Contacts of the helix formed by residues 831 - 844 (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 THR 831 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185 TT 4.2 29.3 + - + +
827M THR* 3.2 20.5 + - - +
828M ALA* 4.2 14.1 - - - +
829M VAL 2.7 2.6 + - - -
830M LYS* 1.3 80.2 - - - +
832M ALA* 1.3 68.9 + - + +
833M GLU 3.4 0.2 - - - -
834M THR* 3.8 6.4 - - - +
835M GLY* 3.3 16.1 + - - -
1077M THR* 4.7 12.9 - - - +
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Residues in contact with ALA 832 (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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175 T 4.9 3.7 - - - +
185 TT 4.1 31.5 - - + +
828M ALA 4.8 3.6 - - - +
829M VAL* 2.8 10.8 + - - +
831M THR* 1.3 86.2 - - + +
833M GLU* 1.3 65.6 + - - +
835M GLY* 3.3 8.8 + - - -
836M TYR* 3.3 12.1 + - - +
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Residues in contact with GLU 833 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829M VAL* 2.8 29.0 + - + +
830M LYS* 4.7 6.7 - - - +
832M ALA* 1.3 76.1 - - - +
834M THR* 1.3 67.2 + - - +
836M TYR* 3.4 7.8 + - + +
837M ILE* 3.2 26.3 + - + +
1098M VAL* 4.3 17.5 - - + +
1099M PRO* 5.0 6.8 - - - +
1102M LYS* 3.0 47.9 + - + +
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Residues in contact with THR 834 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450M LEU* 5.5 0.2 - - + -
830M LYS 2.8 25.1 + - - -
831M THR* 3.8 5.8 - - - +
833M GLU* 1.3 79.2 - - - +
835M GLY* 1.3 68.3 - - - +
837M ILE* 2.8 23.2 + - - +
838M GLN* 2.8 14.5 + - + -
1073M GLY 4.6 4.7 - - - +
1076M ALA* 3.1 23.0 + - + +
1077M THR* 2.9 42.8 - - + +
1098M VAL* 4.5 10.0 - - - +
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Residues in contact with GLY 835 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185 TT 3.5 35.0 - - - +
831M THR 3.3 6.0 + - - -
832M ALA 3.3 7.3 + - - -
833M GLU 3.2 1.0 - - - -
834M THR* 1.3 83.6 - - - +
836M TYR* 1.3 62.2 + - - +
838M GLN* 3.1 8.7 + - - +
839M ARG* 3.0 22.7 + - - +
1133N MET* 5.3 1.6 - - - +
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Residues in contact with TYR 836 (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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165 T 3.9 9.5 + - - -
175 T 3.6 41.5 - - - -
185 TT 4.1 11.6 - - - -
832M ALA 3.3 11.3 + - - +
833M GLU* 3.9 8.5 - - + +
834M THR 3.3 0.2 - - - -
835M GLY* 1.3 74.1 - - - +
837M ILE* 1.3 62.6 + - + +
839M ARG* 3.4 11.4 + - - +
840M ARG* 2.9 80.1 + - + +
1102M LYS* 6.3 1.3 - - - -
1385M THR* 4.4 9.2 - - + +
1386M ARG* 4.9 1.9 + - - -
1402M PHE* 4.4 6.2 - + - -
1403M GLU* 2.4 36.7 + - - -
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Residues in contact with ILE 837 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833M GLU* 3.2 18.8 + - + +
834M THR* 2.8 12.4 + - - +
836M TYR* 1.3 74.8 - - - +
838M GLN* 1.3 67.1 + - - +
840M ARG* 3.5 26.1 - - - +
841M LEU* 3.0 30.6 + - + +
1073M GLY* 5.6 0.2 - - - -
1076M ALA* 5.4 6.5 - - + -
1098M VAL* 4.4 12.8 - - + +
1101M LEU* 4.2 17.5 - - + -
1102M LYS* 4.0 36.1 - - + +
1105M LEU* 3.5 23.5 - - + +
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Residues in contact with GLN 838 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449M SER 4.6 0.6 + - - -
450M LEU* 3.3 38.1 + - + +
834M THR* 2.8 14.1 + - + +
835M GLY* 3.5 10.8 - - - +
837M ILE* 1.3 79.1 - - - +
839M ARG* 1.3 72.0 + - - +
841M LEU* 3.3 4.9 - - - +
842M VAL* 3.1 36.2 + - + +
1069M ALA 5.7 0.8 - - - +
1070M GLN* 4.1 16.8 - - - +
1073M GLY* 4.0 36.3 - - - +
1076M ALA* 6.2 0.4 - - + +
1133N MET* 3.3 26.1 - - + +
1136N ASP* 5.3 2.7 + - - +
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Residues in contact with ARG 839 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175 T 4.2 6.9 + - - -
185 TT 4.5 19.7 - - - +
337M ARG* 2.9 50.0 - - - +
835M GLY 3.0 12.7 + - - +
836M TYR* 3.7 16.0 - - - +
838M GLN* 1.3 82.0 + - - +
840M ARG* 1.3 70.2 + - - +
842M VAL* 2.6 19.4 + - + +
843M LYS* 2.9 23.7 + - + +
1401M SER 3.8 17.4 + - - -
1402M PHE* 3.6 27.6 - - - +
1403M GLU* 5.3 0.2 - - - +
1132N GLU* 2.5 34.6 + - + -
1133N MET* 5.5 4.9 - - + -
1136N ASP* 5.7 3.8 - - - +
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Residues in contact with ARG 840 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836M TYR* 2.9 67.5 + - + +
837M ILE* 3.5 28.1 - - - +
839M ARG* 1.3 80.3 - - - +
841M LEU* 1.3 69.1 + - + +
842M VAL 2.7 0.3 + - - -
843M LYS* 2.9 6.0 + - - +
844M ALA* 2.9 21.4 + - - +
1102M LYS* 4.4 13.1 + - - +
1105M LEU* 4.0 17.0 - - + +
1106M ASN* 2.6 34.3 + - - +
1384M VAL* 3.4 33.5 + - + +
1385M THR* 3.9 7.0 + - - +
1389M PHE* 4.5 1.5 - - + -
1402M PHE* 4.4 18.2 - - + -
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Residues in contact with LEU 841 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837M ILE* 3.0 22.5 + - + +
838M GLN 3.3 9.6 - - - +
840M ARG* 1.3 80.1 - - - +
842M VAL* 1.3 59.9 + - - +
844M ALA* 3.4 4.0 + - - +
845M LEU* 3.1 28.0 - - + +
1069M ALA* 3.9 17.5 - - + +
1072M ILE* 4.0 17.5 - - + -
1073M GLY* 3.9 30.1 - - - +
1101M LEU* 5.7 0.9 - - + -
1105M LEU* 4.0 24.2 - - + -
1371M LEU* 3.5 36.1 - - + -
1384M VAL* 4.0 8.0 - - + +
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Residues in contact with VAL 842 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838M GLN* 3.3 35.2 - - - +
839M ARG* 2.6 15.3 + - + +
841M LEU* 1.3 67.5 - - - +
843M LYS* 1.3 59.2 + - + +
844M ALA 2.6 4.6 + - - -
845M LEU* 2.5 29.0 + - - -
846M GLU* 3.0 13.4 + - + -
1066M VAL* 4.9 13.0 - - + +
1069M ALA* 3.8 19.7 - - + -
1070M GLN* 4.7 8.3 - - + +
1135N ARG* 4.6 7.6 - - - +
1136N ASP* 3.3 36.6 - - + +
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Residues in contact with LYS 843 (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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341M MET* 2.7 37.2 - - - +
839M ARG* 2.9 26.2 + - + +
840M ARG* 3.9 7.4 - - - +
842M VAL* 1.3 78.9 - - + +
844M ALA* 1.3 58.2 + - - +
845M LEU 3.3 0.6 + - - -
846M GLU* 2.8 45.8 + - + +
847M ASP* 6.2 0.2 - - - -
1389M PHE* 3.9 13.9 - - + -
1398M MET* 5.3 5.5 - - - +
1401M SER* 2.8 35.1 + - - +
1402M PHE* 4.3 20.0 - - + -
1425M SER* 3.2 4.6 + - - -
1132N GLU* 4.3 11.2 - - - -
1135N ARG* 3.7 11.9 - - - +
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Residues in contact with ALA 844 (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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840M ARG 2.9 12.0 + - - +
841M LEU 3.5 5.6 - - - +
842M VAL 2.6 5.9 + - - -
843M LYS* 1.3 73.7 - - - +
845M LEU* 1.3 73.9 + - + +
847M ASP* 4.7 3.4 - - - +
848M ILE* 4.7 0.9 - - - +
1374M VAL* 4.1 10.2 - - + +
1384M VAL* 3.9 13.0 - - + -
1389M PHE* 3.3 44.2 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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