Contacts of the helix formed by residues 4556 - 4576 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4552D TYR* 3.3 51.6 + - + +
4553D LEU* 3.5 5.4 - - - +
4555D ARG* 1.3 84.8 - - - +
4557D PHE* 1.3 57.1 + - - +
4558D TYR 3.4 0.7 - - - -
4559D THR* 3.0 26.1 + - - +
4560D LEU* 3.0 22.0 + - + +
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Residues in contact with PHE4557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4553D LEU 3.0 16.4 + - - +
4554D SER* 3.5 13.5 - - - +
4555D ARG 3.3 2.8 - - - -
4556D ASN* 1.3 76.2 - - - +
4558D TYR* 1.3 68.7 - - + +
4560D LEU* 3.2 20.5 + - - +
4561D ARG* 3.5 12.8 + - - +
4655D CYS* 5.1 10.3 - - - -
4658D GLY* 4.8 10.8 - - - +
4659D TYR* 5.4 0.4 - - - +
4662D LEU* 3.7 20.4 - - + -
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Residues in contact with TYR4558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4203D PRO* 5.4 9.9 - - + -
4204D GLN* 4.3 29.9 - - + +
4554D SER 4.9 0.4 + - - -
4555D ARG 4.6 5.6 + - - +
4556D ASN* 4.5 0.2 - - - +
4557D PHE* 1.3 79.5 - - + +
4559D THR* 1.3 64.6 + - + +
4561D ARG* 3.4 19.7 + - + +
4562D PHE* 4.1 3.3 + - - +
4662D LEU* 4.0 33.9 - - + +
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Residues in contact with THR4559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4555D ARG 5.3 1.9 + - - +
4556D ASN* 3.0 33.6 + - - +
4558D TYR* 1.3 77.7 - - + +
4560D LEU* 1.3 63.5 + - - +
4561D ARG 3.2 0.2 - - - -
4562D PHE* 3.2 20.2 + - + +
4563D LEU* 3.2 14.8 - - - +
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Residues in contact with LEU4560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4553D LEU* 5.7 3.8 - - + +
4556D ASN* 3.0 19.7 + - + +
4557D PHE* 3.2 12.9 + - - +
4559D THR* 1.3 77.3 - - - +
4561D ARG* 1.3 61.1 + - - +
4562D PHE 3.4 0.3 + - - -
4563D LEU* 3.6 27.7 + - + +
4564D ALA* 3.7 8.1 + - - +
4651D VAL* 3.3 45.4 - - + +
4654D LEU* 3.8 13.9 - - + +
4655D CYS* 3.5 30.1 - - + +
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Residues in contact with ARG4561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4557D PHE 3.9 11.7 - - - +
4558D TYR* 3.4 13.2 + - + +
4559D THR 3.2 1.0 - - - -
4560D LEU* 1.3 75.7 - - - +
4562D PHE* 1.3 63.8 + - - +
4563D LEU 3.4 0.2 - - - -
4564D ALA* 3.4 33.2 + - - +
4565D LEU* 3.7 7.1 + - - +
4655D CYS* 4.3 20.0 - - - +
4789D TYR* 4.7 8.5 - - - -
4790D LEU* 3.5 28.3 - - - +
4793D TYR* 4.6 11.7 - - - +
4813D ASP* 3.4 35.2 + - - -
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Residues in contact with PHE4562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4558D TYR 4.1 2.3 + - - +
4559D THR* 3.2 18.1 + - - +
4561D ARG* 1.3 76.2 - - - +
4563D LEU* 1.3 65.2 + - + +
4565D LEU* 3.0 24.4 + - + +
4566D PHE* 3.1 30.6 + + + -
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Residues in contact with LEU4563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4559D THR* 3.2 28.0 - - - +
4560D LEU* 3.6 26.0 - - + +
4561D ARG 3.4 0.2 - - - -
4562D PHE* 1.3 76.7 - - + +
4564D ALA* 1.3 61.2 + - - +
4565D LEU 3.0 6.0 + - - -
4566D PHE* 4.3 4.3 - - - +
4567D LEU* 3.2 49.5 + - + +
4647D LEU* 4.8 5.8 - - + -
4648D HIS* 5.2 0.5 - - - -
4651D VAL* 4.3 24.4 - - + +
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Residues in contact with ALA4564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4560D LEU 3.7 7.7 + - - +
4561D ARG* 3.4 35.6 + - - +
4562D PHE 3.2 0.6 - - - -
4563D LEU* 1.3 76.9 - - - +
4565D LEU* 1.3 56.7 + - - +
4568D ALA* 3.6 19.8 + - - +
4648D HIS* 4.8 6.9 + - - -
4651D VAL* 5.2 6.4 - - + +
4793D TYR* 3.8 28.3 + - + +
4814D ILE* 4.9 3.6 - - - +
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Residues in contact with LEU4565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4561D ARG 3.7 6.9 + - - +
4562D PHE* 3.0 17.9 + - + +
4564D ALA* 1.3 80.5 - - - +
4566D PHE* 1.3 62.0 + - - +
4568D ALA 3.8 1.1 + - - -
4569D PHE* 3.6 18.0 + - + -
4814D ILE* 3.2 37.6 - - + +
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Residues in contact with PHE4566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4562D PHE* 3.1 33.0 + + + +
4563D LEU* 3.4 5.6 + - - +
4565D LEU* 1.3 74.5 - - - +
4567D LEU* 1.3 76.0 + - + +
4568D ALA 3.1 1.6 - - - -
4569D PHE* 3.1 25.0 + + + +
4570D ALA* 3.3 16.6 + - + +
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Residues in contact with LEU4567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4563D LEU* 3.2 47.7 + - + +
4566D PHE* 1.3 88.6 - - + +
4568D ALA* 1.3 62.4 + - - +
4570D ALA* 3.7 7.9 - - - +
4571D ILE* 3.1 27.0 + - - +
4644D LEU* 3.7 32.3 - - + +
4647D LEU* 3.7 43.7 - - + -
4648D HIS* 4.2 22.8 - - + +
4651D VAL* 5.5 1.8 - - + -
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Residues in contact with ALA4568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4564D ALA 3.6 21.5 + - - +
4565D LEU 3.8 7.3 + - - +
4566D PHE 3.1 0.8 - - - -
4567D LEU* 1.3 78.4 - - - +
4569D PHE* 1.3 58.3 + - + +
4571D ILE* 3.3 17.6 - - + +
4572D ASN* 2.9 26.8 + - - +
4648D HIS* 5.0 6.3 - - - +
4793D TYR* 5.1 5.2 - - - +
4810D HIS* 5.2 14.6 - - + +
4811D LEU* 6.0 0.4 - - - -
4814D ILE* 4.5 14.6 - - + -
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Residues in contact with PHE4569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4844B VAL* 6.2 4.5 - - + -
4565D LEU* 3.6 11.8 + - + -
4566D PHE* 3.1 18.2 + + + +
4568D ALA* 1.3 78.9 - - + +
4570D ALA* 1.3 57.4 + - - +
4572D ASN* 2.8 26.0 - - - +
4573D PHE* 3.7 12.0 - - - +
4814D ILE* 3.5 35.7 - - + -
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Residues in contact with ALA4570 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4566D PHE* 3.3 17.2 + - + +
4567D LEU* 3.3 12.0 + - - +
4568D ALA 3.2 0.6 - - - -
4569D PHE* 1.3 78.5 - - - +
4571D ILE* 1.3 62.6 + - - +
4572D ASN 3.6 0.2 - - - -
4573D PHE* 3.9 12.3 + - - +
4574D ILE* 4.1 9.2 + - - +
4644D LEU* 4.7 19.5 - - + +
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Residues in contact with ILE4571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4567D LEU 3.1 18.6 + - - +
4568D ALA* 3.3 14.4 - - - +
4570D ALA* 1.3 76.0 - - - +
4572D ASN* 1.3 66.4 + - + +
4573D PHE 3.2 2.0 - - - -
4574D ILE* 3.2 18.0 - - + +
4575D LEU* 3.1 24.2 - - + +
4641D LEU* 5.7 2.5 - - - +
4644D LEU* 5.0 13.9 - - + +
4645D SER* 4.8 19.5 - - - +
4648D HIS* 5.9 8.7 - - + -
4807D PHE* 3.6 60.8 - - + -
4810D HIS* 6.3 0.4 - - - +
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Residues in contact with ASN4572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4847B TYR* 3.1 43.2 + - + +
4568D ALA* 2.9 17.6 + - - +
4569D PHE* 2.8 36.0 - - - +
4571D ILE* 1.3 77.1 - - + +
4573D PHE* 1.3 66.3 + - - +
4574D ILE 3.4 0.2 - - - -
4575D LEU* 3.7 11.3 + - + -
4576D LEU* 3.6 13.0 + - - +
4807D PHE* 5.8 5.8 - - + +
4811D LEU* 5.1 11.4 - - + +
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Residues in contact with PHE4573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4878B MET* 6.3 2.9 - - + -
4569D PHE 3.7 16.6 - - - +
4570D ALA* 3.9 8.5 + - - +
4571D ILE 3.2 0.8 - - - -
4572D ASN* 1.3 83.7 + - - +
4574D ILE* 1.3 62.0 + - + +
4576D LEU* 3.5 12.3 + - + +
4577D PHE* 3.2 52.2 - + - -
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Residues in contact with ILE4574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4570D ALA 4.1 8.0 + - - +
4571D ILE* 3.2 23.6 - - + +
4573D PHE* 1.3 77.4 - - + +
4575D LEU* 1.3 67.6 + - + +
4576D LEU 3.1 2.2 - - - -
4577D PHE* 3.0 41.0 + - + +
4578D TYR 3.9 1.7 + - - -
4630D LEU* 4.4 20.7 - - + +
4632D GLU* 5.2 4.3 - - + -
4637D MET* 3.6 40.2 - - + +
4640D ALA* 5.9 6.7 - - + +
4641D LEU* 5.9 11.7 - - + -
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Residues in contact with LEU4575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4847B TYR* 4.4 9.2 - - - +
4877B MET* 3.6 6.2 - - - +
4571D ILE* 3.1 21.3 - - + +
4572D ASN* 4.0 14.8 - - + +
4573D PHE 3.4 0.6 - - - -
4574D ILE* 1.3 83.5 - - + +
4576D LEU* 1.3 60.6 + - - +
4577D PHE 3.1 0.2 - - - -
4578D TYR* 3.2 24.4 + - + +
4641D LEU* 6.4 2.0 - - + -
4805D PHE* 4.7 22.9 - - + -
4807D PHE* 3.6 42.2 - - + -
4808D ALA 5.8 0.4 - - - +
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Residues in contact with LEU4576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4847B TYR* 4.8 11.4 + - + +
4877B MET* 3.3 11.2 - - - +
4878B MET* 2.9 56.5 + - - +
4881B TYR* 6.4 0.7 - - + -
4572D ASN 3.6 8.7 + - - +
4573D PHE* 3.5 15.8 + - + +
4574D ILE 3.1 1.2 - - - -
4575D LEU* 1.3 77.4 - - - +
4577D PHE* 1.3 61.1 + - + +
4578D TYR 3.2 0.7 - - - -
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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