Contacts of the helix formed by residues 952 - 966 (chain B) in PDB entry 3B7B
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 952 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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919B ASN* 3.8 23.8 - - - -
949B SER* 2.6 30.0 + - - -
950B LEU 3.1 3.0 + - - -
951B ASN* 1.3 85.4 - - - +
953B GLN* 1.3 64.4 + - - +
954B VAL* 3.4 6.4 + - - +
955B TRP* 3.0 15.1 + - - +
956B SER* 3.1 20.6 + - - -
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Residues in contact with GLN 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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919B ASN* 4.8 3.4 - - - +
921B TYR* 3.6 37.7 - - + +
952B SER* 1.3 73.1 - - - +
954B VAL* 1.3 62.2 + - + +
956B SER* 3.3 7.4 + - - -
957B ALA* 2.8 29.6 + - - +
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Residues in contact with VAL 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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916B ALA* 3.6 25.8 - - + +
919B ASN* 3.3 47.6 - - - +
920B ARG 4.2 0.4 - - - +
921B TYR* 3.9 21.5 - - + +
924B VAL* 3.5 26.0 - - + -
948B ALA* 4.1 4.5 - - + -
952B SER* 3.7 4.5 - - - +
953B GLN* 1.3 76.9 - - - +
955B TRP* 1.3 64.9 + - - +
957B ALA* 2.9 6.4 + - - +
958B LEU* 2.8 30.2 + - + +
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Residues in contact with TRP 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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945B LEU* 3.6 37.2 - - + +
948B ALA* 3.9 11.4 - - + +
949B SER 2.9 28.7 - - - +
950B LEU* 3.8 22.8 - - + +
951B ASN* 3.7 30.3 - - - -
952B SER* 3.0 8.7 + - - +
954B VAL* 1.3 81.2 - - - +
956B SER* 1.3 65.0 - - - +
959B GLN* 2.8 67.5 + - + +
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Residues in contact with SER 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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952B SER 3.1 11.4 + - - -
953B GLN* 3.5 10.1 - - - -
954B VAL 3.1 0.4 - - - -
955B TRP* 1.3 90.9 - - - +
957B ALA* 1.3 62.8 + - - +
959B GLN* 3.3 5.4 + - - +
960B MET* 3.1 24.9 + - - +
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Residues in contact with ALA 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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921B TYR* 3.8 21.3 - - + +
924B VAL* 4.4 13.9 - - + -
925B VAL* 4.8 4.3 - - + -
928B LEU* 3.9 8.0 - - + +
953B GLN 2.8 17.8 + - - +
954B VAL 3.6 3.8 - - - +
956B SER* 1.3 77.6 + - - +
958B LEU* 1.3 57.7 + - - +
960B MET* 3.7 7.2 - - - +
961B SER* 3.1 26.2 + - - -
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Residues in contact with LEU 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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912B LEU* 4.2 15.0 - - + -
916B ALA* 3.7 27.8 - - + -
924B VAL* 4.8 1.8 - - + -
928B LEU* 3.4 33.7 - - + -
934B VAL* 4.1 14.9 - - + +
944B PRO* 3.9 1.3 - - + -
945B LEU* 3.4 43.3 - - + +
948B ALA* 3.8 11.2 - - + -
954B VAL* 2.8 18.6 + - + +
957B ALA* 1.3 74.6 - - - +
959B GLN* 1.3 54.9 + - - +
961B SER* 3.1 3.6 + - - -
962B LYS* 2.7 36.9 + - - +
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Residues in contact with GLN 959 (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 LEU* 3.9 19.0 - - + +
955B TRP* 2.8 68.1 + - + +
956B SER* 3.4 9.6 - - - +
958B LEU* 1.3 74.5 - - - +
960B MET* 1.3 53.0 + - - +
962B LYS* 3.1 9.1 + - - +
963B ALA* 2.8 37.6 + - - +
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Residues in contact with MET 960 (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 SER* 3.1 13.5 + - - +
957B ALA* 3.7 7.9 - - - +
959B GLN* 1.3 79.6 - - - +
961B SER* 1.3 54.8 + - - +
963B ALA* 3.7 11.6 - - + +
964B LEU* 2.7 48.6 + - + +
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Residues in contact with SER 961 (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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928B LEU* 3.9 33.0 + - - +
934B VAL* 3.9 14.0 - - - +
957B ALA 3.1 12.3 + - - -
958B LEU* 3.1 9.5 + - - -
960B MET* 1.3 78.1 - - - +
962B LYS* 1.3 69.3 + - - +
964B LEU* 3.9 4.9 - - - +
965B GLN* 3.2 21.1 + - - +
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Residues in contact with LYS 962 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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934B VAL* 4.5 18.3 - - + +
945B LEU* 5.3 7.9 - - + -
958B LEU 2.7 17.6 + - - +
959B GLN* 3.4 15.0 - - - +
961B SER* 1.3 74.2 - - - +
963B ALA* 1.3 62.5 + - - +
965B GLN* 3.1 8.0 - - - +
966B ASP* 3.1 20.4 + - - +
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Residues in contact with ALA 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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959B GLN* 2.8 21.0 + - - +
960B MET* 3.7 14.1 - - + +
962B LYS* 1.3 68.6 - - - +
964B LEU* 1.3 55.1 + - - +
965B GLN 2.6 18.1 + - - -
966B ASP* 2.8 19.9 + - - +
967B SER* 3.4 12.5 + - - -
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Residues in contact with LEU 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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960B MET* 2.7 33.0 + - + +
961B SER* 3.9 5.6 - - - +
963B ALA* 1.3 70.7 - - - +
965B GLN* 1.3 57.3 + - - +
967B SER* 3.5 19.6 - - - +
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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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934B VAL* 6.1 2.9 - - + -
961B SER 3.2 10.5 + - - +
962B LYS* 3.1 12.8 + - - +
963B ALA 2.6 4.9 + - - -
964B LEU* 1.3 75.0 - - - +
966B ASP* 1.3 52.7 + - - +
967B SER* 2.6 21.4 + - - -
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Residues in contact with ASP 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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962B LYS 3.1 8.6 + - - +
963B ALA* 2.8 13.6 + - - +
965B GLN* 1.3 71.0 - - - +
967B SER* 1.3 60.3 + - - +
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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