Contacts of the helix formed by residues 944 - 958 (chain B) in PDB entry 1ONV
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 944 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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941B GLY 5.3 6.5 - - - -
943B SER* 1.3 79.9 - - - +
945B GLU* 1.3 69.2 + - - +
946B ALA 3.2 3.7 - - - +
947B ASP* 3.1 25.2 + - - +
948B GLU* 3.4 15.3 + - - +
951B LYS* 4.6 0.3 + - - -
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Residues in contact with GLU 945 (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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944B SER* 1.3 81.1 + - - +
946B ALA* 1.3 62.3 + - - +
948B GLU* 3.2 38.2 + - - +
949B MET* 3.4 9.9 + - - +
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Residues in contact with ALA 946 (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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478A GLN* 4.0 20.8 + - - +
943B SER* 4.9 12.6 - - - -
944B SER 3.2 1.6 - - - +
945B GLU* 1.3 78.9 - - - +
947B ASP* 1.3 66.7 + - - +
949B MET* 3.0 25.6 + - - +
950B ALA* 3.7 3.1 + - - +
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Residues in contact with ASP 947 (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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471A LYS* 3.4 16.6 + - - +
943B SER* 3.5 32.0 + - - +
944B SER* 3.1 11.2 + - - +
946B ALA* 1.3 80.8 - - - +
948B GLU* 1.3 60.7 + - - +
950B ALA* 3.1 12.4 + - - +
951B LYS* 3.0 34.2 + - - +
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Residues in contact with GLU 948 (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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944B SER* 3.7 15.7 + - - +
945B GLU* 3.5 33.8 - - - +
946B ALA 3.2 0.4 - - - -
947B ASP* 1.3 74.6 - - - +
949B MET* 1.3 65.2 - - - +
951B LYS* 3.0 35.3 + - + +
952B ALA* 3.3 13.0 + - - +
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Residues in contact with MET 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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474A LEU* 3.1 28.2 - - + +
478A GLN* 3.4 50.7 - - + +
479A THR* 5.3 1.3 - - + -
486A SER* 3.4 49.6 - - - +
489A THR* 4.3 6.7 - - - -
490A VAL* 3.3 19.4 - - + +
945B GLU 3.4 5.9 + - - +
946B ALA* 3.0 20.3 + - - +
948B GLU* 1.3 80.1 - - - +
950B ALA* 1.3 57.4 + - - +
952B ALA* 4.0 6.7 + - - +
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Residues in contact with ALA 950 (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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470A THR* 4.4 3.2 + - - -
471A LYS* 3.5 45.1 - - + +
474A LEU* 3.4 17.5 - - + -
478A GLN* 5.9 2.2 - - - +
946B ALA 3.7 2.4 + - - +
947B ASP* 3.1 8.8 + - - +
948B GLU 3.1 0.4 - - - -
949B MET* 1.3 76.2 - - - +
951B LYS* 1.3 65.7 + - - +
952B ALA 3.1 2.2 - - - -
953B LEU* 3.0 15.4 + - - +
954B GLU* 3.3 11.5 + - - +
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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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471A LYS* 3.9 13.7 - - - +
944B SER 4.6 0.6 + - - -
947B ASP* 3.0 43.9 + - - +
948B GLU* 3.0 26.1 + - + +
950B ALA* 1.3 77.4 - - - +
952B ALA* 1.3 56.5 + - - +
954B GLU* 3.2 13.2 + - - +
955B ALA* 2.9 30.4 + - - +
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Residues in contact with ALA 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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490A VAL* 3.7 20.6 - - + -
948B GLU 3.3 7.7 + - - +
949B MET* 4.0 6.1 - - - +
950B ALA 3.1 0.4 - - - -
951B LYS* 1.3 79.8 - - - +
953B LEU* 1.3 61.0 + - - +
955B ALA* 3.4 15.9 + - - +
956B GLU* 3.5 18.5 + - - +
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Residues in contact with LEU 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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470A THR* 3.6 37.9 - - + +
473A LEU* 4.7 4.0 - - + -
474A LEU* 4.7 11.2 - - + +
490A VAL* 3.6 18.8 - - + +
493A LEU* 3.6 9.9 - - + -
494A ALA* 3.4 31.6 - - - +
497A LEU* 3.3 38.8 - - + -
950B ALA* 3.0 13.2 + - - +
952B ALA* 1.3 80.4 - - - +
954B GLU* 1.3 60.6 + - - +
956B GLU* 3.3 19.7 + - - +
957B LEU* 3.5 9.4 + - + +
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Residues in contact with GLU 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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470A THR* 3.5 32.4 + - + +
471A LYS* 5.0 11.4 - - - +
511A MET* 2.9 40.7 - - + +
950B ALA 3.3 5.4 + - - +
951B LYS* 3.2 15.5 + - - +
953B LEU* 1.3 76.0 - - - +
955B ALA* 1.3 61.7 + - - +
957B LEU* 3.5 2.6 + - - +
958B ASN* 2.9 37.1 + - + +
961B MET* 4.9 5.3 - - + +
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Residues in contact with ALA 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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951B LYS 2.9 18.1 + - - +
952B ALA* 3.5 10.8 - - - +
953B LEU 3.2 0.4 - - - -
954B GLU* 1.3 77.5 - - - +
956B GLU* 1.3 65.5 + - + +
958B ASN* 3.3 17.2 + - - +
959B ASP* 4.2 2.4 + - - +
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Residues in contact with GLU 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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494A ALA* 3.8 25.3 - - + +
498A LYS* 2.7 58.0 + - + +
952B ALA 3.5 14.3 - - - +
953B LEU 3.5 7.0 - - - +
954B GLU 3.1 0.6 - - - -
955B ALA* 1.3 78.1 - - - +
957B LEU* 1.3 61.6 + - - +
958B ASN 3.0 5.6 + - - -
959B ASP* 3.1 7.4 + - - +
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Residues in contact with LEU 957 (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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470A THR* 4.4 9.6 - - + -
497A LEU* 2.6 63.5 - - + +
498A LYS* 3.6 0.9 - - - +
502A PRO* 3.6 15.3 - - + -
513A PHE* 3.8 36.1 - - + -
953B LEU 3.5 5.3 + - - +
954B GLU 3.5 5.7 + - - +
956B GLU* 1.3 79.3 - - - +
958B ASN* 1.3 62.6 + - - +
959B ASP 3.0 1.4 + - - -
960B LEU* 2.9 39.3 - - + +
961B MET* 3.0 24.1 + - + +
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Residues in contact with ASN 958 (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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511A MET* 5.6 1.2 - - - +
954B GLU* 2.9 25.1 + - + +
955B ALA* 3.3 15.5 + - - +
956B GLU 3.0 0.4 - - - -
957B LEU* 1.3 76.9 - - - +
959B ASP* 1.3 63.1 + - - +
961B MET* 3.4 31.4 - - - +
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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