Contacts of the helix formed by residues 4556 - 4576 (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 ASN4556 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4552H TYR* 3.3 51.6 + - + +
4553H LEU* 3.5 5.4 - - - +
4555H ARG* 1.3 84.4 - - - +
4557H PHE* 1.3 58.0 + - - +
4558H TYR 3.4 0.7 - - - -
4559H THR* 3.0 26.8 + - - +
4560H LEU* 3.0 21.3 + - + +
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Residues in contact with PHE4557 (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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4553H LEU 3.0 16.2 + - - +
4554H SER* 3.5 13.2 - - - +
4555H ARG 3.3 2.6 - - - -
4556H ASN* 1.3 76.9 - - - +
4558H TYR* 1.3 66.9 + - + +
4560H LEU* 3.2 22.1 + - - +
4561H ARG* 3.5 13.2 + - - +
4655H CYS* 5.1 8.7 - - - -
4658H GLY* 4.8 10.3 - - - +
4659H TYR* 5.9 0.4 - - - -
4662H LEU* 3.7 21.1 - - + -
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Residues in contact with TYR4558 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4203H PRO* 5.4 9.6 - - + -
4204H GLN* 4.3 30.3 - - + +
4554H SER 4.9 0.6 + - - -
4555H ARG 4.6 5.7 + - - +
4556H ASN* 3.4 0.4 - - - +
4557H PHE* 1.3 78.7 - - + +
4559H THR* 1.3 64.1 + - + +
4561H ARG* 3.4 20.5 + - + +
4562H PHE* 4.1 3.1 + - - +
4662H LEU* 4.0 35.6 - - + +
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Residues in contact with THR4559 (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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4555H ARG 5.3 1.1 + - - +
4556H ASN* 3.0 34.4 + - - +
4558H TYR* 1.3 75.5 - - + +
4560H LEU* 1.3 63.1 + - - +
4561H ARG 3.2 0.2 - - - -
4562H PHE* 3.2 19.8 + - - +
4563H LEU* 3.2 13.2 - - - +
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Residues in contact with LEU4560 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4553H LEU* 5.7 3.6 - - + +
4556H ASN* 3.0 19.8 + - + +
4557H PHE* 3.2 11.4 + - - +
4559H THR* 1.3 78.9 - - - +
4561H ARG* 1.3 61.4 + - - +
4562H PHE 3.4 0.5 + - - -
4563H LEU* 3.6 27.0 + - + +
4564H ALA* 3.7 8.3 + - - +
4651H VAL* 3.3 46.1 - - + +
4654H LEU* 3.8 14.8 - - + +
4655H CYS* 3.5 30.1 - - + +
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Residues in contact with ARG4561 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4557H PHE 3.5 12.1 + - - +
4558H TYR* 3.4 13.2 + - + +
4559H THR 3.2 0.8 - - - -
4560H LEU* 1.3 75.5 - - - +
4562H PHE* 1.3 63.5 + - - +
4564H ALA* 3.4 35.2 + - - +
4565H LEU* 3.7 7.3 + - - +
4655H CYS* 4.3 19.8 - - - +
4789H TYR* 4.7 8.3 - - - -
4790H LEU* 3.5 27.5 - - - +
4793H TYR* 4.6 11.7 - - - +
4813H ASP* 3.4 35.0 + - - -
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Residues in contact with PHE4562 (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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4558H TYR 4.1 3.0 + - - +
4559H THR* 3.2 17.8 + - + +
4561H ARG* 1.3 76.5 - - - +
4563H LEU* 1.3 64.8 + - + +
4565H LEU* 3.0 25.9 + - + +
4566H PHE* 3.1 29.8 + + + +
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Residues in contact with LEU4563 (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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4559H THR* 3.2 27.6 - - - +
4560H LEU* 3.6 28.3 - - + +
4561H ARG 3.4 0.2 - - - -
4562H PHE* 1.3 76.9 - - + +
4564H ALA* 1.3 60.9 + - - +
4565H LEU 3.0 6.3 + - - -
4566H PHE* 4.3 4.5 - - - +
4567H LEU* 3.2 51.4 + - + +
4647H LEU* 4.8 5.8 - - + -
4648H HIS* 5.2 0.5 - - - -
4651H VAL* 4.3 23.7 - - + +
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Residues in contact with ALA4564 (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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4560H LEU 3.7 6.8 + - - +
4561H ARG* 3.4 36.5 + - - +
4562H PHE 3.2 0.4 - - - -
4563H LEU* 1.3 77.1 - - - +
4565H LEU* 1.3 56.2 + - - +
4568H ALA* 3.6 19.6 - - - +
4648H HIS* 4.8 6.6 + - - -
4651H VAL* 5.2 6.1 - - + +
4793H TYR* 3.8 28.0 + - + +
4814H ILE* 4.9 3.1 - - - +
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Residues in contact with LEU4565 (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 3.7 7.1 + - - +
4562H PHE* 3.0 17.9 + - + +
4564H ALA* 1.3 79.4 - - - +
4566H PHE* 1.3 61.9 + - - +
4567H LEU 3.6 0.4 - - - -
4568H ALA 4.0 1.1 - - - -
4569H PHE* 3.6 18.3 + - + -
4814H ILE* 3.2 38.4 - - + +
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Residues in contact with PHE4566 (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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4562H PHE* 3.1 33.4 + + + +
4563H LEU* 3.4 5.8 + - - +
4565H LEU* 1.3 74.8 - - - +
4567H LEU* 1.3 76.2 + - + +
4568H ALA 3.1 1.6 - - - -
4569H PHE* 3.1 24.4 + + + +
4570H ALA* 3.3 17.0 + - + +
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Residues in contact with LEU4567 (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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4563H LEU* 3.2 48.0 + - + +
4566H PHE* 1.3 88.8 - - + +
4568H ALA* 1.3 61.2 + - - +
4569H PHE 3.3 0.2 - - - -
4570H ALA* 3.3 8.4 + - - +
4571H ILE* 3.1 26.3 + - - +
4644H LEU* 3.7 32.0 - - + +
4647H LEU* 3.7 43.1 - - + -
4648H HIS* 4.2 23.3 - - + +
4651H VAL* 5.5 2.2 - - + -
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Residues in contact with ALA4568 (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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4564H ALA 3.6 22.1 + - - +
4565H LEU 3.8 6.4 + - - +
4566H PHE 3.1 0.8 - - - -
4567H LEU* 1.3 79.3 - - - +
4569H PHE* 1.3 58.7 + - + +
4571H ILE* 3.3 18.0 - - - +
4572H ASN* 2.9 27.2 + - - +
4648H HIS* 5.0 5.5 - - - +
4793H TYR* 5.1 5.2 - - - +
4810H HIS* 5.2 14.1 - - + +
4811H LEU* 6.0 0.7 - - - -
4814H ILE* 4.5 15.0 - - + -
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Residues in contact with PHE4569 (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* 6.2 4.5 - - + -
4565H LEU* 3.6 10.5 + - + -
4566H PHE* 3.1 17.5 + + + +
4568H ALA* 1.3 79.6 - - + +
4570H ALA* 1.3 56.9 + - - +
4572H ASN* 2.8 25.7 - - - +
4573H PHE* 3.7 12.3 - - - +
4814H ILE* 3.5 36.1 - - + -
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Residues in contact with ALA4570 (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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4566H PHE* 3.3 18.1 + - + +
4567H LEU* 3.3 11.8 + - - +
4568H ALA 3.2 0.8 - - - -
4569H PHE* 1.3 78.6 - - - +
4571H ILE* 1.3 62.0 + - - +
4573H PHE* 3.9 13.3 + - - +
4574H ILE* 4.1 8.8 + - - +
4644H LEU* 4.7 19.1 - - + +
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Residues in contact with ILE4571 (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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4567H LEU 3.1 18.1 + - - +
4568H ALA* 3.3 14.4 - - + +
4570H ALA* 1.3 75.2 - - - +
4572H ASN* 1.3 66.4 + - + +
4573H PHE 3.2 1.8 - - - -
4574H ILE* 3.2 18.1 - - + +
4575H LEU* 3.1 24.6 - - + +
4641H LEU* 5.7 2.9 - - - +
4644H LEU* 5.0 14.6 - - + +
4645H SER* 4.8 19.1 - - - +
4648H HIS* 5.9 9.0 - - + -
4807H PHE* 3.6 59.5 - - + -
4810H HIS* 6.3 0.2 - - - +
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Residues in contact with ASN4572 (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* 3.1 43.2 + - + +
4568H ALA* 2.9 18.2 + - - +
4569H PHE* 2.8 37.2 - - - +
4571H ILE* 1.3 77.1 - - + +
4573H PHE* 1.3 67.7 + - - +
4574H ILE 3.4 0.2 - - - -
4575H LEU* 3.7 11.2 + - + -
4576H LEU* 3.6 13.7 + - - +
4807H PHE* 5.8 6.1 - - + +
4811H LEU* 5.1 10.9 - - + +
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Residues in contact with PHE4573 (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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4878F MET* 6.3 2.9 - - + -
4569H PHE 3.7 16.2 - - - +
4570H ALA* 3.9 8.5 + - - +
4571H ILE 3.2 0.8 - - - -
4572H ASN* 1.3 83.8 + - - +
4574H ILE* 1.3 62.3 + - + +
4576H LEU* 3.5 12.5 + - + +
4577H PHE* 3.2 51.4 - + - -
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Residues in contact with ILE4574 (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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4570H ALA 4.1 8.0 + - - +
4571H ILE* 3.2 23.3 - - + +
4573H PHE* 1.3 77.6 - - + +
4575H LEU* 1.3 68.7 + - + +
4576H LEU 3.1 2.0 - - - -
4577H PHE* 2.9 40.3 + - + +
4578H TYR 3.9 2.3 + - - -
4630H LEU* 4.4 20.7 - - + +
4632H GLU* 5.2 4.0 - - + -
4637H MET* 3.6 40.6 - - + +
4640H ALA* 5.9 6.7 - - + +
4641H LEU* 5.9 11.7 - - + +
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Residues in contact with LEU4575 (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* 4.4 9.2 - - - +
4877F MET* 3.6 6.2 - - - +
4571H ILE* 3.1 22.4 + - + +
4572H ASN* 4.0 14.6 - - + +
4573H PHE 3.4 0.4 - - - -
4574H ILE* 1.3 83.1 - - + +
4576H LEU* 1.3 60.7 + - - +
4578H TYR* 3.2 23.9 + - + +
4641H LEU* 6.4 2.0 - - + -
4805H PHE* 4.7 22.4 - - + -
4807H PHE* 3.6 42.0 - - + -
4808H ALA 5.8 0.7 - - - +
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Residues in contact with LEU4576 (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* 4.8 11.4 + - + +
4877F MET* 3.3 11.3 - - - +
4878F MET* 2.9 55.9 + - - +
4881F TYR* 6.4 0.4 - - + -
4572H ASN 3.6 9.1 + - - +
4573H PHE* 3.5 14.9 + - + +
4574H ILE 3.1 0.8 - - - -
4575H LEU* 1.3 78.5 - - - +
4577H PHE* 1.3 60.4 + - + +
4578H TYR 3.2 1.3 - - - -
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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