Contacts of the helix formed by residues 962 - 973 (chain B) in PDB entry 5LPN
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 962 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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960B SER* 3.4 2.9 + - - -
961B SER* 1.3 82.1 + - - +
963B PRO* 1.3 68.6 - - - +
964B GLU* 3.9 3.3 + - - +
965B GLN* 3.4 28.2 + - - +
966B GLN* 2.9 27.7 + - - +
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Residues in contact with PRO 963 (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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70A ARG* 3.3 41.2 - - - +
71A PHE* 5.0 2.6 - - - -
961B SER 3.3 6.7 - - - +
962B SER* 1.3 88.1 - - - +
964B GLU* 1.3 58.7 + - + +
966B GLN* 3.0 22.7 - - - +
967B LYS* 3.0 22.3 + - - +
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Residues in contact with GLU 964 (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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70A ARG* 3.9 28.1 + - - +
962B SER* 3.9 3.4 + - - +
963B PRO* 1.3 79.3 - - + +
965B GLN* 1.3 60.6 + - - +
967B LYS* 2.6 42.9 + - + +
968B LYS* 2.9 49.5 + - - +
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Residues in contact with GLN 965 (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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960B SER* 3.3 25.3 - - - +
962B SER* 3.3 30.0 + - - +
963B PRO 3.2 0.2 - - - -
964B GLU* 1.3 75.0 - - - +
966B GLN* 1.3 64.7 + - - +
968B LYS* 3.3 17.6 + - - +
969B LEU* 2.9 52.0 + - - +
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Residues in contact with GLN 966 (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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42A ILE* 4.2 29.5 - - + +
71A PHE* 5.6 1.3 - - + -
956B LEU* 3.8 15.9 - - + +
957B ARG* 4.4 26.7 + - - +
960B SER* 3.9 25.1 + - - +
961B SER* 4.8 4.6 + - - +
962B SER 2.9 16.5 + - - +
963B PRO* 3.0 22.8 + - - +
965B GLN* 1.3 75.3 - - - +
967B LYS* 1.3 54.6 + - - -
969B LEU* 3.1 7.7 + - - +
970B TRP* 2.8 30.0 + - - +
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Residues in contact with LYS 967 (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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70A ARG* 3.1 33.4 + - + +
71A PHE* 3.7 31.5 - - + -
73A THR* 6.2 2.0 - - - -
74A ILE* 4.2 22.4 - - + -
963B PRO 3.0 6.4 + - - +
964B GLU* 2.6 50.8 + - + +
966B GLN* 1.3 75.3 - - - +
968B LYS* 1.3 65.7 + - + +
970B TRP* 3.1 4.7 + - - +
971B VAL* 3.0 29.0 + - + +
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Residues in contact with LYS 968 (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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964B GLU* 2.9 41.4 + - + +
965B GLN* 3.3 20.2 + - - +
967B LYS* 1.3 76.0 - - + +
969B LEU* 1.3 58.9 + - + +
971B VAL* 3.4 8.3 + - - +
972B GLY* 2.9 23.9 + - - -
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Residues in contact with LEU 969 (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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956B LEU* 3.3 33.0 - - + +
959B GLN* 4.3 22.2 - - + +
960B SER* 3.6 26.5 - - - +
965B GLN* 2.9 31.8 + - - +
966B GLN* 3.6 5.2 - - - +
968B LYS* 1.3 76.7 - - - +
970B TRP* 1.3 59.1 + - - +
972B GLY* 2.9 16.7 + - - +
973B GLN* 3.2 13.0 + - - +
974B LEU 4.5 0.5 + - - -
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Residues in contact with TRP 970 (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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42A ILE* 3.1 36.4 + - + -
43A GLY* 3.7 11.2 - - - -
44A ILE* 3.3 49.5 + - + +
71A PHE* 5.3 1.6 - + + -
74A ILE* 4.2 21.5 - - + -
953B GLU* 6.3 2.5 - - + -
956B LEU* 4.2 12.3 - - + +
966B GLN 2.8 13.4 + - - +
967B LYS* 3.5 8.3 - - - +
969B LEU* 1.3 73.6 - - - +
971B VAL* 1.3 78.9 + - + +
974B LEU* 3.2 33.3 + - + +
975B LEU* 3.1 64.1 + - + -
978B VAL* 4.6 5.7 - - + +
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Residues in contact with VAL 971 (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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74A ILE* 3.8 27.8 - - + -
967B LYS* 3.0 16.7 + - + +
968B LYS* 3.6 10.3 - - - +
970B TRP* 1.3 86.4 - - + +
972B GLY* 1.3 65.2 + - - +
973B GLN 3.4 0.2 + - - -
975B LEU* 3.9 28.4 - - + +
976B GLN* 4.8 4.9 - - - +
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Residues in contact with GLY 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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968B LYS 2.9 14.9 + - - -
969B LEU* 2.9 9.5 + - - -
971B VAL* 1.3 79.6 - - - +
973B GLN* 1.3 58.5 + - - +
976B GLN* 4.4 12.6 - - - +
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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
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948B GLU* 4.7 7.7 + - - +
952B LEU* 3.3 34.2 - - + +
969B LEU 3.2 6.8 + - - +
972B GLY* 1.3 78.2 - - - +
974B LEU* 1.3 69.1 + - - +
975B LEU 3.1 3.5 + - - -
976B GLN* 3.5 13.0 + - - +
977B LEU* 3.5 10.8 + - + +
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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