Contacts of the helix formed by residues 948 - 956 (chain B) in PDB entry 5MJ6
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 948 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907B TYR* 5.7 1.4 + - - -
914B LEU* 3.8 28.6 - - + +
944B PHE* 3.0 56.1 + - + +
945B VAL 3.8 2.0 - - - -
947B GLU* 1.3 88.1 - - - +
949B TRP* 1.3 64.2 + - - +
950B ASN 3.3 2.7 - - - -
951B LYS* 3.1 11.2 + - + +
952B LEU* 2.9 28.5 + - + +
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Residues in contact with TRP 949 (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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945B VAL* 3.2 34.2 + - + +
946B LYS 3.6 9.9 - - - +
947B GLU 3.4 3.0 + - - -
948B ASN* 1.3 77.7 - - - +
950B ASN* 1.3 76.0 + - - +
952B LEU* 3.2 9.7 + - + +
953B VAL* 3.0 48.9 + - + +
958B LEU* 3.9 16.4 - - + +
963B ILE* 3.8 22.0 - - + -
966B ILE* 5.6 1.1 - - + -
967B VAL* 3.6 28.5 - - + -
986B PHE* 3.7 18.2 - + + -
987B PHE* 3.6 26.7 - + - -
990B GLN* 3.7 33.5 - - - +
994B THR* 4.3 8.4 + - + +
997B LEU* 6.0 0.4 - - + -
1000B VAL* 5.9 1.1 - - + -
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Residues in contact with ASN 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947B GLU 5.3 0.2 + - - -
948B ASN 3.3 0.6 - - - -
949B TRP* 1.3 92.8 - - - +
951B LYS* 1.3 62.5 + - - +
953B VAL* 3.3 6.6 + - - +
954B GLN* 3.0 22.2 + - - +
990B GLN* 4.3 9.7 + - - +
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Residues in contact with LYS 951 (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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914B LEU* 4.3 29.4 - - + +
915B ASN* 5.9 2.9 - - - -
948B ASN* 3.1 14.2 + - + +
950B ASN* 1.3 78.8 - - - +
952B LEU* 1.3 61.2 + - - +
954B GLN* 3.2 38.5 + - - +
955B LYS* 3.2 24.5 + - + +
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Residues in contact with LEU 952 (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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914B LEU* 3.8 11.2 - - + -
924B LEU* 3.5 32.5 - - + -
928B ILE* 5.0 2.7 - - + -
944B PHE* 4.8 4.5 - - + +
945B VAL* 3.9 38.1 - - + +
948B ASN* 2.9 25.5 + - + +
949B TRP* 3.5 10.5 - - + +
951B LYS* 1.3 76.8 - - - +
953B VAL* 1.3 51.5 + - + +
955B LYS* 3.0 5.9 + - - -
956B PHE* 2.8 44.8 + - + +
963B ILE* 4.3 13.2 - - + -
966B ILE* 4.5 22.0 - - + -
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Residues in contact with VAL 953 (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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949B TRP* 3.0 53.4 + - + +
950B ASN* 3.3 7.8 + - - +
952B LEU* 1.3 75.5 - - - +
954B GLN* 1.3 61.6 + - - +
956B PHE 3.1 20.3 - - - +
957B PRO* 3.6 4.4 - - + +
958B LEU* 4.0 34.8 - - + +
963B ILE* 4.5 6.7 - - + -
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Residues in contact with GLN 954 (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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270B SER* 4.9 6.6 - - - -
950B ASN 3.0 13.5 + - - +
951B LYS* 3.3 39.1 + - + +
952B LEU 3.1 0.2 - - - -
953B VAL* 1.3 80.5 - - - +
955B LYS* 1.3 63.3 + - + +
956B PHE* 4.7 0.3 - - - -
957B PRO* 5.1 1.4 - - - +
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Residues in contact with LYS 955 (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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269B SER 5.0 9.1 + - - -
270B SER* 4.3 23.9 - - - +
271B TYR* 5.0 11.0 + - + +
272B TYR* 5.8 1.9 - - - +
914B LEU* 3.6 33.0 + - + -
915B ASN 5.9 1.0 - - - -
916B GLY 5.9 0.2 - - - +
921B THR* 3.7 31.9 + - + +
951B LYS* 3.2 21.6 + - + +
952B LEU* 3.0 8.3 + - - +
954B GLN* 1.3 82.1 - - + +
956B PHE* 1.3 83.5 + - + +
957B PRO* 4.2 4.5 - - - +
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Residues in contact with PHE 956 (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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271B TYR* 4.3 9.4 - + + -
426B GLU* 3.5 32.3 - - + -
921B THR* 3.9 34.3 - - + -
924B LEU* 4.8 4.9 - - + -
952B LEU* 2.8 34.2 + - + -
953B VAL* 3.1 15.3 - - - +
955B LYS* 1.3 91.1 - - + +
957B PRO* 1.3 71.7 - - + +
960B SER* 3.6 14.6 - - - +
962B THR* 3.8 31.2 - - + -
963B ILE* 3.2 25.0 - - + +
966B ILE* 4.7 5.6 - - + -
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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