Contacts of the helix formed by residues 3563 - 3572 (chain D) in PDB entry 1PXX
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 SER3563 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3343D ILE* 4.0 6.1 - - - +
3347D ASP* 3.3 15.9 - - - -
3561D THR 4.4 3.7 + - - -
3562D ALA* 1.3 76.0 - - - +
3564D ILE* 1.3 63.9 + - - +
3565D GLN* 3.5 11.0 + - - +
3566D SER* 3.0 39.1 + - - -
3567D LEU* 3.1 11.3 + - - +
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Residues in contact with ILE3564 (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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3197D MET* 5.3 1.6 - - + -
3201D PHE* 4.1 15.9 - - + -
3301D TYR* 4.4 6.3 - - + +
3343D ILE* 4.1 5.8 - - + +
3347D ASP* 2.6 28.9 + - - +
3563D SER* 1.3 73.9 - - - +
3565D GLN* 1.3 66.1 + - + +
3567D LEU* 4.0 19.5 - - + -
3568D ILE* 3.1 43.9 + - + +
3578D THR* 3.7 9.1 - - + +
3579D SER* 4.7 16.6 - - - -
3580D PHE* 3.8 41.1 - - + -
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Residues in contact with GLN3565 (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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3563D SER* 3.0 10.2 + - - +
3564D ILE* 1.3 86.6 - - + +
3566D SER* 1.3 58.8 + - - +
3568D ILE* 3.3 0.7 + - - +
3569D CYS* 2.8 35.5 + - + +
3575D CYS* 4.3 6.7 - - - -
3576D PRO 3.6 20.8 + - - -
3577D PHE* 3.9 15.8 - - - +
3578D THR* 3.5 30.3 + - - +
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Residues in contact with SER3566 (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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3339D GLU* 5.4 2.1 + - - -
3561D THR 4.1 5.0 + - - -
3562D ALA* 4.0 6.4 - - - -
3563D SER* 3.0 33.4 + - - -
3565D GLN* 1.3 79.0 - - - +
3567D LEU* 1.3 65.3 + - - +
3569D CYS* 3.8 8.5 - - - -
3570D ASN* 2.9 43.1 + - - -
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Residues in contact with LEU3567 (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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3201D PHE* 5.1 0.2 - - + -
3301D TYR* 5.0 4.0 - - + -
3304D ILE* 4.0 20.2 - - + +
3305D TRP* 3.5 59.2 - - + +
3308D GLU* 4.0 22.2 - - + -
3339D GLU* 4.8 7.2 - - - +
3343D ILE* 4.4 8.7 - - + -
3563D SER 3.1 15.0 + - - +
3564D ILE* 4.0 26.2 - - + +
3566D SER* 1.3 78.6 + - - +
3568D ILE* 1.3 65.4 + - + +
3570D ASN* 4.8 2.0 - - - +
3571D ASN* 2.8 29.6 + - - +
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Residues in contact with ILE3568 (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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3197D MET* 3.9 13.2 - - + -
3301D TYR* 5.0 1.1 - - + -
3304D ILE* 4.4 16.6 - - + -
3423D VAL* 4.0 16.4 - - + -
3564D ILE* 3.1 45.1 - - + +
3565D GLN* 3.3 6.8 + - - +
3567D LEU* 1.3 85.1 - - + +
3569D CYS* 1.3 59.8 + - - +
3572D VAL* 2.7 40.3 + - + +
3576D PRO* 3.5 42.8 - - + +
3578D THR* 3.8 13.9 - - + -
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Residues in contact with CYS3569 (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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3565D GLN* 2.8 20.3 + - + +
3566D SER* 3.2 11.2 + - - +
3568D ILE* 1.3 80.0 - - - +
3570D ASN* 1.3 67.9 + - - +
3571D ASN 3.2 1.0 + - - -
3572D VAL 3.6 11.6 - - - +
3575D CYS* 2.0 57.4 + - - +
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Residues in contact with ASN3570 (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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3308D GLU* 4.5 2.2 + - - -
3311D ARG* 3.4 52.9 - - - +
3566D SER* 2.9 34.7 + - - +
3567D LEU* 4.8 0.8 - - - +
3569D CYS* 1.3 78.5 - - - +
3571D ASN* 1.3 64.5 + - - +
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Residues in contact with ASN3571 (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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3304D ILE* 3.7 17.7 + - + +
3307D ARG* 3.2 59.8 + - + +
3308D GLU* 2.8 37.0 + - - +
3311D ARG* 3.7 5.2 - - - +
3567D LEU* 2.8 27.1 + - - +
3568D ILE 3.2 1.2 + - - +
3569D CYS 3.2 0.6 - - - -
3570D ASN* 1.3 86.2 - - - +
3572D VAL* 1.3 67.3 + - + +
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Residues in contact with VAL3572 (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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3304D ILE* 4.1 29.4 - - + -
3307D ARG* 4.3 2.7 - - - +
3419D LEU* 3.8 13.7 - - + +
3420D THR* 3.6 37.2 - - - +
3423D VAL* 4.3 3.8 - - + -
3568D ILE* 2.7 32.4 + - + +
3569D CYS 3.6 8.7 - - - +
3571D ASN* 1.3 81.0 - - + +
3573D LYS* 1.3 68.9 + - - +
3574D GLY 3.4 0.3 + - - -
3575D CYS* 3.2 13.2 + - - -
3576D PRO* 4.0 16.2 - - + -
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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