Contacts of the helix formed by residues 920 - 926 (chain B) in PDB entry 4Z2M
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 GLY 920 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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917B PHE* 3.9 6.8 + - - -
918B GLU 3.2 4.2 + - - -
919B GLN* 1.3 79.0 - - - +
921B GLY* 1.3 65.3 + - - +
922B TRP 3.3 1.0 + - - -
923B SER* 3.3 24.1 + - - -
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Residues in contact with GLY 921 (chain B).
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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916B PHE* 3.3 35.1 + - - -
917B PHE* 3.9 24.2 - - - +
919B GLN* 3.2 16.2 - - - +
920B GLY* 1.3 75.3 - - - +
922B TRP* 1.3 58.4 + - - -
923B SER 3.1 4.6 + - - -
924B PHE* 3.4 10.2 - - - -
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Residues in contact with TRP 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841B GLU* 3.1 23.8 + - + +
842B LEU* 3.5 29.7 - - + +
860B VAL* 4.1 15.7 - - + -
864B TYR* 3.7 29.0 + + - -
894B THR* 5.6 1.0 - - - +
902B TRP* 4.1 9.6 - + - -
906B MET* 3.5 29.8 - - + -
909B ILE* 3.5 17.5 - - + -
916B PHE* 3.6 12.2 - + - -
917B PHE* 4.7 10.0 - + - -
920B GLY 3.3 2.2 + - - -
921B GLY* 1.3 68.5 - - - -
923B SER* 1.3 61.2 + - - +
924B PHE* 2.9 43.7 + + - -
925B LEU* 3.0 28.9 + - + +
926B GLU 4.2 0.5 + - - -
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Residues in contact with SER 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919B GLN* 3.9 9.5 + - - -
920B GLY* 3.3 27.9 + - - -
921B GLY 3.1 1.0 - - - -
922B TRP* 1.3 77.5 - - - +
924B PHE* 1.3 55.7 + - - +
925B LEU 3.0 1.1 - - - -
926B GLU* 2.8 36.0 + - - +
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Residues in contact with PHE 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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900B LEU* 4.8 3.4 - - + -
902B TRP* 5.1 0.4 - + - -
905B ILE* 3.9 38.4 - - + -
916B PHE* 3.8 15.7 - + - -
919B GLN* 3.7 25.8 - - - +
921B GLY 3.4 19.6 + - - -
922B TRP* 2.9 32.8 + + - -
923B SER* 1.3 79.8 + - - +
925B LEU* 1.3 83.9 + - + +
926B GLU* 3.3 6.9 + - - +
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Residues in contact with LEU 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B LEU* 4.2 16.6 - - + -
844B HIS* 4.1 18.8 - - + +
894B THR* 3.5 32.4 - - + +
895B GLU 3.9 12.1 - - - +
900B LEU* 3.8 22.9 - - + -
902B TRP* 4.2 7.4 - - + -
922B TRP* 3.0 31.9 + - + +
923B SER 3.0 0.8 - - - -
924B PHE* 1.3 110.6 - - + +
926B GLU* 1.3 71.3 + - - +
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Residues in contact with GLU 926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894B THR* 4.1 18.4 - - - +
895B GLU* 4.2 10.4 + - - +
922B TRP 4.2 0.6 + - - -
923B SER* 2.8 23.2 + - - +
924B PHE* 4.3 7.2 - - - +
925B LEU* 1.3 88.5 - - - +
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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