Contacts of the helix formed by residues 919 - 926 (chain A) in PDB entry 2X2M
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 ALA 919 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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917A TRP 3.8 2.0 + - - -
918A MET* 1.3 75.6 - - - +
920A ILE* 1.3 68.0 - - - +
921A GLU* 3.2 19.3 - - - +
922A SER* 2.9 17.3 + - - +
923A LEU* 2.9 13.4 + - - +
932A SER* 3.5 31.8 + - - -
935A TRP* 3.5 27.6 - - + +
936A SER* 5.1 0.2 + - - -
995A ARG* 4.1 0.4 - - - +
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Residues in contact with ILE 920 (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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918A MET 3.8 0.8 + - - -
919A ALA* 1.3 71.3 - - - +
921A GLU* 1.3 71.9 + - + +
923A LEU* 3.3 4.9 + - - -
924A PHE* 3.1 44.9 + - + +
935A TRP* 4.0 26.8 - - + -
964A LEU* 3.7 42.8 - - + +
965A LYS* 3.9 13.5 - - + +
969A ARG* 4.8 3.8 - - - +
990A GLN* 3.8 37.0 - - + +
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Residues in contact with GLU 921 (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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919A ALA* 3.2 17.1 - - - +
920A ILE* 1.3 77.3 - - + +
922A SER* 1.3 60.1 + - - +
924A PHE* 5.0 0.2 - - - -
925A ASP* 3.0 37.8 + - - +
926A HIS 3.1 6.8 + - - -
927A ILE* 3.2 26.1 + - + +
929A THR* 4.8 4.2 + - - +
932A SER* 3.8 11.4 + - - -
990A GLN 5.1 0.4 - - - +
992A PRO* 3.6 25.9 - - + +
995A ARG* 2.7 41.4 + - - +
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Residues in contact with SER 922 (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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918A MET* 3.5 16.2 - - - +
919A ALA* 2.9 16.2 + - - +
921A GLU* 1.3 77.7 - - - +
923A LEU* 1.3 66.5 + - - +
926A HIS* 3.1 22.1 + - - +
927A ILE 2.8 23.9 + - - +
928A TYR* 3.6 25.1 + - - -
932A SER* 3.5 22.2 - - - -
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Residues in contact with LEU 923 (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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915A VAL* 4.0 31.2 - - + +
918A MET* 3.7 22.8 - - + +
919A ALA 2.9 11.4 + - - +
920A ILE 3.6 7.6 - - - +
922A SER* 1.3 80.6 - - - +
924A PHE* 1.3 66.7 + - + +
926A HIS* 3.9 0.7 - - - -
960A LEU* 4.6 12.3 - - + -
961A PHE* 3.7 41.4 - - + +
964A LEU* 3.6 30.5 - - + -
766B PRO* 4.6 7.0 - - + +
2012B FMT 2.9 26.9 - - - +
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Residues in contact with PHE 924 (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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920A ILE* 3.1 36.9 + - + +
921A GLU* 5.0 0.4 - - - -
923A LEU* 1.3 87.6 - - + +
925A ASP* 1.3 73.7 - - - +
926A HIS* 3.6 0.7 - - - -
961A PHE* 3.5 47.1 - + + -
964A LEU* 5.1 1.3 - - + -
965A LYS* 4.1 27.6 - - + -
700B GLY* 2.8 32.5 + - - -
703B SER* 3.6 29.4 - - - -
2012B FMT 3.8 3.9 - - - +
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Residues in contact with ASP 925 (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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906A VAL* 5.1 4.3 - - - +
921A GLU* 3.0 24.1 + - - +
924A PHE* 1.3 89.5 - - - +
926A HIS* 1.3 70.4 + - - +
927A ILE* 3.2 27.0 + - + +
700B GLY 5.1 0.7 + - - -
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Residues in contact with HIS 926 (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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906A VAL* 3.4 8.1 - - + +
907A LYS* 2.8 49.5 + - + +
908A ARG* 3.0 17.5 + - - -
909A SER 3.2 10.3 + - - -
910A GLN* 3.3 27.6 + - - -
911A GLY 5.3 0.4 - - - -
918A MET* 6.2 0.2 - - + -
921A GLU 3.1 2.6 + - - -
922A SER 3.1 17.7 + - - -
923A LEU 3.9 1.1 - - - -
924A PHE 4.0 2.7 - - - -
925A ASP* 1.3 79.5 - - - +
927A ILE* 1.3 59.7 + - - +
928A TYR* 3.6 13.4 - + + -
701B PRO* 4.2 7.9 - - + +
2012B FMT 2.6 35.2 + - - -
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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