Contacts of the helix formed by residues 889 - 898 (chain M) in PDB entry 2JA7
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 889 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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888M GLY* 1.3 73.4 - - - +
890M ASP* 1.3 65.0 + - - +
891M ALA* 2.8 13.7 + - - +
892M ALA* 3.1 26.0 + - - +
893M PHE* 3.1 20.6 + - - +
1295M THR* 4.4 4.9 - - - -
1297M GLU* 3.8 35.9 - - - +
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Residues in contact with ASP 890 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888M GLY 3.6 0.8 + - - -
889M SER* 1.3 72.1 - - - +
891M ALA* 1.3 64.3 + - - +
893M PHE* 3.5 17.4 - - - +
894M GLU* 3.7 6.6 + - - +
933M TYR* 5.6 0.2 + - - -
940M ARG* 3.8 26.1 + - - +
941M LYS* 4.8 7.8 + - - -
944M ARG* 5.0 2.8 + - - -
1294M PRO 5.4 2.1 - - - +
1295M THR 3.6 12.7 + - - +
1296M GLY* 3.6 19.4 - - - -
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Residues in contact with ALA 891 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889M SER* 2.8 11.9 - - - +
890M ASP* 1.3 78.8 - - - +
892M ALA* 1.3 63.9 + - - +
894M GLU* 3.0 23.0 + - - +
895M LYS* 3.5 5.2 + - - +
1295M THR* 4.5 3.0 + - - +
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Residues in contact with ALA 892 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888M GLY* 5.1 4.3 - - - -
889M SER* 3.1 23.0 + - - +
891M ALA* 1.3 78.4 - - - +
893M PHE* 1.3 62.4 + - - +
895M LYS* 3.4 12.8 + - - +
896M ARG* 3.2 24.1 + - - +
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Residues in contact with PHE 893 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884M ASP 5.7 0.7 - - - -
885M THR* 4.0 21.3 - - + -
887M GLY 5.6 1.8 - - - -
888M GLY* 5.3 1.5 - - - +
889M SER 3.1 11.2 + - - +
890M ASP* 3.5 18.8 - - - +
891M ALA 3.0 0.4 + - - -
892M ALA* 1.3 77.0 - - - +
894M GLU* 1.3 61.8 + - - +
896M ARG* 3.3 1.7 + - - +
897M TYR* 3.0 43.8 + + + +
933M TYR* 3.5 26.2 - + - -
936M LEU* 3.8 32.3 - - + -
937M VAL* 3.7 23.6 - - + -
940M ARG* 3.5 38.6 - - - +
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Residues in contact with GLU 894 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890M ASP 3.7 4.8 + - - +
891M ALA* 3.0 11.7 + - - +
893M PHE* 1.3 76.5 - - - +
895M LYS* 1.3 54.6 + - - +
896M ARG 2.6 16.9 + - - -
898M ARG* 2.9 48.6 + - + +
906M HIS* 4.2 19.2 + - - -
933M TYR* 3.2 24.0 + - + +
1029M ARG* 4.4 0.2 + - - -
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Residues in contact with LYS 895 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891M ALA 3.5 5.4 + - - +
892M ALA* 3.4 15.3 + - - +
894M GLU* 1.3 76.9 - - - +
896M ARG* 1.3 56.8 + - - +
1029M ARG* 3.5 19.4 + - - +
1033M GLN* 5.3 4.9 + - - -
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Residues in contact with ARG 896 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884M ASP* 3.7 28.5 + - - +
892M ALA 3.2 14.1 + - - +
893M PHE* 6.0 0.4 - - - +
894M GLU 2.6 8.1 + - - -
895M LYS* 1.3 75.9 - - - +
897M TYR* 1.3 82.4 + - + +
898M ARG 3.6 0.4 - - - -
1029M ARG* 3.0 28.4 - - - +
1030M ARG* 2.7 40.1 + - + +
1034M GLU* 3.0 34.7 + - - +
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Residues in contact with TYR 897 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884M ASP* 3.4 23.3 - - - +
885M THR* 4.1 13.0 + - - -
893M PHE* 3.0 32.7 + + + +
896M ARG* 1.3 108.1 + - + +
898M ARG* 1.3 62.9 + - - +
899M VAL* 3.6 5.4 + - - +
929M LEU* 5.7 0.2 - - - +
932M GLU* 4.0 15.8 - - - +
933M TYR* 3.7 13.1 - - + +
936M LEU* 3.1 33.5 - - + +
1024M SER* 3.2 39.0 + - - -
1027M ALA* 3.8 12.1 - - + +
1029M ARG* 4.4 6.4 - - - +
1030M ARG* 3.3 17.8 + - - +
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Residues in contact with ARG 898 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894M GLU* 2.9 40.1 + - + +
897M TYR* 1.3 77.3 - - - +
899M VAL* 1.3 78.8 + - - +
900M ASP* 4.5 18.5 + - - +
906M HIS* 4.6 17.8 - - + +
926M GLN* 4.7 1.2 + - - -
930M ASP* 2.8 29.3 + - - +
933M TYR* 3.2 44.8 - - + +
1029M ARG* 2.8 31.7 + - - -
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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