Contacts of the helix formed by residues 852 - 863 (chain A) in PDB entry 3ZFM
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 PRO 852 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720A VAL* 3.7 25.6 - - + -
820A MET* 4.2 3.1 - - + -
850A ASP 3.6 6.5 - - - +
851A CYS* 1.4 88.8 - - - +
853A SER* 1.3 59.9 + - - +
854A ALA 3.3 5.2 - - - +
855A LEU* 3.2 28.6 + - + +
856A HIS* 3.0 25.5 + - - +
889A SER 4.7 0.2 - - - +
890A LEU* 3.4 42.8 - - + +
892A ALA 3.4 8.1 - - - +
893A MET* 4.4 2.9 - - + -
894A ALA 4.6 0.2 - - - -
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Residues in contact with SER 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851A CYS 3.9 0.6 + - - -
852A PRO* 1.3 69.0 - - - +
854A ALA* 1.3 60.4 + - - +
856A HIS* 4.0 5.8 - - - +
857A GLN* 3.1 31.4 + - - +
889A SER 5.9 0.2 - - - -
892A ALA* 2.9 27.3 + - - -
893A MET 4.4 0.9 - - - -
894A ALA 4.1 14.9 - - - +
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Residues in contact with ALA 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852A PRO* 3.3 2.4 - - + +
853A SER* 1.3 78.5 - - - +
855A LEU* 1.3 61.6 + - - +
857A GLN* 4.2 4.7 - - - +
858A LEU* 3.4 17.2 + - - +
879A THR* 5.4 0.3 - - - +
883A MET* 3.4 33.8 - - + +
889A SER* 3.6 27.8 + - - +
890A LEU* 5.4 0.4 - - + -
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Residues in contact with LEU 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A VAL* 4.2 0.7 - - + -
724A VAL* 3.7 22.0 - - + -
727A LEU* 4.6 5.4 - - + -
816A MET* 3.3 31.8 - - + +
820A MET* 3.6 26.2 - - + -
851A CYS* 3.9 8.1 - - - -
852A PRO* 3.2 34.0 + - + +
854A ALA* 1.3 75.7 - - - +
856A HIS* 1.3 63.3 + - - +
858A LEU 3.3 1.9 + - - -
859A MET* 3.2 21.3 + - + +
880A LEU* 4.0 13.2 - - + -
883A MET* 3.8 20.2 - - + -
890A LEU* 4.0 11.0 - - + -
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Residues in contact with HIS 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845A LEU 3.6 18.4 - - - -
847A PRO* 3.4 53.6 - - + +
851A CYS* 4.1 3.1 - - - +
852A PRO 3.0 16.0 + - - +
853A SER* 3.6 6.5 + - - +
855A LEU* 1.3 75.4 - - - +
857A GLN* 1.3 61.9 + - - +
859A MET* 3.3 21.0 + - - +
860A LEU* 3.1 51.9 + - + +
863A TRP* 4.6 4.9 - + - -
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Residues in contact with GLN 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853A SER* 3.1 20.0 + - - +
854A ALA* 4.2 5.6 - - - +
856A HIS* 1.3 73.1 - - - +
858A LEU* 1.4 60.0 + - - +
860A LEU* 3.1 26.7 + - - +
861A ASP* 3.0 60.2 + - - +
864A GLN* 5.3 3.2 - - - +
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Residues in contact with LEU 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A MET* 3.8 24.7 - - + -
854A ALA 3.4 15.9 + - - +
855A LEU 3.3 7.1 + - - +
857A GLN* 1.4 77.8 - - - +
859A MET* 1.4 61.7 + - - +
861A ASP* 3.2 15.9 + - - +
862A CYS* 3.0 28.0 + - - -
871A PRO* 4.1 13.2 - - + -
875A GLN 6.0 0.2 - - - -
876A ILE* 4.1 33.7 - - + -
879A THR* 3.9 30.1 - - + +
880A LEU* 3.8 24.0 - - + -
883A MET* 4.8 1.3 - - + -
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Residues in contact with MET 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813A GLY* 4.0 2.7 - - - +
816A MET* 3.8 47.3 - - + +
817A TRP* 4.0 17.9 - - - -
820A MET* 4.0 7.0 - - + -
848A PRO* 4.2 5.6 - - + -
851A CYS* 3.7 29.4 - - - -
855A LEU 3.2 16.1 + - - +
856A HIS* 3.4 19.1 - - - +
858A LEU* 1.4 74.6 - - - +
860A LEU* 1.3 57.6 + - - +
862A CYS* 3.1 8.0 + - - +
863A TRP* 3.0 65.0 + - + -
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Residues in contact with LEU 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844A ARG* 4.0 31.1 + - + -
856A HIS* 3.1 46.0 + - + +
857A GLN* 3.1 33.2 + - - +
859A MET* 1.3 73.2 - - - +
861A ASP* 1.3 61.1 - - - +
863A TRP* 3.2 20.6 + - + +
864A GLN* 3.0 24.6 + - - +
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Residues in contact with ASP 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857A GLN* 3.0 46.1 + - - +
858A LEU* 3.4 18.2 - - - +
860A LEU* 1.3 71.6 - - - +
862A CYS* 1.4 65.2 + - - +
864A GLN* 3.2 30.9 + - + +
869A HIS 5.5 1.3 - - - +
870A ARG* 3.4 9.7 - - - +
871A PRO* 3.4 24.6 - - + +
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Residues in contact with CYS 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809A VAL* 3.4 38.8 - - - +
810A TRP* 3.4 13.5 + - - -
812A TYR* 4.1 12.3 - - - -
813A GLY* 3.7 14.6 - - - -
816A MET* 4.5 2.0 - - - -
858A LEU* 3.0 25.3 + - - -
859A MET* 3.1 8.5 + - - +
861A ASP* 1.4 75.0 - - - +
863A TRP* 1.4 58.6 + - - +
870A ARG* 3.2 22.2 + - - -
871A PRO* 4.2 4.5 - - - -
876A ILE* 4.1 17.3 - - - -
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Residues in contact with TRP 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810A TRP* 3.1 46.6 + + + -
813A GLY* 3.1 37.8 - - - -
814A ILE* 3.4 21.1 - - + +
817A TRP* 4.1 8.5 - + + -
827A TYR* 6.0 0.2 - - - -
844A ARG* 3.1 52.4 + - + +
845A LEU* 3.8 40.2 - - + -
856A HIS* 4.6 2.0 - + - -
859A MET* 3.0 48.2 + - + +
860A LEU* 3.2 20.4 + - + +
861A ASP 3.1 0.6 - - - -
862A CYS* 1.4 77.5 - - - +
864A GLN* 1.4 63.4 + - - +
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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