Contacts of the helix formed by residues 4784 - 4799 (chain B) 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 ASP4784 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4667B VAL* 5.8 8.5 - - + -
4780B VAL* 2.9 19.8 + - + +
4781B ILE* 3.4 15.7 + - + +
4783B THR* 1.3 78.0 - - - +
4785B ASN* 1.3 62.2 + - - +
4786B SER* 4.2 14.1 - - - +
4787B PHE* 4.2 6.1 - - + +
4788B LEU* 3.0 30.9 + - - +
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Residues in contact with ASN4785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4783B THR 3.6 3.5 + - - +
4784B ASP* 1.3 74.7 - - - +
4786B SER* 1.3 71.2 + - - +
4788B LEU* 4.0 5.4 - - - +
4789B TYR* 3.1 23.7 + - - +
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Residues in contact with SER4786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4659B TYR* 3.4 23.6 + - - -
4667B VAL* 4.7 11.8 - - - +
4784B ASP* 4.2 8.5 - - - +
4785B ASN* 1.3 86.2 + - - +
4787B PHE* 1.3 63.6 + - - +
4789B TYR* 3.4 13.3 + - - +
4790B LEU* 3.5 19.1 + - - +
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Residues in contact with PHE4787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4656B ILE* 4.4 28.3 - - + -
4659B TYR* 4.0 32.1 + + + -
4660B ASN* 5.9 5.2 - - - -
4664B VAL* 4.9 2.9 - - + -
4781B ILE* 3.2 49.8 - - + +
4782B PHE* 4.0 29.6 - + - -
4784B ASP* 3.6 7.0 + - + +
4785B ASN 3.4 0.2 - - - -
4786B SER* 1.3 79.6 + - - +
4788B LEU* 1.3 63.4 + - - +
4790B LEU* 3.4 5.9 + - + +
4791B GLY* 2.9 29.9 + - - -
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Residues in contact with LEU4788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4782B PHE 4.8 10.1 - - - +
4783B THR 5.6 0.2 - - - -
4784B ASP 3.0 18.6 + - - +
4785B ASN* 4.1 6.5 - - - +
4787B PHE* 1.3 78.2 - - - +
4789B TYR* 1.3 60.4 + - - +
4791B GLY* 4.4 2.0 - - - +
4792B TRP* 2.9 30.3 + - - +
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Residues in contact with TYR4789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4561B ARG* 4.7 6.5 - - - -
4785B ASN 3.1 19.0 + - - +
4786B SER* 3.7 7.0 - - - +
4787B PHE 3.2 0.6 - - - -
4788B LEU* 1.3 79.8 - - - +
4790B LEU* 1.3 77.6 + - + +
4792B TRP* 3.5 18.3 + + + +
4793B TYR* 3.6 10.9 + - - +
4812B LEU 5.3 0.2 + - - -
4813B ASP* 2.7 39.5 + - + -
4816B MET* 3.9 17.7 - - + +
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Residues in contact with LEU4790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4561B ARG* 3.5 32.8 - - - +
4655B CYS* 3.8 27.4 - - + +
4656B ILE* 5.3 9.5 - - + +
4659B TYR* 4.9 24.0 - - + -
4786B SER 3.5 11.6 + - - +
4787B PHE* 3.4 9.9 + - + +
4788B LEU 3.4 0.2 - - - -
4789B TYR* 1.3 99.3 - - + +
4791B GLY* 1.3 62.9 + - - +
4793B TYR* 3.4 15.6 + - + +
4794B MET* 3.7 10.0 + - - +
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Residues in contact with GLY4791 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4656B ILE* 5.9 5.6 - - - -
4787B PHE* 2.9 22.8 + - - -
4788B LEU* 3.8 2.7 - - - -
4790B LEU* 1.3 76.7 - - - +
4792B TRP* 1.3 64.2 + - - +
4794B MET* 3.2 16.2 + - - +
4795B VAL* 3.3 14.4 + - - +
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Residues in contact with TRP4792 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4788B LEU 2.9 18.8 + - - +
4789B TYR* 3.9 13.7 - + + +
4790B LEU 3.3 0.6 - - - -
4791B GLY* 1.3 77.0 - - - +
4793B TYR* 1.3 72.9 + + + +
4795B VAL* 3.2 26.5 - - + +
4796B MET* 3.6 17.4 + - + +
4809B ALA* 4.1 35.2 - - + -
4810B HIS* 5.8 1.1 - + - -
4812B LEU* 6.0 3.1 - - + -
4813B ASP* 5.9 4.0 - - + -
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Residues in contact with TYR4793 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4561B ARG* 4.6 10.8 - - - +
4564B ALA* 3.8 29.7 + - + +
4568B ALA* 5.1 1.0 - - - +
4648B HIS* 2.4 45.0 + + - -
4652B ALA* 4.3 19.3 - - + -
4789B TYR 3.6 8.5 + - - +
4790B LEU* 3.4 13.1 + - + +
4791B GLY 3.2 0.6 - - - -
4792B TRP* 1.3 89.1 - + + +
4794B MET* 1.3 51.0 + - - +
4796B MET* 4.1 2.2 + - - -
4797B SER* 2.6 29.8 + - - -
4810B HIS* 3.4 37.9 + + + +
4813B ASP* 3.2 37.2 - - + +
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Residues in contact with MET4794 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4652B ALA* 4.9 11.0 - - + +
4653B PHE* 5.7 1.1 - - + +
4656B ILE* 3.9 27.4 - - + -
4790B LEU 3.7 7.0 + - - +
4791B GLY* 3.2 10.6 + - - +
4793B TYR* 1.3 78.3 - - - +
4795B VAL* 1.3 64.9 + - - +
4796B MET 3.3 1.6 - - - -
4797B SER* 3.2 20.8 + - - -
4798B LEU* 3.7 9.4 + - - +
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Residues in contact with VAL4795 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4791B GLY 3.3 11.4 + - - +
4792B TRP* 3.2 33.4 - - + +
4794B MET* 1.3 77.7 - - - +
4796B MET* 1.3 60.6 + - + +
4797B SER 3.5 0.3 + - - -
4798B LEU* 3.6 12.3 + - - +
4799B LEU* 3.4 22.0 - - + +
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Residues in contact with MET4796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4792B TRP* 3.6 27.2 + - + +
4793B TYR 4.4 1.1 - - - +
4794B MET 3.3 0.4 - - - -
4795B VAL* 1.3 80.7 - - + +
4797B SER* 1.3 64.2 + - - +
4799B LEU* 3.3 20.7 + - + +
4800B GLY* 3.6 6.9 + - - -
4806B PHE* 4.7 11.6 - - + +
4809B ALA* 5.3 6.7 - - + -
4810B HIS* 3.8 26.7 + - + +
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Residues in contact with SER4797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4648B HIS* 4.3 10.1 - - - -
4649B THR* 3.6 37.1 - - - +
4652B ALA* 4.1 10.9 - - - +
4793B TYR 2.6 25.5 + - - -
4794B MET* 3.2 13.7 + - - -
4796B MET* 1.3 79.3 - - - +
4798B LEU* 1.3 62.3 + - - +
4800B GLY* 3.3 11.3 + - - -
4801B HIS* 3.8 5.0 - - - -
4807B PHE* 5.6 0.5 - - - -
4810B HIS* 4.0 12.1 + - - -
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Residues in contact with LEU4798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4649B THR* 5.3 5.4 - - + -
4794B MET 3.7 8.0 + - - +
4795B VAL* 3.6 11.7 + - - +
4796B MET 3.3 0.6 - - - -
4797B SER* 1.3 80.2 - - - +
4799B LEU* 1.3 66.1 + - + +
4800B GLY 3.3 0.7 + - - -
4801B HIS* 3.6 28.1 + - + +
4802B TYR* 4.4 1.6 + - - +
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Residues in contact with LEU4799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4795B VAL* 3.4 24.7 - - + +
4796B MET* 3.3 13.0 + - - +
4797B SER 3.2 0.8 - - - -
4798B LEU* 1.3 79.4 - - + +
4800B GLY* 1.3 63.2 + - - +
4801B HIS 3.3 0.4 - - - -
4802B TYR* 3.2 24.4 + - + +
4804B ASN 3.6 9.0 - - - +
4806B PHE* 4.1 45.4 - - + -
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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