Contacts of the helix formed by residues 941 - 955 (chain B) in PDB entry 3BBT
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 LYS 941 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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810B GLU* 4.1 19.8 + - - +
875B GLN* 3.7 28.2 + - - +
937B ASP 5.8 3.4 - - - -
939B ARG 5.0 2.0 - - - +
940B PRO* 1.3 76.1 - - - +
942B PHE* 1.3 61.4 + - - +
943B LYS* 3.1 18.6 - - + +
944B GLU* 2.9 42.7 + - + +
945B LEU* 3.1 14.0 + - - +
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Residues in contact with PHE 942 (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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803B ALA* 3.9 14.2 - - + +
806B MET* 3.5 58.8 - - + -
807B MET* 3.5 23.2 - - + +
810B GLU* 3.6 26.7 + - + +
874B HIS* 3.6 22.2 - - + -
875B GLN* 5.5 0.2 - - - -
877B ASP* 3.7 17.7 - - + -
878B VAL* 3.7 12.1 - - + -
881B TYR* 3.8 22.9 - + + -
940B PRO 4.3 0.4 + - - -
941B LYS* 1.3 72.8 - - - +
943B LYS* 1.3 60.1 + - - +
944B GLU 3.4 0.2 - - - -
945B LEU* 3.7 18.2 - - + -
946B ALA* 3.3 23.9 + - - +
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Residues in contact with LYS 943 (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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807B MET* 3.8 29.3 - - + +
810B GLU* 5.5 11.9 - - - +
941B LYS* 3.1 15.2 - - + -
942B PHE* 1.3 78.1 - - - +
944B GLU* 1.3 64.2 + - + +
946B ALA* 3.9 2.1 - - - +
947B ALA* 3.1 24.7 + - - +
954D ARG* 5.4 19.7 - - + +
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Residues in contact with GLU 944 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939B ARG 4.9 1.2 - - - +
940B PRO* 3.9 17.4 - - + +
941B LYS* 2.9 42.5 + - + +
943B LYS* 1.3 79.2 - - + +
945B LEU* 1.3 56.7 + - - +
947B ALA* 3.4 6.5 + - - +
948B GLU* 3.0 30.6 + - - +
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Residues in contact with LEU 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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803B ALA* 4.4 4.5 - - + -
878B VAL* 4.0 18.2 - - + -
881B TYR* 3.7 31.2 - - + +
927B VAL* 3.8 27.6 - - + -
931B CYS* 3.8 17.5 - - - -
940B PRO* 3.9 14.8 - - + +
941B LYS 3.1 16.6 + - - +
942B PHE* 3.7 30.7 - - + +
944B GLU* 1.3 72.4 - - - +
946B ALA* 1.3 65.4 + - - +
948B GLU* 3.2 5.2 + - - +
949B PHE* 3.0 33.1 + - + -
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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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800B VAL* 4.2 16.9 - - + +
803B ALA* 3.8 18.2 - - + +
804B LYS* 4.5 10.5 - - + -
807B MET* 4.1 14.6 - - - -
942B PHE 3.3 17.3 + - - +
943B LYS 3.9 3.4 - - - +
945B LEU* 1.3 78.1 - - - +
947B ALA* 1.3 56.0 + - - +
949B PHE* 4.1 0.2 - - - -
950B SER* 2.9 36.4 + - - +
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Residues in contact with ALA 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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943B LYS 3.1 16.0 + - - +
944B GLU* 3.6 7.2 - - - +
946B ALA* 1.3 77.3 - - - +
948B GLU* 1.3 56.8 + - - +
950B SER* 3.7 6.9 - - - -
951B ARG* 3.2 26.5 + - - +
954B ARG* 5.3 0.2 + - - -
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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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927B VAL* 4.0 28.0 - - + -
944B GLU 3.0 18.0 + - - +
945B LEU* 3.2 6.9 + - - +
947B ALA* 1.3 76.6 - - - +
949B PHE* 1.3 63.7 + - + +
951B ARG* 2.7 48.4 + - - +
952B MET* 3.0 47.6 + - + +
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Residues in contact with PHE 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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796B LEU* 3.7 24.1 - - + +
799B CYS* 3.7 21.5 - - + -
800B VAL* 3.5 19.6 - - + +
881B TYR* 3.5 33.2 - + - -
885B ILE* 3.7 17.7 - - + -
889B MET* 4.6 4.5 - - + -
924B VAL* 4.0 24.2 - - + -
927B VAL* 3.7 33.4 - - + -
928B MET* 6.1 0.4 - - + -
945B LEU* 3.0 29.5 + - + +
948B GLU* 1.3 72.9 - - + +
950B SER* 1.3 56.8 + - - +
952B MET* 3.6 12.6 - - - +
953B ALA* 2.8 33.1 + - - +
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Residues in contact with SER 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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800B VAL* 3.3 23.1 - - - +
804B LYS* 4.5 6.1 + - - -
946B ALA* 2.9 20.4 + - - +
947B ALA* 3.7 8.3 - - - -
949B PHE* 1.3 77.2 - - - +
951B ARG* 1.3 61.2 + - - +
953B ALA* 3.2 15.4 + - - +
954B ARG* 3.5 22.8 + - - +
804D LYS* 5.2 2.9 + - - -
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Residues in contact with ARG 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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947B ALA 3.2 15.4 + - - +
948B GLU* 2.7 35.9 + - - +
950B SER* 1.3 78.6 - - - +
952B MET* 1.3 63.4 + - - +
954B ARG* 3.4 37.9 - - - +
955B ASP* 4.4 2.3 + - - +
959B TYR* 3.8 30.5 + - - -
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Residues in contact with MET 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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796B LEU* 3.4 18.5 - - + +
923B ASP* 4.2 9.2 - - + +
924B VAL* 3.3 41.7 - - + +
927B VAL* 4.5 3.4 - - + -
948B GLU* 3.0 45.4 + - + +
949B PHE* 3.7 18.8 - - - +
951B ARG* 1.3 77.2 - - - +
953B ALA* 1.3 61.7 + - - +
954B ARG 3.2 2.2 - - - -
955B ASP 3.2 23.5 - - - +
959B TYR* 3.6 46.8 - - + -
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Residues in contact with ALA 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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793B GLN* 3.1 31.1 + - - +
796B LEU* 4.4 11.4 - - + -
797B ASN* 3.6 22.7 - - - +
800B VAL* 4.6 4.7 - - + -
949B PHE 2.8 18.4 + - - +
950B SER* 3.2 11.4 + - - +
952B MET* 1.3 74.8 - - - +
954B ARG* 1.3 63.8 + - - +
955B ASP 3.4 0.2 - - - -
956B PRO* 3.8 2.9 - - - +
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Residues in contact with ARG 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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793B GLN* 5.0 0.5 - - - +
947B ALA 5.3 0.2 + - - -
950B SER* 3.5 14.3 + - - +
951B ARG* 3.4 43.1 - - - +
952B MET 3.2 0.2 - - - -
953B ALA* 1.3 80.2 - - - +
955B ASP* 1.3 58.7 + - + +
956B PRO* 3.4 7.1 - - - +
807D MET* 6.2 2.3 - - - +
811D GLU* 5.7 1.0 - - - +
943D LYS* 5.3 19.0 + - - +
947D ALA* 5.6 7.9 - - - +
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Residues in contact with ASP 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 ARG 4.4 2.1 + - - +
952B MET 3.2 10.6 + - - +
954B ARG* 1.3 78.9 - - + +
956B PRO* 1.3 65.5 - - - +
957B GLN* 4.4 7.1 + - - +
958B ARG* 3.3 45.6 + - + +
959B TYR* 3.4 11.9 - - + -
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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