Contacts of the helix formed by residues 4556 - 4576 (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 ASN4556 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4552B TYR* 3.3 51.3 + - + +
4553B LEU* 3.5 6.1 - - - +
4555B ARG* 1.3 84.1 - - - +
4557B PHE* 1.3 58.4 + - - +
4558B TYR 3.4 0.7 - - - -
4559B THR* 3.0 25.9 + - - +
4560B LEU* 3.0 21.6 + - + +
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Residues in contact with PHE4557 (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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4553B LEU 3.0 15.9 + - - +
4554B SER* 3.5 14.6 - - - +
4555B ARG 3.3 2.6 - - - -
4556B ASN* 1.3 75.8 - - - +
4558B TYR* 1.3 67.3 + - + +
4560B LEU* 3.2 21.7 + - - +
4561B ARG* 3.5 12.6 + - - +
4655B CYS* 5.1 10.1 - - - -
4658B GLY* 4.8 9.4 - - - +
4659B TYR* 5.4 1.1 - - - +
4662B LEU* 3.7 22.0 - - + -
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Residues in contact with TYR4558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4203B PRO* 5.4 11.0 - - + -
4204B GLN* 4.3 29.4 - - + +
4554B SER 4.9 0.2 + - - -
4555B ARG 4.6 6.9 + - - +
4556B ASN 3.4 0.4 - - - -
4557B PHE* 1.3 78.5 - - - +
4559B THR* 1.3 63.5 + - + +
4561B ARG* 3.4 20.4 + - + +
4562B PHE* 4.1 2.9 + - - +
4662B LEU* 4.0 32.9 - - + +
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Residues in contact with THR4559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4555B ARG 5.3 1.1 + - - +
4556B ASN* 3.0 35.1 + - - +
4558B TYR* 1.3 76.3 - - + +
4560B LEU* 1.3 61.8 + - - +
4561B ARG 3.2 0.2 - - - -
4562B PHE* 3.2 20.5 + - + +
4563B LEU* 3.2 13.6 - - - +
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Residues in contact with LEU4560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4553B LEU* 5.7 4.3 - - + +
4556B ASN* 3.0 18.7 + - + +
4557B PHE* 3.2 12.7 + - - +
4559B THR* 1.3 78.8 - - - +
4561B ARG* 1.3 60.9 + - - +
4562B PHE 3.2 0.9 + - - -
4563B LEU* 3.6 26.9 + - + +
4564B ALA* 3.7 8.5 + - - +
4651B VAL* 3.3 46.4 - - + +
4654B LEU* 3.8 13.2 - - + +
4655B CYS* 3.5 31.2 - - + +
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Residues in contact with ARG4561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4557B PHE 3.9 11.7 - - - +
4558B TYR* 3.4 13.4 + - + +
4559B THR 3.2 0.8 - - - -
4560B LEU* 1.3 77.2 - - - +
4562B PHE* 1.3 63.4 + - - +
4563B LEU 3.4 0.2 - - - -
4564B ALA* 3.4 33.8 + - - +
4565B LEU* 3.7 7.3 + - - +
4655B CYS* 4.3 19.8 - - - +
4789B TYR* 4.7 8.3 - - - -
4790B LEU* 3.5 28.9 - - - +
4793B TYR* 4.6 11.1 - - - -
4813B ASP* 3.4 34.6 + - - -
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Residues in contact with PHE4562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4558B TYR 4.1 2.3 + - - +
4559B THR* 3.2 18.7 + - + +
4561B ARG* 1.3 77.5 - - - +
4563B LEU* 1.3 66.3 + - + +
4565B LEU* 3.0 25.1 + - + +
4566B PHE* 3.1 31.2 + + + -
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Residues in contact with LEU4563 (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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4559B THR* 3.2 28.0 - - - +
4560B LEU* 3.6 26.7 - - + +
4561B ARG 3.4 0.2 - - - -
4562B PHE* 1.3 74.8 - - + +
4564B ALA* 1.3 61.0 + - - +
4565B LEU 3.0 6.4 + - - -
4566B PHE* 4.3 4.9 - - - +
4567B LEU* 3.2 48.8 + - + +
4647B LEU* 4.8 5.8 - - + -
4648B HIS* 5.2 0.5 - - - -
4651B VAL* 4.3 23.5 - - + +
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Residues in contact with ALA4564 (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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4560B LEU 3.7 7.2 + - - +
4561B ARG* 3.4 36.5 + - - +
4562B PHE 3.2 0.4 - - - -
4563B LEU* 1.3 76.9 - - - +
4565B LEU* 1.3 56.2 + - - +
4568B ALA* 3.6 19.8 + - - +
4648B HIS* 4.8 6.9 + - + -
4651B VAL* 5.2 6.6 - - + +
4793B TYR* 3.8 28.5 + - + +
4814B ILE* 4.9 3.1 - - - +
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Residues in contact with LEU4565 (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 3.7 6.2 + - - +
4562B PHE* 3.0 17.5 + - + +
4564B ALA* 1.3 80.2 - - - +
4566B PHE* 1.3 62.8 + - - +
4567B LEU 3.6 0.4 - - - -
4568B ALA 3.8 1.3 + - - -
4569B PHE* 3.6 17.9 + - + -
4814B ILE* 3.2 37.9 - - + +
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Residues in contact with PHE4566 (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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4562B PHE* 3.1 33.7 + + + +
4563B LEU* 3.4 5.6 + - - +
4565B LEU* 1.3 73.7 - - - +
4567B LEU* 1.3 76.9 + - + +
4568B ALA 3.1 1.3 - - - -
4569B PHE* 3.1 24.0 + + + +
4570B ALA* 3.3 16.4 + - + +
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Residues in contact with LEU4567 (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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4563B LEU* 3.2 47.6 + - + +
4566B PHE* 1.3 89.8 - - + +
4568B ALA* 1.3 60.9 + - - +
4570B ALA* 3.3 8.3 + - - +
4571B ILE* 3.1 26.0 + - - +
4644B LEU* 3.8 31.8 - - + +
4647B LEU* 3.7 42.0 - - + -
4648B HIS* 4.2 23.5 - - + +
4651B VAL* 5.5 2.0 - - + -
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Residues in contact with ALA4568 (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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4564B ALA 3.6 21.5 + - - +
4565B LEU 3.8 7.9 + - - +
4566B PHE 3.1 0.8 - - - -
4567B LEU* 1.3 78.9 - - - +
4569B PHE* 1.3 59.4 + - + +
4571B ILE* 3.3 18.0 - - + +
4572B ASN* 2.9 26.6 + - - +
4648B HIS* 5.0 5.4 - - - +
4793B TYR* 5.1 5.2 - - - +
4810B HIS* 5.2 14.4 - - + +
4811B LEU* 5.9 1.1 - - - +
4814B ILE* 4.5 15.5 - - + -
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Residues in contact with PHE4569 (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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4565B LEU* 3.6 11.8 + - + -
4566B PHE* 3.1 18.4 + + + +
4568B ALA* 1.3 79.1 - - - +
4570B ALA* 1.3 57.4 + - - +
4572B ASN* 2.8 25.2 - - - +
4573B PHE* 3.7 12.3 - - - +
4814B ILE* 3.5 34.8 - - + -
4844H VAL* 6.2 4.7 - - + -
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Residues in contact with ALA4570 (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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4566B PHE* 3.3 17.2 + - + +
4567B LEU* 3.3 11.5 + - + +
4568B ALA 3.2 0.6 - - - -
4569B PHE* 1.3 77.3 - - - +
4571B ILE* 1.3 63.3 + - - +
4573B PHE* 3.9 13.0 + - - +
4574B ILE* 4.1 9.0 + - - +
4644B LEU* 4.7 18.5 - - + +
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Residues in contact with ILE4571 (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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4567B LEU 3.1 17.9 + - - +
4568B ALA* 3.3 14.6 - - - +
4570B ALA* 1.3 75.9 - - - +
4572B ASN* 1.3 66.1 + - + +
4573B PHE 3.2 1.6 - - - -
4574B ILE* 3.2 17.1 - - + +
4575B LEU* 3.1 24.7 - - + +
4641B LEU* 5.7 2.7 - - - +
4644B LEU* 5.0 15.7 - - + +
4645B SER* 4.8 19.3 - - - +
4648B HIS* 5.9 9.2 - - + -
4807B PHE* 3.6 59.5 - - + -
4810B HIS* 6.3 0.2 - - - +
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Residues in contact with ASN4572 (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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4568B ALA* 2.9 18.0 + - - +
4569B PHE* 2.8 37.6 - - - +
4571B ILE* 1.3 76.9 - - + +
4573B PHE* 1.3 66.5 + - - +
4574B ILE 3.4 0.2 - - - -
4575B LEU* 3.7 10.9 + - + -
4576B LEU* 3.6 13.7 + - - +
4807B PHE* 5.8 6.1 - - + +
4811B LEU* 5.1 11.1 - - + +
4847H TYR* 3.1 43.9 + - + +
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Residues in contact with PHE4573 (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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4569B PHE 3.7 17.0 - - - +
4570B ALA* 3.9 8.7 + - - +
4571B ILE 3.2 1.0 - - - -
4572B ASN* 1.3 82.8 + - - +
4574B ILE* 1.3 62.7 + - + +
4576B LEU* 3.5 12.8 + - + +
4577B PHE* 3.2 52.1 - + - -
4878H MET* 6.3 2.7 - - + -
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Residues in contact with ILE4574 (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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4570B ALA 4.1 8.7 + - - +
4571B ILE* 3.2 23.1 - - + +
4573B PHE* 1.3 77.4 - - + +
4575B LEU* 1.3 68.3 + - + +
4576B LEU 3.1 2.0 - - - -
4577B PHE* 3.0 40.5 + - + +
4578B TYR 3.9 1.9 + - - -
4630B LEU* 4.4 21.7 - - + +
4632B GLU* 5.2 4.0 - - + -
4637B MET* 3.6 40.8 - - + +
4640B ALA* 5.9 5.6 - - + +
4641B LEU* 5.9 11.2 - - + -
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Residues in contact with LEU4575 (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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4571B ILE* 3.1 22.2 - - + +
4572B ASN* 4.0 14.1 - - + +
4573B PHE 3.4 0.6 - - - -
4574B ILE* 1.3 83.6 - - + +
4576B LEU* 1.3 60.1 + - - +
4577B PHE 3.1 0.2 - - - -
4578B TYR* 3.2 23.6 + - + +
4641B LEU* 6.4 2.0 - - + -
4805B PHE* 4.7 23.8 - - + -
4807B PHE* 3.6 42.0 - - + -
4808B ALA 5.8 0.9 - - - +
4847H TYR* 4.4 9.0 - - - +
4877H MET* 3.6 6.1 - - - +
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Residues in contact with LEU4576 (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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4572B ASN 3.6 8.8 + - - +
4573B PHE* 3.5 16.2 + - + +
4574B ILE 3.1 1.0 - - - -
4575B LEU* 1.3 77.9 - - - +
4577B PHE* 1.3 61.0 + - + +
4578B TYR 3.2 1.1 - - - -
4847H TYR* 4.8 10.7 + - + +
4877H MET* 3.3 10.1 - - - +
4878H MET* 2.9 56.7 + - - +
4881H TYR* 6.4 0.4 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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