Contacts of the helix formed by residues 835 - 841 (chain D) in PDB entry 1ZYR
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 SER 835 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804D LEU* 5.2 2.7 - - - -
827D ILE 2.9 14.0 + - - -
828D LYS* 4.8 0.9 - - - -
829D VAL* 2.7 49.8 + - - +
831D GLY* 3.7 6.8 + - - -
834D THR* 1.3 75.7 - - - +
836D VAL* 1.3 55.1 + - - +
837D GLY 2.5 2.4 + - - -
838D ARG* 2.5 51.7 + - - +
839D LEU* 3.7 2.8 + - - +
863D VAL* 5.2 2.7 - - - -
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Residues in contact with VAL 836 (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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804D LEU* 5.7 2.0 - - - +
816D HIS* 4.4 11.7 - - + +
817D GLU* 4.6 14.8 - - + -
820D GLU* 3.3 35.0 - - + +
825D ALA* 4.0 5.6 - - + +
826D PRO 2.6 31.6 - - - +
827D ILE* 3.9 0.2 - - - -
829D VAL* 3.6 13.0 - - + +
834D THR 4.3 0.8 + - - -
835D SER* 1.3 68.1 - - - +
837D GLY* 1.3 65.9 + - - +
838D ARG 3.2 0.2 - - - -
839D LEU* 3.0 25.3 + - + +
840D LYS* 3.2 17.9 + - + +
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Residues in contact with GLY 837 (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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827D ILE* 3.1 38.6 + - - -
835D SER 2.5 7.5 + - - -
836D VAL* 1.3 80.7 - - - +
838D ARG* 1.3 56.7 + - - -
839D LEU 2.8 7.1 + - - -
840D LYS* 3.4 11.3 + - - +
841D TYR* 3.6 17.1 + - - +
863D VAL 3.6 12.1 - - - +
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Residues in contact with ARG 838 (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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831D GLY 3.2 25.1 + - - -
832D ARG 3.4 12.7 + - - -
833D GLU 4.0 0.8 + - - -
834D THR* 3.4 27.4 - - + +
835D SER* 2.5 25.9 + - - +
837D GLY* 1.3 69.2 - - - -
839D LEU* 1.3 60.8 + - - +
841D TYR 3.8 5.6 - - - +
842D VAL* 3.9 4.5 - - - +
863D VAL* 3.5 41.2 + - + +
864D VAL* 4.8 4.0 - - - +
865D THR* 2.9 25.1 + - - +
874D GLU* 2.8 46.6 + - - -
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Residues in contact with LEU 839 (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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64B GLU* 5.4 2.9 - - - +
65B PHE* 4.7 26.2 - - + -
806D PHE* 4.3 28.7 - - + -
812D ALA 5.8 0.2 - - - +
813D LEU* 4.7 13.7 - - + -
817D GLU* 4.5 23.8 - - + +
834D THR* 4.4 19.1 - - + +
835D SER 4.4 3.4 - - - +
836D VAL* 3.5 22.9 - - + +
837D GLY 2.8 2.8 + - - -
838D ARG* 1.3 82.1 - - - +
840D LYS* 1.3 67.4 + - - +
841D TYR 3.5 0.2 - - - -
842D VAL* 3.2 17.3 - - - +
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Residues in contact with LYS 840 (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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64B GLU* 5.4 3.3 - - - +
154B GLU* 3.3 42.9 + - + -
168B ASP* 4.6 10.2 - - - +
817D GLU* 5.2 4.6 + - - -
820D GLU* 3.0 28.3 + - - -
821D VAL* 5.2 2.0 - - - +
827D ILE* 5.9 3.9 - - + +
836D VAL* 3.2 17.5 + - + +
837D GLY* 4.0 3.1 - - - +
839D LEU* 1.3 80.1 - - - +
841D TYR* 1.3 106.2 + - + +
842D VAL* 3.9 2.1 + - - +
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Residues in contact with TYR 841 (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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150B TYR* 5.7 3.1 - + - -
152B PRO* 5.1 14.8 - - + -
168B ASP* 5.4 5.6 - - - -
827D ILE* 4.7 24.4 - - + +
837D GLY 3.6 16.0 + - - +
838D ARG 3.8 1.7 - - - +
840D LYS* 1.3 115.3 + - + +
842D VAL* 1.3 70.4 + - - +
843D PHE* 3.5 25.4 - + + -
857D ILE* 3.5 36.1 + - + +
858D VAL* 4.1 26.5 - - + -
863D VAL 5.4 0.2 - - - -
864D VAL* 3.7 9.9 - - + +
865D THR 3.7 14.2 + - - -
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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