Contacts of the helix formed by residues 5486 - 5507 (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 SER5486 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5451E TYR* 4.5 2.6 + - - -
5454E SER* 5.9 0.2 - - - -
5484E GLY 3.4 4.2 + - - -
5485E ALA* 1.3 74.2 - - - +
5487E GLU* 1.3 66.6 + - - +
5488E GLU* 3.6 10.4 + - - +
5489E GLU* 3.0 21.4 + - - +
5490E ILE* 2.9 25.2 + - - +
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Residues in contact with GLU5487 (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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5486E SER* 1.3 76.0 - - - +
5488E GLU* 1.3 56.2 + - - +
5490E ILE* 3.3 21.8 + - + +
5491E ARG* 2.9 46.4 + - + +
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Residues in contact with GLU5488 (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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5451E TYR* 2.9 35.7 + - + +
5486E SER* 3.1 8.9 + - - +
5487E GLU* 1.3 80.6 - - - +
5489E GLU* 1.3 61.7 + - - +
5491E ARG* 3.4 28.0 + - - +
5492E LEU* 3.1 23.5 + - + +
5531E ALA* 4.0 24.3 - - + +
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Residues in contact with GLU5489 (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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5451E TYR* 3.6 25.6 - - + +
5453E PRO* 3.3 11.8 - - - +
5454E SER* 2.5 51.6 + - - -
5455E PHE* 3.6 13.8 - - + -
5473E PHE* 5.7 0.2 - - - +
5474E SER* 5.4 2.5 + - - +
5479E PRO* 3.8 14.7 - - + +
5485E ALA* 3.4 15.6 - - + +
5486E SER* 3.0 18.1 + - - +
5488E GLU* 1.3 80.1 - - - +
5490E ILE* 1.3 62.8 + - - +
5492E LEU* 3.5 4.7 + - + +
5493E SER* 3.2 22.7 + - - -
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Residues in contact with ILE5490 (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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5479E PRO* 4.0 16.4 - - + +
5480E PHE* 3.8 25.7 - - + -
5485E ALA* 4.0 26.0 - - + +
5486E SER 2.9 17.9 + - - +
5487E GLU* 3.5 27.8 - - + +
5489E GLU* 1.3 78.1 - - - +
5491E ARG* 1.3 63.5 + - + +
5493E SER* 3.4 4.0 + - - -
5494E LYS* 3.1 35.2 + - + +
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Residues in contact with ARG5491 (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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5487E GLU* 2.9 25.1 + - + +
5488E GLU* 3.6 33.6 + - - +
5489E GLU 3.3 0.2 - - - -
5490E ILE* 1.3 77.2 - - + +
5492E LEU* 1.3 64.3 + - - +
5494E LYS* 3.3 12.0 + - + +
5495E MET* 3.0 23.9 + - - +
5531E ALA 5.5 4.6 + - - -
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Residues in contact with LEU5492 (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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5449E PHE* 4.1 3.6 - - + -
5451E TYR* 3.4 52.0 - - + -
5474E SER* 3.8 17.9 - - - +
5488E GLU* 3.1 17.2 + - + +
5489E GLU* 3.6 5.8 - - + +
5491E ARG* 1.3 76.5 - - - +
5493E SER* 1.3 57.9 + - - +
5495E MET* 3.2 29.1 + - + +
5496E VAL* 2.9 35.7 + - + +
5529E ILE* 3.8 14.8 - - + -
5530E GLY 3.8 17.9 - - - +
5531E ALA* 6.2 0.7 - - - -
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Residues in contact with SER5493 (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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5474E SER* 2.7 39.0 + - - +
5477E GLY* 3.3 20.3 - - - -
5479E PRO* 3.9 14.1 - - - -
5480E PHE* 3.8 4.8 - - - -
5489E GLU 3.2 11.8 + - - -
5490E ILE 3.8 7.6 - - - -
5492E LEU* 1.3 79.8 - - - +
5494E LYS* 1.3 57.0 - - - +
5496E VAL 3.3 0.2 + - - -
5497E MET* 2.8 39.9 + - - +
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Residues in contact with LYS5494 (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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5160E HIS* 4.6 10.3 - - - +
5161E GLU* 4.3 3.1 - - - +
5480E PHE* 3.4 32.5 - - + -
5490E ILE* 3.1 25.6 + - + +
5491E ARG* 3.6 12.1 - - + +
5493E SER* 1.3 76.1 - - - +
5495E MET* 1.3 63.1 + - - +
5497E MET* 3.6 11.2 + - + +
5498E LYS* 3.0 24.3 + - - +
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Residues in contact with MET5495 (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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5491E ARG 3.0 12.6 + - - +
5492E LEU* 3.5 22.2 - - + +
5494E LYS* 1.3 78.2 - - - +
5496E VAL* 1.3 61.8 + - + +
5498E LYS* 3.0 8.5 + - - +
5499E PHE* 2.8 52.8 + - + +
5514E LEU* 4.1 16.6 - - + +
5515E PRO* 3.9 19.5 - - + -
5529E ILE* 3.6 23.8 - - + -
5533E THR* 3.2 33.4 - - + +
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Residues in contact with VAL5496 (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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5449E PHE* 4.7 4.3 - - + -
5471E GLU* 5.1 0.9 - - + +
5474E SER* 4.0 16.2 - - - -
5475E VAL* 3.5 38.4 - - + +
5492E LEU* 2.9 24.1 + - + +
5493E SER 3.8 2.2 - - - +
5495E MET* 1.3 76.7 - - + +
5497E MET* 1.3 59.4 + - - +
5499E PHE* 3.1 6.9 + - + -
5500E TRP* 2.8 50.4 + - + +
5529E ILE* 4.0 31.9 - - + -
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Residues in contact with MET5497 (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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5156E ALA 4.4 1.6 - - - +
5157E LEU* 3.9 37.1 - - + +
5160E HIS* 4.0 21.3 - - + +
5161E GLU* 3.4 9.0 - - + +
5474E SER 3.4 13.2 - - - +
5475E VAL 3.4 12.1 - - - +
5477E GLY* 3.9 18.2 - - - -
5480E PHE* 3.4 36.6 - - + -
5493E SER* 2.8 26.6 + - - +
5494E LYS* 4.0 7.0 - - - +
5496E VAL* 1.3 71.8 - - - +
5498E LYS* 1.3 57.9 + - - +
5500E TRP* 3.8 6.1 - - - +
5501E ALA* 2.8 33.3 + - - +
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Residues in contact with LYS5498 (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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5161E GLU* 3.4 27.1 + - - +
5494E LYS 3.0 20.5 + - - +
5495E MET 3.0 5.8 + - - +
5497E MET* 1.3 75.7 - - - +
5499E PHE* 1.3 59.2 + - - +
5501E ALA* 4.0 0.3 - - - +
5502E ASN* 2.9 49.5 + - - +
5505E ARG* 5.3 1.3 - - - +
5511E GLY* 6.1 0.2 - - - -
5512E GLU 4.7 15.8 + - - +
5514E LEU* 3.4 27.4 - - + -
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Residues in contact with PHE5499 (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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5495E MET* 2.8 49.9 + - + -
5496E VAL* 3.5 8.5 - - - +
5498E LYS* 1.3 74.8 - - - +
5500E TRP* 1.3 74.1 + - + +
5503E PHE* 2.9 24.3 + - - +
5509E PRO* 3.3 29.1 - - - +
5510E ASN* 4.6 1.8 - - - -
5514E LEU* 3.6 19.7 - - + -
5515E PRO* 3.3 39.5 - - + -
5517E TRP* 3.7 31.2 - + + -
5527E LEU* 3.5 25.8 - - + -
5529E ILE* 5.0 3.4 - - + -
5533E THR* 4.7 0.2 - - + -
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Residues in contact with TRP5500 (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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5136E MET* 4.0 14.2 - - + +
5157E LEU* 5.6 3.1 - - + -
5218E PHE* 4.1 8.7 - + - -
5244E ILE* 3.7 21.8 - - + +
5246E GLU* 3.0 24.3 + - + -
5347E MET* 3.9 13.5 - - - -
5447E TYR* 3.7 44.9 - + - -
5449E PHE* 6.4 0.7 - + - -
5471E GLU* 5.4 2.0 - - + -
5475E VAL* 3.6 34.4 - - + +
5496E VAL* 2.8 47.2 + - + +
5497E MET* 3.8 6.1 - - - +
5499E PHE* 1.3 83.0 - - + +
5501E ALA* 1.3 57.1 + - - +
5503E PHE* 3.2 10.4 + - - +
5504E ALA* 2.9 26.3 + - - +
5517E TRP* 3.9 21.8 - + - -
5529E ILE* 4.2 11.9 - - + -
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Residues in contact with ALA5501 (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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5136E MET* 4.4 7.1 - - - -
5157E LEU* 5.3 0.9 - - + -
5161E GLU* 3.4 30.3 - - + +
5163E VAL* 4.1 8.4 - - + +
5497E MET 2.8 22.3 + - - +
5500E TRP* 1.3 70.5 - - - +
5502E ASN* 1.3 60.3 + - - +
5504E ALA* 3.1 9.2 + - - +
5505E ARG* 2.8 48.7 + - - +
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Residues in contact with ASN5502 (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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5498E LYS* 2.9 33.4 + - - +
5499E PHE 3.7 0.2 - - - +
5501E ALA* 1.3 75.9 - - - +
5503E PHE* 1.3 53.1 + - - +
5505E ARG* 2.8 35.2 + - - +
5506E ASN* 2.7 39.8 + - - +
5508E ASN 3.2 8.9 - - - +
5509E PRO 3.0 30.8 + - - +
5510E ASN 3.6 12.0 + - - +
5511E GLY* 3.8 6.4 - - - -
5514E LEU* 3.4 18.4 - - - +
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Residues in contact with PHE5503 (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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5216E THR* 4.7 1.3 - - + -
5242E ARG* 2.8 26.1 - - + -
5243E ALA 3.4 19.3 - - - -
5244E ILE* 3.7 23.6 - - + -
5345E PRO* 3.6 31.4 - - + -
5347E MET* 3.6 29.8 - - + -
5445E TYR* 3.9 17.3 - + - -
5499E PHE 2.9 13.8 + - - +
5500E TRP 3.3 8.1 - - - +
5502E ASN* 1.3 78.0 - - - +
5504E ALA* 1.3 58.5 + - - +
5507E GLY* 2.6 55.1 + - - -
5508E ASN 3.5 8.0 + - - -
5509E PRO* 3.9 12.8 - - + -
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Residues in contact with ALA5504 (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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5134E PRO* 4.2 12.2 - - + +
5135E VAL 5.2 0.4 - - - +
5136E MET* 3.8 28.0 - - + -
5163E VAL* 5.3 0.4 - - + -
5214E SER* 3.5 12.6 + - - -
5216E THR* 3.2 28.0 + - + +
5242E ARG* 2.7 20.8 + - - +
5500E TRP 2.9 13.2 + - - +
5501E ALA* 3.1 8.7 + - - +
5503E PHE* 1.3 76.5 - - - +
5505E ARG* 1.3 57.0 + - - +
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Residues in contact with ARG5505 (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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5134E PRO* 3.8 24.9 - - + +
5161E GLU* 2.9 48.3 + - - -
5162E ASN* 4.6 2.8 + - - +
5163E VAL* 4.0 4.8 - - - +
5214E SER* 4.8 2.2 + - - -
5242E ARG* 3.4 13.3 + - - -
5498E LYS* 4.9 2.6 - - - +
5501E ALA* 2.8 28.5 + - - +
5502E ASN* 2.8 32.6 + - - +
5504E ALA* 1.3 79.5 - - - +
5506E ASN* 1.3 74.7 + - - +
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Residues in contact with ASN5506 (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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5242E ARG* 4.0 9.2 + - - +
5345E PRO* 5.4 0.2 - - - +
5502E ASN* 2.7 28.9 + - - +
5505E ARG* 1.3 91.2 - - - +
5507E GLY* 1.3 60.1 + - - +
5508E ASN* 3.0 20.1 + - + +
5510E ASN 5.0 4.4 + - - -
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Residues in contact with GLY5507 (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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5242E ARG* 3.5 9.5 - - - +
5345E PRO* 3.8 31.1 - - - +
5443E PRO* 4.3 4.7 - - - +
5445E TYR* 3.5 16.6 + - - -
5503E PHE* 2.6 34.5 + - - -
5506E ASN* 1.3 73.9 - - - +
5508E ASN* 1.3 58.2 + - - +
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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
------------------------------------------------------------
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