Contacts of the helix formed by residues 5471 - 5476 (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 GLU5471 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5220E GLU* 3.1 25.1 - - - +
5246E GLU* 2.8 34.6 - - - +
5247E SER* 4.4 2.2 + - - -
5351E ASN* 2.9 25.7 + - - +
5447E TYR* 4.2 14.1 - - + +
5449E PHE* 3.6 39.2 - - + -
5469E GLY* 3.4 7.1 + - - -
5470E ASP* 1.3 72.4 - - - +
5472E LEU* 1.3 74.5 + - - +
5473E PHE 3.2 0.2 - - - -
5474E SER* 2.9 14.7 + - - -
5475E VAL* 2.9 18.8 + - + +
5496E VAL* 6.2 0.7 - - + -
5500E TRP* 5.4 1.8 - - + -
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Residues in contact with LEU5472 (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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5101E PHE* 3.7 52.0 - - + +
5103E ASN* 6.0 0.7 - - - -
5138E TRP* 3.3 38.8 - - + -
5152E TYR* 4.4 10.3 - - + +
5220E GLU* 3.7 7.9 - - + +
5246E GLU* 4.0 2.2 - - - +
5469E GLY* 3.1 22.2 + - - +
5471E GLU* 1.3 95.3 - - - +
5473E PHE* 1.3 58.7 + - + +
5475E VAL* 3.8 4.4 - - + +
5476E PHE* 2.9 42.4 + - + +
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Residues in contact with PHE5473 (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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5100E LEU 3.4 25.1 - - - -
5101E PHE* 4.4 9.4 - + - -
5102E THR 3.5 22.7 - - - -
5103E ASN* 4.8 3.6 - - + -
5453E PRO* 3.7 21.3 - - + -
5455E PHE* 3.5 55.9 - + + -
5456E SER* 5.1 2.9 - - - -
5469E GLY 4.2 11.9 - - - -
5470E ASP* 3.7 19.7 - - - +
5471E GLU 3.2 1.0 - - - -
5472E LEU* 1.3 77.6 - - + +
5474E SER* 1.3 59.2 + - - +
5476E PHE* 5.4 0.4 - - - -
5477E GLY 3.4 0.5 + - - -
5478E ALA* 2.9 42.3 + - + +
5479E PRO* 3.4 5.5 - - - +
5482E LYS* 4.1 2.9 - - - -
5489E GLU* 5.7 0.4 - - - +
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Residues in contact with SER5474 (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* 3.8 12.1 - - - -
5451E TYR* 5.3 1.0 - - - -
5453E PRO* 6.1 0.3 - - - +
5470E ASP 4.4 1.1 + - - -
5471E GLU 2.9 9.8 + - - -
5473E PHE* 1.3 77.4 - - - +
5475E VAL* 1.3 66.1 + - - +
5477E GLY 3.2 2.8 + - - -
5479E PRO* 5.1 0.4 - - - -
5489E GLU* 5.4 2.4 + - - +
5492E LEU* 3.8 23.2 - - - +
5493E SER* 2.7 41.1 + - - +
5496E VAL* 4.0 20.9 - - - -
5497E MET* 3.4 8.0 - - - +
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Residues in contact with VAL5475 (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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5157E LEU* 3.9 15.1 - - + +
5218E PHE* 4.0 16.4 - - + -
5246E GLU* 4.1 14.1 - - - +
5471E GLU* 2.9 20.7 + - + +
5472E LEU* 3.8 5.8 - - - +
5474E SER* 1.3 76.5 - - - +
5476E PHE* 1.3 73.6 + - + +
5496E VAL* 3.5 24.2 - - + -
5497E MET* 3.4 19.4 - - - +
5500E TRP* 3.6 40.4 - - + +
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Residues in contact with PHE5476 (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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5103E ASN* 3.0 35.1 + - + +
5138E TRP* 3.4 63.7 - + + -
5152E TYR* 4.2 24.5 - + + -
5153E ASP 3.9 19.2 - - - +
5154E GLY* 4.6 3.6 - - - -
5156E ALA* 3.8 11.0 - - - +
5157E LEU* 4.6 9.9 + - + -
5165E VAL* 4.6 15.9 - - + -
5167E THR* 5.0 1.8 - - + -
5218E PHE* 4.0 14.4 - + - -
5472E LEU* 2.9 25.5 + - + +
5475E VAL* 1.3 86.7 - - + +
5477E GLY* 1.3 62.7 + - - +
5478E ALA 3.4 1.8 - - - -
5497E MET* 4.6 1.8 - - - -
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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
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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