Contacts of the helix formed by residues 5357 - 5364 (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 TRP5357 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3367C PRO* 4.5 17.2 - - + +
3368C LEU* 5.6 0.4 - - - +
3369C SER* 3.9 21.1 + - - -
3370C GLU* 4.9 2.0 - - + -
5100E LEU* 4.8 3.1 - - + -
5355E PHE 3.5 2.0 + - - -
5356E GLY* 1.3 79.2 - - - +
5358E LEU* 1.3 92.9 + - + +
5360E PRO* 3.1 8.5 - - - +
5361E MET* 2.9 64.6 + - + +
5457E SER* 3.7 29.6 - - - -
5459E MET* 3.7 37.3 + - + -
5460E LYS* 3.7 28.0 - - + -
5461E PRO* 3.7 16.5 - - + +
5464E VAL* 4.2 11.7 - - + -
5467E ASP* 3.1 15.2 + - - +
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Residues in contact with LEU5358 (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 4.9 2.2 - - - +
5097E LEU* 4.9 0.4 - - + -
5100E LEU* 3.5 34.3 - - + -
5101E PHE* 3.4 40.4 - - + -
5357E TRP* 1.3 87.1 - - + +
5359E ILE* 1.3 58.6 + - + +
5361E MET* 3.4 5.1 - - + +
5363E LEU* 2.8 50.3 + - + +
5467E ASP* 2.8 25.4 + - - +
5468E HIS* 3.9 28.0 - - + +
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Residues in contact with ILE5359 (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 4.5 22.4 - - + +
5354E GLU 3.4 21.1 - - - +
5355E PHE* 3.4 24.5 - - + -
5358E LEU* 1.3 74.0 - - + +
5360E PRO* 1.3 67.1 - - + +
5363E LEU* 3.1 6.8 + - - -
5364E MET* 2.8 54.3 + - + +
5425E MET* 5.2 2.2 - - + -
5426E PHE* 3.7 24.9 - - + -
5467E ASP* 5.0 1.0 + - - -
5468E HIS* 3.6 33.4 - - + -
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Residues in contact with PRO5360 (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 27.1 - - - +
5355E PHE* 3.3 49.8 - - + +
5357E TRP 3.1 15.9 - - - +
5359E ILE* 1.3 97.2 - - + +
5361E MET* 1.3 57.8 + - - -
5364E MET* 3.5 1.1 + - + -
5365E SER* 3.2 2.6 + - - -
5366E TYR* 2.8 49.6 + - + +
5368E LEU* 5.0 0.7 - - + -
5418E LEU* 5.0 0.9 - - + -
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Residues in contact with MET5361 (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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3308C LEU* 4.0 6.5 - - + -
3365C SER 5.2 3.2 - - - +
3367C PRO* 4.0 29.8 - - + -
3369C SER* 3.8 4.7 + - - +
5E COA 3.1 39.1 + - - +
5096E LEU* 4.6 4.7 - - + -
5100E LEU* 3.7 22.4 - - + -
5357E TRP* 2.9 51.1 + - + +
5358E LEU* 3.4 6.5 - - + +
5360E PRO* 1.3 76.9 - - - +
5363E LEU* 1.3 90.9 + - + +
5365E SER* 3.2 13.0 + - - -
5459E MET* 6.0 0.9 - - + -
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Residues in contact with LEU5363 (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 2.8 101.1 + - + +
5096E LEU* 3.9 13.0 - - + -
5097E LEU* 4.5 2.7 - - + +
5100E LEU* 4.3 4.5 - - + -
5304E LEU 3.6 2.8 - - - +
5358E LEU* 2.8 43.3 + - + +
5359E ILE* 3.7 5.4 - - - +
5361E MET* 1.3 102.4 - - + +
5364E MET* 1.3 58.7 + - + +
5365E SER* 3.3 4.5 + - - -
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Residues in contact with MET5364 (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 4.0 22.2 - - + +
5304E LEU* 3.5 24.2 - - + +
5305E SER* 3.7 6.0 - - - +
5306E LEU* 3.0 31.0 + - + +
5317E PRO* 4.0 24.2 - - + -
5318E LEU* 5.7 1.1 - - + -
5355E PHE* 5.2 1.3 - - - -
5359E ILE* 2.8 43.7 + - + +
5360E PRO* 4.4 3.4 - - + +
5363E LEU* 1.3 75.6 - - + +
5365E SER* 1.3 69.0 + - - +
5366E TYR* 3.2 5.8 + - + +
5388E LEU* 3.7 40.4 - - + -
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Residues in contact with SER5365 (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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3C COA 3.4 36.2 + - - -
3361C MET* 5.2 3.3 - - - +
3365C SER* 2.8 38.6 + - - +
5E COA 4.5 8.7 + - - -
5305E SER* 4.4 2.3 + - - -
5306E LEU* 4.6 1.9 - - - +
5360E PRO 3.8 1.8 - - - -
5361E MET 3.2 13.2 + - - -
5363E LEU 3.2 4.8 + - - -
5364E MET* 1.3 79.9 - - - +
5366E TYR* 1.3 65.5 + - - +
5367E PRO* 3.3 9.9 - - - +
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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