - - +
5411E VAL* 1.3 58.4 + - - +
5413E LYS* 3.6 11.0 - - + +
5414E LYS 3.1 12.5 + - - -
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Residues in contact with VAL5411 (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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3370C GLU 5.7 2.0 - - - +
3371C GLY 6.3 0.7 - - - -
3372C GLN* 4.8 13.5 - - - +
3411C VAL* 4.2 32.1 - - + -
5371E GLY* 5.4 1.8 - - - -
5372E GLN* 3.3 37.2 - - + +
5409E ASP* 2.7 26.7 + - - +
5410E THR* 1.3 73.1 - - - +
5412E LYS* 1.3 57.3 + - + +
5414E LYS* 3.1 24.5 - - + +
5415E ASP* 3.2 14.0 + - - +
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Residues in contact with LYS5412 (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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5407E THR* 4.1 17.0 + - + +
5409E ASP* 3.0 36.1 + - + +
5411E VAL* 1.3 73.7 - - + +
5413E LYS* 1.3 56.1 + - - +
5414E LYS 3.0 1.8 - - - -
5415E ASP* 2.9 15.3 + - + +
5416E LEU* 2.7 43.7 + - + +
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Residues in contact with LYS5413 (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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5373E LEU* 3.3 26.4 - - - +
5374E ASP* 5.0 0.4 - - - +
5375E GLN* 3.2 40.5 + - + +
5404E LEU* 3.1 37.7 - - + +
5407E THR* 2.9 36.7 + - + +
5408E ASP* 4.4 10.8 + - - +
5409E ASP 3.0 14.5 + - - +
5410E THR* 3.5 12.6 - - + +
5412E LYS* 1.3 77.0 - - - +
5414E LYS* 1.3 57.9 + - - +
5416E LEU* 4.3 2.9 - - - -
5417E PHE* 2.9 25.5 + - - +
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Residues in contact with LYS5414 (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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3369C SER 3.0 21.8 - - - +
3370C GLU* 2.8 60.2 + - - +
5368E LEU* 5.4 8.3 - - + -
5371E GLY 3.2 27.4 - - - +
5373E LEU* 4.0 15.7 - - + -
5410E THR 3.1 10.2 + - - +
5411E VAL* 3.1 13.2 - - + +
5412E LYS 3.0 0.2 - - - -
5413E LYS* 1.3 76.2 - - - +
5415E ASP* 1.3 77.9 + - - +
5417E PHE* 3.3 6.8 + - + +
5418E LEU* 3.1 46.5 + - + +
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Residues in contact with ASP5415 (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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3370C GLU* 4.0 5.5 - - - +
3372C GLN* 4.2 9.6 + - - +
5411E VAL* 3.2 16.4 + - - +
5412E LYS* 2.9 18.6 + - + +
5414E LYS* 1.3 104.7 + - - +
5416E LEU* 1.3 64.5 + - + +
5418E LEU* 3.1 16.2 + - - +
5419E ASP* 3.1 20.8 + - - +
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Residues in contact with LEU5416 (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* 3.0 32.4 - - + +
5404E LEU* 3.4 16.2 - - + -
5406E GLY* 5.8 1.6 - - - +
5407E THR* 3.7 30.1 - - + -
5412E LYS* 2.7 24.3 + - + +
5413E LYS* 4.5 0.2 - - - -
5415E ASP* 1.3 71.5 - - + +
5417E PHE* 1.3 64.2 + - - +
5419E ASP* 3.1 17.4 + - + +
5420E LEU* 3.0 23.2 + - - +
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Residues in contact with PHE5417 (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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5366E TYR* 3.4 25.4 - + - -
5368E LEU* 5.3 3.1 - - + -
5373E LEU* 3.9 15.5 - - + -
5378E ALA* 3.3 42.0 - - + -
5381E LEU* 3.9 11.2 - - + -
5382E LEU* 3.9 30.3 - - + -
5400E THR* 5.6 1.6 - - + -
5404E LEU* 3.9 9.2 - - + -
5413E LYS 2.9 19.5 + - - +
5414E LYS* 3.4 7.2 - - + +
5415E ASP 3.1 0.4 - - - -
5416E LEU* 1.3 77.0 - - - +
5418E LEU* 1.3 69.7 + - + +
5420E LEU* 3.2 23.2 + - + +
5421E ILE* 3.2 39.6 + - + +
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Residues in contact with LEU5418 (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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3369C SER* 4.4 3.8 - - - +
3370C GLU* 3.4 15.0 - - - +
5353E GLN* 6.1 0.4 - - - +
5355E PHE* 3.7 44.4 - - + +
5356E GLY* 4.3 3.6 - - - +
5360E PRO* 5.0 1.6 - - + -
5368E LEU* 3.9 25.8 - - + -
5414E LYS* 3.2 46.7 - - + +
5415E ASP* 3.1 9.7 + - - +
5417E PHE* 1.3 86.1 - - + +
5419E ASP* 1.3 62.4 + - - +
5421E ILE* 3.6 3.3 + - + +
5422E ALA* 3.1 23.6 + - - +
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Residues in contact with ASP5419 (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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5352E LYS 4.8 9.0 - - - +
5353E GLN* 5.4 8.0 - - - +
5403E TYR* 4.5 8.1 - - + -
5415E ASP* 3.1 19.4 + - - +
5416E LEU* 3.4 24.7 - - + +
5418E LEU* 1.3 76.3 - - - +
5420E LEU* 1.3 61.9 + - - +
5422E ALA* 3.6 5.6 - - - +
5423E ASP* 2.8 41.7 + - - +
5540E LYS* 6.2 0.7 - - - +
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Residues in contact with LEU5420 (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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5382E LEU* 4.0 33.2 - - + -
5389E VAL* 5.2 0.7 - - + -
5391E ILE* 4.4 1.3 - - + -
5399E ALA 3.8 28.3 - - - +
5400E THR* 4.4 4.9 - - - -
5403E TYR* 3.5 31.6 - - + -
5404E LEU* 5.6 0.9 - - + -
5416E LEU 3.0 8.3 + - - +
5417E PHE* 3.2 21.1 + - + +
5419E ASP* 1.3 77.6 - - - +
5421E ILE* 1.3 66.3 + - + +
5423E ASP* 3.2 2.9 + - - +
5424E VAL* 3.0 26.8 + - + +
5547E TRP* 3.6 29.4 - - + -
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Residues in contact with ILE5421 (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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5355E PHE* 3.6 48.5 - - + -
5366E TYR* 3.3 27.4 - - + +
5382E LEU* 4.7 3.1 - - + -
5385E SER* 4.9 2.2 - - - +
5388E LEU* 5.2 3.4 - - + -
5389E VAL* 4.2 19.1 - - + -
5417E PHE* 3.2 36.9 + - + +
5418E LEU* 4.0 6.3 - - + +
5420E LEU* 1.3 83.6 - - + +
5422E ALA* 1.3 57.3 + - - +
5424E VAL* 3.3 2.1 + - - +
5425E MET* 3.0 41.7 + - + +
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Residues in contact with ALA5422 (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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5352E LYS 5.6 2.0 - - - +
5353E GLN* 5.1 1.8 - - - -
5354E GLU* 4.0 14.3 - - + +
5355E PHE* 3.9 24.8 - - - +
5418E LEU 3.1 18.6 + - - +
5419E ASP* 3.6 8.3 - - - +
5421E ILE* 1.3 77.1 - - - +
5423E ASP* 1.3 60.3 + - - +
5425E MET* 4.8 0.2 - - - -
5426E PHE* 2.9 36.1 + - - +
5427E GLY 3.1 6.5 + - - -
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Residues in contact with ASP5423 (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* 2.6 40.8 + - - +
5419E ASP* 2.8 23.6 + - - +
5420E LEU 3.2 2.9 + - - +
5422E ALA* 1.3 80.2 - - - +
5424E VAL* 1.3 61.8 + - - +
5427E GLY* 3.5 6.4 + - - +
5428E VAL* 2.8 38.0 + - + +
5429E PRO* 3.4 1.0 - - - +
5540E LYS* 2.9 34.8 + - - -
5543E GLU* 3.6 14.3 - - + +
5547E TRP* 4.2 5.4 - - - +
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Residues in contact with VAL5424 (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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5251E LEU 5.2 0.3 - - - +
5252E THR* 5.7 0.3 - - - -
5253E SER* 5.6 4.4 + - - +
5388E LEU 5.2 0.4 - - - +
5389E VAL* 3.6 38.1 - - + +
5391E ILE* 4.6 2.2 - - + -
5420E LEU* 3.0 21.7 + - + +
5421E ILE 4.0 3.4 - - - +
5423E ASP* 1.3 76.2 - - - +
5425E MET* 1.3 58.6 + - - +
5428E VAL* 5.0 3.4 - - - -
5429E PRO* 3.2 20.4 - - - +
5547E TRP* 3.4 42.8 - - + -
5551E PHE* 3.9 18.6 - - + -
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Residues in contact with MET5425 (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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5E COA 4.6 11.2 - - + -
5252E THR* 3.1 32.7 + - + +
5253E SER 6.0 0.4 - - - +
5254E VAL* 4.0 26.9 - - + -
5355E PHE* 3.8 20.6 - - + -
5359E ILE* 5.2 1.3 - - + -
5388E LEU* 3.8 40.4 - - + +
5389E VAL* 4.5 2.0 - - + -
5421E ILE* 3.0 39.5 + - + +
5424E VAL* 1.3 79.1 - - - +
5426E PHE* 1.3 86.4 + - + +
5429E PRO* 3.5 8.4 - - - +
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Residues in contact with PHE5426 (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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5E COA 4.8 6.3 - - + -
5221E SER* 4.7 4.0 - - - -
5247E SER* 3.2 36.1 - - - -
5248E GLY* 4.0 5.4 - - - -
5252E THR* 4.4 12.6 - - + -
5255E LEU* 6.4 0.4 - - + -
5350E ILE* 4.3 6.7 - - + -
5354E GLU* 3.4 39.7 - - + +
5355E PHE* 5.1 1.3 - + - -
5359E ILE* 3.7 32.5 - - + -
5422E ALA* 2.9 15.5 + - - +
5425E MET* 1.3 106.6 - - + +
5427E GLY* 1.3 63.7 + - - +
5429E PRO* 3.6 4.0 - - - -
5430E SER* 2.7 34.4 + - - +
5468E HIS* 3.7 10.8 - + - -
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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
------------------------------------------------------------
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