Contacts of the helix formed by residues 4806 - 4815 (chain H) in PDB entry 6X34
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 PHE4806 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4796H MET* 4.7 13.0 - - + +
4799H LEU* 4.1 48.9 + - + +
4800H GLY* 4.8 2.1 - - - +
4802H TYR* 6.0 2.7 - + + -
4804H ASN* 3.8 23.0 + - + -
4805H PHE* 1.3 83.8 - - - +
4807H PHE* 1.3 65.6 + - - +
4808H ALA* 3.1 7.4 - - - +
4809H ALA* 3.2 29.6 + - + +
4810H HIS* 4.0 7.6 + - - -
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Residues in contact with PHE4807 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4571H ILE* 3.6 43.5 - - + -
4572H ASN* 5.8 5.4 - - + +
4575H LEU* 3.6 35.0 - - + -
4645H SER* 5.0 12.1 - - - -
4648H HIS* 5.6 4.3 - + - -
4797H SER 5.6 0.7 - - - -
4800H GLY* 3.4 40.4 - - - -
4805H PHE* 3.7 20.3 - - + +
4806H PHE* 1.3 76.2 - - - +
4808H ALA* 1.3 63.0 + - - +
4809H ALA 3.2 0.4 - - - -
4810H HIS* 3.1 40.6 + + + +
4811H LEU* 3.3 9.9 + - - +
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Residues in contact with ALA4808 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4847F TYR* 4.9 8.1 - - + -
4848F LEU* 3.3 22.6 - - + +
4851F VAL* 3.8 36.1 - - + -
4575H LEU* 5.8 1.0 - - - +
4805H PHE* 5.4 7.5 - - + -
4806H PHE* 3.1 2.8 - - - -
4807H PHE* 1.3 77.4 - - - +
4809H ALA* 1.3 61.3 + - - +
4811H LEU* 3.1 23.3 + - - +
4812H LEU* 3.7 2.4 + - - +
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Residues in contact with ALA4809 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4848F LEU* 6.4 0.2 - - - -
4792H TRP* 4.1 31.2 - - + -
4796H MET* 5.3 5.2 - - + -
4806H PHE* 3.2 22.3 + - + +
4808H ALA* 1.3 77.9 - - - +
4810H HIS* 1.3 68.0 + - + +
4812H LEU* 3.1 21.2 + - - +
4813H ASP* 3.8 3.1 + - - +
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Residues in contact with HIS4810 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4568H ALA* 5.2 11.9 - - + +
4571H ILE* 6.3 0.2 - - - +
4648H HIS* 3.3 30.5 + + - +
4792H TRP* 5.8 2.0 - + - -
4793H TYR* 3.4 40.3 + + + +
4796H MET* 3.8 39.9 - - + +
4797H SER* 4.0 7.2 + - - -
4800H GLY* 6.0 0.2 - - - -
4806H PHE 4.6 4.0 + - - -
4807H PHE* 3.1 41.7 + + + +
4809H ALA* 1.3 79.8 - - - +
4811H LEU* 1.3 60.0 + - - +
4813H ASP* 3.2 14.5 + - - +
4814H ILE* 3.4 11.8 + - - +
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Residues in contact with LEU4811 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4844F VAL* 4.9 16.6 - - + +
4847F TYR* 4.9 10.5 - - + -
4848F LEU* 4.1 14.5 - - + +
4568H ALA* 6.0 2.0 - - - -
4572H ASN* 5.1 12.1 - - + +
4807H PHE 3.3 7.1 + - - +
4808H ALA* 3.1 19.0 + - - +
4810H HIS* 1.3 76.4 - - - +
4812H LEU* 1.3 56.9 + - - +
4813H ASP 3.3 0.2 - - - -
4814H ILE* 3.2 25.3 - - + +
4815H ALA* 3.8 8.1 + - - +
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Residues in contact with LEU4812 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4848F LEU* 4.7 15.7 - - + +
4792H TRP* 6.0 3.6 - - + -
4808H ALA 3.7 4.2 + - - +
4809H ALA* 3.1 15.3 + - - +
4810H HIS 3.1 0.8 - - - -
4811H LEU* 1.3 77.2 - - - +
4813H ASP* 1.3 63.2 + - - +
4815H ALA* 3.8 15.0 + - - +
4816H MET* 4.1 5.4 + - - +
4825H LEU* 5.6 4.9 - - - +
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Residues in contact with ASP4813 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4561H ARG* 3.4 27.5 + - - -
4789H TYR* 2.7 35.0 + - - +
4792H TRP* 5.9 4.2 - - + -
4793H TYR* 3.2 38.2 - - + +
4809H ALA 3.8 2.5 + - - +
4810H HIS* 3.2 12.5 + - - +
4812H LEU* 1.3 76.1 - - - +
4814H ILE* 1.3 64.3 + - - +
4815H ALA 3.1 2.0 - - - -
4816H MET* 3.0 20.1 + - - +
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Residues in contact with ILE4814 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4844F VAL* 5.7 5.4 - - + -
4564H ALA 5.2 2.2 - - - +
4565H LEU* 3.2 49.4 - - + +
4568H ALA* 4.5 9.9 - - + -
4569H PHE* 3.5 37.2 - - + -
4810H HIS 3.4 4.5 + - - +
4811H LEU* 3.2 33.2 - - + +
4813H ASP* 1.3 79.1 - - - +
4815H ALA* 1.3 61.5 + - - +
4816H MET 3.0 9.6 - - - +
4818H VAL* 5.8 0.7 - - - +
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Residues in contact with ALA4815 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4841F LEU* 4.1 23.2 - - + +
4844F VAL* 4.9 11.0 - - + -
4811H LEU 3.8 8.6 + - - +
4812H LEU* 3.9 12.8 - - - +
4813H ASP 3.1 0.4 - - - -
4814H ILE* 1.3 84.1 - - + +
4816H MET* 1.3 59.6 + - - +
4818H VAL* 4.0 6.4 - - - +
4821H LEU* 3.8 23.4 - - - +
4825H LEU* 5.9 6.7 - - + -
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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