Contacts of the helix formed by residues 983 - 990 (chain B) in PDB entry 5JPM
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 983 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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981B THR* 3.2 1.3 + - - -
982B ALA* 1.3 77.5 + - - +
984B ASP* 1.3 64.8 + - - +
985B PRO* 3.3 7.9 - - - -
986B LEU* 3.4 17.4 + - - +
987B ASP* 3.1 39.7 + - - +
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Residues in contact with ASP 984 (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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981B THR* 3.6 32.3 - - - +
982B ALA* 3.6 5.6 + - - +
983B SER* 1.3 73.7 - - - +
985B PRO* 1.3 69.7 - - + +
987B ASP* 3.4 3.3 + - - +
988B THR* 2.8 31.4 + - - +
1290B THR* 3.5 34.4 - - + +
1316B TRP* 4.3 7.2 - - + +
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Residues in contact with PRO 985 (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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982B ALA 5.6 0.2 - - - +
983B SER* 3.5 5.2 - - - -
984B ASP* 1.3 93.6 - - + +
986B LEU* 1.3 66.6 + - + +
988B THR* 3.2 1.6 + - - -
989B LEU* 3.0 29.3 + - - +
1027B TYR* 3.4 30.5 - - + +
1316B TRP* 3.6 48.7 - - + +
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Residues in contact with LEU 986 (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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983B SER* 3.4 20.1 + - - +
985B PRO* 1.3 84.7 - - + +
987B ASP* 1.3 62.9 + - - +
989B LEU 5.2 0.4 - - - -
990B GLY* 2.8 33.7 + - - +
992B GLU* 5.3 0.9 + - - +
993B GLY 5.2 0.2 + - - -
1027B TYR* 4.0 15.7 - - + +
1028B LEU* 5.9 3.4 - - + -
1033B GLN* 3.3 31.9 - - + +
1036B THR* 4.7 17.7 - - + -
1037B LEU* 5.1 13.1 - - + +
1320B HIS* 6.2 0.4 - - + -
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Residues in contact with ASP 987 (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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981B THR* 2.3 40.0 + - + +
983B SER* 3.1 26.6 + - - +
984B ASP* 4.0 4.3 - - - +
986B LEU* 1.3 80.2 - - - +
988B THR* 1.3 61.1 + - - +
990B GLY 4.5 0.2 - - - -
992B GLU* 3.8 14.3 - - + +
993B GLY* 3.6 14.9 + - - -
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Residues in contact with THR 988 (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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984B ASP* 2.8 20.4 + - - +
985B PRO 3.8 2.7 - - - -
987B ASP* 1.3 80.4 - - - +
989B LEU* 1.3 59.5 + - + +
990B GLY 3.7 0.4 - - - -
993B GLY* 3.3 3.2 - - - -
994B ALA* 2.8 23.4 + - - +
1297B GLY* 5.0 11.7 - - - +
1299B PHE* 6.0 1.3 - - + -
1309B LEU* 3.7 29.5 - - + +
1312B LEU* 5.8 0.7 - - + -
1316B TRP* 3.8 19.8 - - + -
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Residues in contact with LEU 989 (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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985B PRO 3.0 12.4 + - - +
986B LEU* 5.2 0.4 - - - -
988B THR* 1.3 90.3 - - + +
990B GLY* 1.3 64.7 + - - +
994B ALA* 3.8 12.3 - - + +
995B LEU* 3.4 23.4 + - - +
1020B PRO 4.8 2.0 - - - +
1023B ALA* 4.3 4.3 - - + +
1024B ALA* 3.8 31.2 - - + +
1027B TYR* 3.8 36.8 - - + -
1028B LEU* 4.6 5.9 - - + +
1309B LEU* 4.5 18.2 - - + +
1313B SER* 4.3 6.3 - - - -
1316B TRP* 3.8 27.4 - - + -
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Residues in contact with GLY 990 (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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986B LEU* 2.8 23.1 + - - +
988B THR 3.7 1.8 - - - -
989B LEU* 1.3 76.1 - - - +
991B SER* 1.3 66.7 + - - -
992B GLU 3.2 2.9 - - - -
993B GLY 3.0 9.3 + - - +
995B LEU* 3.2 23.3 + - - +
1028B LEU* 5.5 1.3 - - - -
1037B LEU* 3.9 20.4 - - - -
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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