Contacts of the helix formed by residues 920 - 929 (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 ARG 920 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B SO4 3.6 22.6 + - - +
2B SO4 2.8 44.1 + - - -
853B LYS* 4.9 0.8 - - - +
883B ALA 3.3 19.5 - - - +
884B PHE* 3.3 23.2 + - - -
885B SER* 3.4 17.8 + - - +
886B GLY* 3.5 14.8 - - - -
915B ALA* 3.1 15.4 + - + +
918B GLU* 3.2 26.0 + - + +
919B ASN* 1.3 73.2 + - - +
921B TYR* 1.3 66.3 + - - +
922B ASP 3.4 2.2 - - - -
923B CYS* 2.7 27.2 + - + -
924B VAL* 3.1 13.1 + - - +
954B VAL* 4.2 0.6 - - - +
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Residues in contact with TYR 921 (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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1B SO4 2.9 17.6 + - - +
919B ASN* 3.3 4.5 + - - +
920B ARG* 1.3 72.1 - - - +
922B ASP* 1.3 76.5 + - - +
923B CYS 2.8 0.7 + - - -
924B VAL* 3.0 4.1 + - + +
925B VAL* 2.8 49.9 + - + +
953B GLN* 3.6 60.6 - - + +
954B VAL* 3.9 14.6 - - + +
957B ALA* 3.8 12.2 - - + +
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Residues in contact with ASP 922 (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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1B SO4 3.4 23.8 + - - +
886B GLY 5.5 0.9 - - - +
888B VAL* 3.4 26.4 - - + +
920B ARG 3.2 0.8 + - - -
921B TYR* 1.3 88.8 - - - +
923B CYS* 1.3 57.6 + - - +
925B VAL* 3.4 6.4 + - - +
926B LEU* 2.9 28.8 + - - +
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Residues in contact with CYS 923 (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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882B ALA 4.2 8.7 - - - -
883B ALA* 4.4 7.2 - - - -
886B GLY* 3.9 27.8 - - - -
887B CYS 4.5 0.7 - - - -
888B VAL* 3.4 25.4 - - - +
891B ALA* 4.6 9.0 - - - -
915B ALA* 3.9 11.0 - - + -
920B ARG* 2.7 23.9 + - + +
922B ASP* 1.3 71.4 - - - +
924B VAL* 1.3 66.7 + - - +
925B VAL 3.0 1.3 - - - -
926B LEU* 3.0 4.8 + - - +
927B PHE* 2.7 35.1 + - + -
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Residues in contact with VAL 924 (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* 3.9 20.0 - - + -
915B ALA* 3.7 19.7 - - + +
916B ALA* 3.7 7.6 - - + +
920B ARG 3.1 14.8 + - - +
921B TYR* 3.0 10.9 + - - +
923B CYS* 1.3 73.9 - - - +
925B VAL* 1.3 65.8 + - + +
927B PHE* 4.3 0.4 - - - -
928B LEU* 2.7 51.9 + - + +
954B VAL* 3.5 33.7 - - + +
957B ALA* 4.4 10.3 - - + -
958B LEU* 4.8 2.0 - - + -
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Residues in contact with VAL 925 (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* 2.8 60.1 + - + +
922B ASP* 3.5 9.4 - - - +
924B VAL* 1.3 83.9 - - + +
926B LEU* 1.3 56.9 + - - +
928B LEU* 4.1 5.5 - - - +
929B SER* 2.9 38.1 + - - -
957B ALA* 4.8 4.3 - - + -
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Residues in contact with LEU 926 (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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888B VAL* 4.1 16.2 - - + +
891B ALA* 3.8 28.5 - - + -
892B GLU* 3.9 24.2 - - + +
895B LEU* 4.2 13.7 - - + -
922B ASP 2.9 16.9 + - - +
923B CYS* 3.0 4.5 + - - +
925B VAL* 1.3 75.6 - - - +
927B PHE* 1.3 68.3 + - + +
929B SER* 2.8 21.4 + - - +
930B ARG* 3.1 47.6 - - - +
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Residues in contact with PHE 927 (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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879B LEU* 4.0 23.1 - - + -
883B ALA* 3.8 18.6 - - + -
891B ALA* 4.4 8.3 - - + -
895B LEU* 4.1 11.9 - - + -
901B LEU* 3.5 20.6 - - + -
911B PRO* 3.5 27.8 - - + -
912B LEU* 3.7 28.9 - - + -
915B ALA* 4.2 7.4 - - + -
923B CYS* 2.7 30.4 + - + +
924B VAL 3.6 2.7 - - - +
926B LEU* 1.3 85.5 - - + +
928B LEU* 1.3 56.7 + - - +
930B ARG* 2.9 18.9 + - - +
931B ASP 3.0 9.9 + - - -
932B SER* 3.0 25.6 + - - +
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Residues in contact with LEU 928 (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* 3.4 33.4 - - + -
924B VAL* 2.7 33.7 + - + +
925B VAL* 4.1 3.6 - - - +
927B PHE* 1.3 66.3 - - - +
929B SER* 1.3 58.0 + - - +
930B ARG 2.8 9.7 + - - -
931B ASP* 3.1 12.5 + - - +
932B SER 4.3 5.4 - - - +
934B VAL* 4.0 10.5 - - + -
957B ALA* 3.9 21.5 - - + +
958B LEU* 3.4 26.5 - - + -
961B SER* 3.9 23.6 + - - +
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Residues in contact with SER 929 (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 VAL* 2.9 21.2 + - - +
926B LEU* 2.8 27.9 + - - +
928B LEU* 1.3 76.4 - - - +
930B ARG* 1.3 64.4 + - - +
931B ASP 3.6 0.4 - - - -
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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