Contacts of the helix formed by residues 4556 - 4576 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4552F TYR* 3.3 51.5 + - + +
4553F LEU* 3.5 5.4 - - - +
4554F SER 3.4 0.2 - - - -
4555F ARG* 1.3 84.9 - - - +
4557F PHE* 1.3 58.4 + - - +
4558F TYR 3.4 0.9 - - - -
4559F THR* 3.0 26.4 + - - +
4560F LEU* 3.0 21.2 + - + +
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Residues in contact with PHE4557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4553F LEU 3.0 16.2 + - - +
4554F SER* 3.5 13.7 - - - +
4555F ARG 3.3 2.6 - - - -
4556F ASN* 1.3 75.2 - - - +
4558F TYR* 1.3 67.2 + - + +
4560F LEU* 3.2 21.7 + - - +
4561F ARG* 3.5 12.6 + - - +
4655F CYS* 5.1 10.1 - - - -
4658F GLY* 4.8 9.9 - - - +
4659F TYR* 5.4 0.7 - - - +
4662F LEU* 3.7 21.3 - - + -
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Residues in contact with TYR4558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4203F PRO* 5.4 9.4 - - + -
4204F GLN* 4.3 30.0 - - + +
4554F SER 4.9 0.4 + - - -
4555F ARG 4.6 6.5 + - - +
4556F ASN 3.4 0.2 - - - -
4557F PHE* 1.3 78.5 - - + +
4559F THR* 1.3 64.0 + - + +
4561F ARG* 3.4 20.1 + - + +
4562F PHE* 4.1 3.3 + - - +
4662F LEU* 4.0 34.6 - - + +
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Residues in contact with THR4559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4555F ARG 5.3 1.1 + - - +
4556F ASN* 3.0 34.8 + - - +
4558F TYR* 1.3 75.8 - - + +
4560F LEU* 1.3 63.8 + - - +
4562F PHE* 3.2 20.2 + - + +
4563F LEU* 3.2 13.7 - - - +
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Residues in contact with LEU4560 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4553F LEU* 5.7 4.0 - - + +
4556F ASN* 3.0 19.5 + - + +
4557F PHE* 3.2 12.0 + - - +
4559F THR* 1.3 79.4 - - - +
4561F ARG* 1.3 60.7 + - - +
4562F PHE 3.4 0.9 + - - -
4563F LEU* 3.6 26.6 + - + +
4564F ALA* 3.7 8.7 + - - +
4651F VAL* 3.3 46.1 - - + +
4654F LEU* 3.8 14.1 - - + +
4655F CYS* 3.5 30.7 - - + +
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Residues in contact with ARG4561 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4557F PHE 3.5 11.6 + - - +
4558F TYR* 3.4 13.7 + - + +
4559F THR 3.2 1.2 - - - -
4560F LEU* 1.3 76.2 - - - +
4562F PHE* 1.3 62.5 + - - +
4564F ALA* 3.4 36.1 + - - +
4565F LEU* 3.7 7.1 + - - +
4655F CYS* 4.3 19.6 - - - +
4789F TYR* 4.7 8.1 - - - -
4790F LEU* 3.5 28.5 - - - +
4793F TYR* 4.6 11.5 - - - -
4813F ASP* 3.4 35.4 + - - -
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Residues in contact with PHE4562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4558F TYR 4.1 2.3 + - - +
4559F THR* 3.2 17.9 + - - +
4561F ARG* 1.3 76.4 - - - +
4563F LEU* 1.3 65.0 + - + +
4565F LEU* 3.0 25.1 + - + +
4566F PHE* 3.1 30.9 + + + +
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Residues in contact with LEU4563 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4559F THR* 3.2 27.6 - - - +
4560F LEU* 3.6 27.8 - - + +
4562F PHE* 1.3 77.3 - - + +
4564F ALA* 1.3 60.7 + - - +
4565F LEU 3.0 6.0 + - - -
4566F PHE* 4.3 4.5 - - - +
4567F LEU* 3.2 50.7 + - + +
4647F LEU* 4.8 6.1 - - + -
4648F HIS* 5.2 0.7 - - - -
4651F VAL* 4.3 23.3 - - + -
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Residues in contact with ALA4564 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4560F LEU 3.7 6.3 + - - +
4561F ARG* 3.4 36.9 + - - +
4562F PHE 3.2 1.0 - - - -
4563F LEU* 1.3 77.2 - - - +
4565F LEU* 1.3 56.0 + - - +
4568F ALA* 3.6 18.8 - - - +
4648F HIS* 4.8 7.3 + - - -
4651F VAL* 5.2 6.1 - - + +
4793F TYR* 3.8 27.8 + - + +
4814F ILE* 4.9 3.1 - - - +
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Residues in contact with LEU4565 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4561F ARG 3.7 6.5 + - - +
4562F PHE* 3.0 18.4 + - + +
4564F ALA* 1.3 79.9 - - - +
4566F PHE* 1.3 62.3 + - - +
4567F LEU 3.6 0.2 - - - -
4568F ALA 3.8 1.1 + - - -
4569F PHE* 3.6 17.8 + - + -
4814F ILE* 3.2 38.2 - - + +
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Residues in contact with PHE4566 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4562F PHE* 3.1 32.7 + + + +
4563F LEU* 3.4 5.6 + - - +
4565F LEU* 1.3 73.4 - - - +
4567F LEU* 1.3 76.4 + - + +
4568F ALA 3.1 1.6 - - - -
4569F PHE* 3.1 24.6 + + + +
4570F ALA* 3.3 17.1 + - + +
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Residues in contact with LEU4567 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4563F LEU* 3.2 47.7 + - + +
4566F PHE* 1.3 88.1 - - + +
4568F ALA* 1.3 60.6 + - - +
4570F ALA* 3.3 8.7 + - - +
4571F ILE* 3.1 26.6 + - - +
4644F LEU* 3.8 28.8 - - + +
4647F LEU* 3.7 46.0 - - + -
4648F HIS* 4.2 22.4 - - + +
4651F VAL* 5.5 2.0 - - + -
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Residues in contact with ALA4568 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4564F ALA 3.6 21.9 + - - +
4565F LEU 3.8 6.4 + - - +
4566F PHE 3.1 0.8 - - - -
4567F LEU* 1.3 79.2 - - - +
4569F PHE* 1.3 57.7 + - + +
4571F ILE* 3.3 17.4 - - + +
4572F ASN* 2.9 28.0 + - - +
4648F HIS* 5.0 5.5 - - - +
4793F TYR* 5.1 4.7 - - - +
4810F HIS* 5.2 13.9 - - + +
4811F LEU* 5.9 1.1 - - - +
4814F ILE* 4.5 15.7 - - + -
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Residues in contact with PHE4569 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4844D VAL* 6.2 4.7 - - + -
4565F LEU* 3.6 10.7 + - + -
4566F PHE* 3.1 17.7 + + + +
4568F ALA* 1.3 78.9 - - + +
4570F ALA* 1.3 57.6 + - - +
4572F ASN* 2.8 26.1 - - - +
4573F PHE* 3.7 11.6 - - - +
4814F ILE* 3.5 34.5 - - + -
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Residues in contact with ALA4570 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4566F PHE* 3.3 17.6 + - + +
4567F LEU* 3.3 11.6 + - - +
4568F ALA 3.2 1.0 - - - -
4569F PHE* 1.3 78.8 - - - +
4571F ILE* 1.3 61.6 + - - +
4572F ASN 3.6 0.2 - - - -
4573F PHE* 3.9 12.5 + - - +
4574F ILE* 4.1 8.8 + - - +
4644F LEU* 4.7 19.1 - - + +
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Residues in contact with ILE4571 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4567F LEU 3.1 18.3 + - - +
4568F ALA* 3.3 14.1 - - - +
4570F ALA* 1.3 76.3 - - - +
4572F ASN* 1.3 66.6 + - + +
4573F PHE 3.2 2.0 - - - -
4574F ILE* 3.2 17.8 - - + +
4575F LEU* 3.1 24.3 - - + +
4641F LEU* 5.7 2.9 - - - +
4644F LEU* 5.0 13.9 - - + +
4645F SER* 4.8 19.1 - - - +
4648F HIS* 5.9 9.2 - - + -
4807F PHE* 3.6 59.9 - - + -
4810F HIS* 6.3 0.2 - - - +
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Residues in contact with ASN4572 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4847D TYR* 3.1 42.8 + - + +
4568F ALA* 2.9 18.7 + - - +
4569F PHE* 2.8 37.1 - - - +
4571F ILE* 1.3 77.5 - - + +
4573F PHE* 1.3 67.6 + - - +
4574F ILE 3.4 0.2 - - - -
4575F LEU* 3.7 10.7 + - + -
4576F LEU* 3.6 13.5 + - - +
4807F PHE* 5.8 6.1 - - + +
4811F LEU* 5.1 11.5 - - + +
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Residues in contact with PHE4573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4878D MET* 6.3 2.7 - - + -
4569F PHE 3.7 16.2 - - - +
4570F ALA* 4.0 8.1 - - - +
4571F ILE 3.2 1.2 - - - -
4572F ASN* 1.3 83.8 + - - +
4574F ILE* 1.3 60.9 + - + +
4576F LEU* 3.5 12.5 + - + +
4577F PHE* 3.2 52.5 - + - -
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Residues in contact with ILE4574 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4570F ALA 4.1 7.4 + - - +
4571F ILE* 3.2 24.0 - - + +
4573F PHE* 1.3 78.0 - - + +
4575F LEU* 1.3 68.6 + - + +
4576F LEU 3.1 2.2 - - - -
4577F PHE* 3.0 40.0 + - + +
4578F TYR 3.9 2.1 + - - -
4630F LEU* 4.4 20.7 - - + +
4632F GLU* 5.2 4.0 - - + -
4637F MET* 3.6 41.1 - - + +
4640F ALA* 5.9 7.0 - - + +
4641F LEU* 5.9 11.9 - - + -
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Residues in contact with LEU4575 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4847D TYR* 4.4 9.0 - - - +
4877D MET* 3.6 5.9 - - - +
4571F ILE* 3.1 22.4 - - + +
4572F ASN* 4.0 15.3 - - + +
4573F PHE 3.4 0.6 - - - -
4574F ILE* 1.3 84.2 - - + +
4576F LEU* 1.3 61.0 + - - +
4577F PHE 3.1 0.2 - - - -
4578F TYR* 3.2 24.3 + - + +
4641F LEU* 6.4 1.8 - - + -
4805F PHE* 4.7 22.9 - - + -
4807F PHE* 3.6 41.5 - - + -
4808F ALA 5.8 0.7 - - - +
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Residues in contact with LEU4576 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4847D TYR* 4.8 10.7 + - + +
4877D MET* 3.3 10.1 - - - +
4878D MET* 2.9 55.9 + - - +
4881D TYR* 6.4 0.7 - - + -
4572F ASN 3.6 9.7 + - - +
4573F PHE* 3.5 15.6 + - + +
4574F ILE 3.1 0.8 - - - -
4575F LEU* 1.3 78.7 - - - +
4577F PHE* 1.3 59.9 + - + +
4578F TYR 3.2 0.9 - - - -
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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
------------------------------------------------------------
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