Contacts of the helix formed by residues 971 - 986 (chain B) in PDB entry 5JP2
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 ASN 971 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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952B LYS 4.9 2.9 + - - +
953B LEU 2.8 24.9 + - - +
954B LEU 4.8 0.2 - - - +
955B TYR* 2.5 42.1 + - + -
969B TRP 3.9 0.4 + - - -
970B PHE* 1.3 70.0 - - - +
972B MET* 1.3 58.7 + - - +
973B GLN* 3.3 15.0 + - - +
974B ALA* 2.9 36.8 + - + +
975B LEU* 2.8 29.9 + - - +
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Residues in contact with MET 972 (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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925B PHE* 3.7 36.3 - - + -
929B PRO 4.9 4.9 - - - +
931B ALA* 4.0 15.9 - - + +
932B PRO 3.6 21.1 - - - +
933B VAL* 3.9 17.3 - - + -
934B LEU* 3.5 25.4 - - + +
970B PHE* 3.5 21.7 + - - +
971B ASN* 1.3 73.6 + - - +
973B GLN* 1.3 65.3 + - - +
975B LEU* 3.8 13.0 - - + +
976B THR* 2.5 40.3 + - - +
1132B TYR* 3.7 3.4 - - - +
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Residues in contact with GLN 973 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929B PRO* 3.2 32.9 + - + +
930B ASN* 5.3 3.6 + - - +
971B ASN* 3.3 9.8 - - - +
972B MET* 1.3 87.0 + - - +
974B ALA* 1.3 60.5 + - - +
976B THR* 3.5 6.7 - - - -
977B LEU* 3.2 29.3 + - + +
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Residues in contact with ALA 974 (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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952B LYS 4.0 11.7 - - - +
953B LEU* 3.9 16.7 - - + +
971B ASN* 2.9 26.1 + - + +
973B GLN* 1.3 75.2 - - - +
975B LEU* 1.3 59.2 + - - +
977B LEU* 3.2 9.9 + - - +
978B HIS* 2.8 31.5 + - - +
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Residues in contact with LEU 975 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917B PHE* 4.0 22.7 - - + -
925B PHE* 3.9 23.8 - - + -
934B LEU* 4.7 1.8 - - + -
953B LEU* 3.9 14.0 - - + +
970B PHE* 3.8 39.0 - - + -
971B ASN 2.8 22.0 + - - +
972B MET* 3.8 20.4 - - + +
974B ALA* 1.3 72.2 - - - +
976B THR* 1.3 58.0 + - - +
978B HIS* 3.2 1.6 + - + +
979B LEU* 2.9 55.6 + - + +
994B VAL* 4.6 7.4 - - + -
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Residues in contact with THR 976 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925B PHE* 3.7 48.7 + - + +
926B THR* 3.9 1.3 - - - +
928B ASN 5.5 0.5 + - - -
929B PRO* 5.8 2.5 - - + +
972B MET* 2.5 24.9 + - - +
973B GLN* 3.5 8.3 - - - -
975B LEU* 1.3 77.1 - - - +
977B LEU* 1.3 60.0 + - + +
979B LEU* 3.2 4.9 + - - +
980B GLN* 2.8 56.4 + - + +
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Residues in contact with LEU 977 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973B GLN* 3.2 15.2 + - + +
974B ALA* 3.2 10.6 + - - +
976B THR* 1.3 79.9 - - + +
978B HIS* 1.3 63.5 + - - +
980B GLN* 3.3 23.5 + - - +
981B ARG* 3.0 24.6 + - - +
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Residues in contact with HIS 978 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950B ASN* 6.0 1.8 - - - -
953B LEU* 4.0 26.8 - - + +
974B ALA 2.8 17.6 + - - +
975B LEU* 3.6 4.9 - - + +
977B LEU* 1.3 77.6 - - - +
979B LEU* 1.3 64.3 + - + +
981B ARG* 3.3 18.0 + - - +
982B GLU* 3.1 48.6 + - + +
993B ASN 4.6 3.2 + - - -
994B VAL* 3.9 32.1 - - + +
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Residues in contact with LEU 979 (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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917B PHE* 4.0 35.2 - - + -
921B ILE* 4.5 7.2 - - + -
922B THR* 4.2 17.9 - - + +
925B PHE* 3.6 35.7 - - + -
975B LEU* 2.9 29.9 + - + +
976B THR* 3.8 2.2 - - - +
978B HIS* 1.3 76.3 - - + +
980B GLN* 1.3 66.3 + - - +
982B GLU* 3.1 6.2 + - + +
983B ALA* 2.9 24.3 + - - +
992B TYR* 4.2 18.9 - - + -
994B VAL* 4.1 16.2 - - + -
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Residues in contact with GLN 980 (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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922B THR* 5.1 6.3 - - - +
926B THR* 3.0 41.9 + - - +
976B THR* 2.8 43.0 + - + +
977B LEU* 3.3 23.1 + - - +
979B LEU* 1.3 73.0 - - - +
981B ARG* 1.3 61.9 + - - +
983B ALA* 3.5 5.8 + - - +
984B GLU* 3.0 38.3 + - - +
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Residues in contact with ARG 981 (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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977B LEU 3.0 13.6 + - - +
978B HIS* 3.6 20.0 + - - +
979B LEU 3.1 0.2 - - - -
980B GLN* 1.3 74.1 - - - +
982B GLU* 1.3 83.2 + - - +
984B GLU* 3.1 13.9 + - + +
985B LEU* 2.9 53.1 + - + +
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Residues in contact with GLU 982 (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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978B HIS* 3.1 43.9 + - + +
979B LEU* 3.6 8.5 - - + +
981B ARG* 1.3 87.7 + - + +
983B ALA* 1.3 64.2 + - - +
985B LEU* 3.3 14.4 + - - +
986B ASN* 3.1 18.5 + - - +
992B TYR* 3.9 32.4 - - + -
993B ASN 4.9 9.9 - - - +
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Residues in contact with ALA 983 (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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922B THR* 4.8 9.0 - - + +
979B LEU 2.9 15.6 + - - +
980B GLN* 3.7 7.0 - - - +
982B GLU* 1.3 76.1 - - - +
984B GLU* 1.3 63.0 + - - +
986B ASN 3.0 1.0 + - - -
987B PRO* 2.8 31.0 - - + +
992B TYR* 3.3 33.1 - - + +
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Residues in contact with GLU 984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980B GLN* 3.0 30.5 + - - +
981B ARG* 3.4 12.7 - - - +
983B ALA* 1.3 77.5 - - + +
985B LEU* 1.3 65.5 + - + +
987B PRO* 3.9 10.1 - - - +
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Residues in contact with LEU 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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981B ARG* 2.9 58.8 + - + +
982B GLU* 3.7 15.9 - - - +
984B GLU* 1.3 83.0 - - + +
986B ASN* 1.3 60.2 + - + +
987B PRO* 3.7 4.1 - - - +
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Residues in contact with ASN 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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982B GLU 3.1 9.3 + - - +
983B ALA 3.0 3.4 + - - +
985B LEU* 1.3 79.4 - - + +
987B PRO* 1.3 64.8 - - - +
988B GLN* 3.1 9.9 + - - +
989B ALA* 3.3 33.0 + - + +
992B TYR* 3.3 16.8 + - + -
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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