Contacts of the helix formed by residues 935 - 950 (chain E) in PDB entry 2BT4
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 VAL 935 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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820E LEU* 4.5 3.1 - - + -
828E TYR 4.7 8.7 - - - +
829E GLY* 6.2 0.7 - - - -
831E ASP* 3.3 32.3 - - + +
836E VAL* 3.3 33.2 - - + -
839E LEU* 4.1 22.4 - - + +
907E ILE* 4.1 17.8 - - + +
934E GLY* 1.3 72.1 - - - -
936E GLN* 1.3 63.5 + - - +
937E GLY 3.1 0.2 - - - -
938E TYR* 3.1 28.1 + - + +
939E VAL 3.9 1.4 + - - -
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Residues in contact with GLN 936 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839E LEU* 5.1 1.3 - - - -
933E CYS 3.3 9.9 - - - +
934E GLY 3.1 0.6 - - - -
935E VAL* 1.3 81.7 - - - +
937E GLY* 1.3 57.0 + - - +
939E VAL* 2.9 33.6 + - + +
940E PHE* 3.0 39.5 + - + -
2343L GLU* 3.5 22.2 + - - +
2344L ARG* 2.9 36.0 + - - +
2347L ALA* 3.4 16.5 - - - +
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Residues in contact with GLY 937 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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905E VAL* 3.6 18.8 - - - +
906E HIS 5.8 0.4 - - - -
930E VAL* 3.8 25.4 - - - +
933E CYS* 3.4 6.9 + - - +
934E GLY 3.1 11.0 + - - -
935E VAL 3.1 2.4 - - - -
936E GLN* 1.3 78.6 - - - +
938E TYR* 1.3 59.8 + - - +
940E PHE* 3.3 8.2 + - - +
941E GLY 3.0 17.8 + - - -
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Residues in contact with TYR 938 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811E ILE* 4.2 14.6 - - + -
813E ASN* 2.6 31.4 + - - -
817E LEU* 4.1 3.5 - - - +
833E LEU* 4.5 4.5 - - + +
836E VAL* 3.8 28.3 - - + -
839E LEU* 5.9 0.9 - - + -
840E CYS* 3.8 21.7 - - - -
877E VAL* 4.6 11.9 - - + +
879E ASN* 3.1 31.3 + - + -
905E VAL* 4.2 17.9 - - + -
907E ILE* 3.9 28.5 - - + +
935E VAL* 3.1 24.2 + - - +
937E GLY* 1.3 76.5 - - - +
939E VAL* 1.3 58.9 + - + +
941E GLY* 3.2 2.1 + - - -
942E VAL* 2.9 32.9 + - - +
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Residues in contact with VAL 939 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839E LEU* 3.9 39.7 - - + +
840E CYS* 5.6 1.1 - - - -
843E ALA* 4.0 27.8 - - + -
936E GLN* 2.9 24.7 + - + +
938E TYR* 1.3 73.9 - - + +
940E PHE* 1.3 61.9 + - + +
942E VAL* 3.2 2.5 + - - +
943E GLU* 2.8 53.6 + - - +
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Residues in contact with PHE 940 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930E VAL* 4.3 11.9 - - + -
933E CYS* 4.0 31.0 - - + -
936E GLN* 3.0 43.4 + - + -
937E GLY* 3.6 13.5 - - - +
938E TYR 3.2 0.2 - - - -
939E VAL* 1.3 81.5 - - + +
941E GLY* 1.3 58.4 + - - +
943E GLU* 3.4 17.7 + - - -
944E ARG* 2.9 25.1 + - - +
2330L VAL* 5.2 0.9 - - + -
2340L PHE* 3.4 58.9 - + + -
2343L GLU* 3.2 25.1 - - + -
2344L ARG* 3.9 7.6 - - + -
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Residues in contact with GLY 941 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877E VAL* 3.7 14.8 - - - -
903E VAL* 3.9 26.9 - - - +
905E VAL* 4.8 0.2 - - - -
930E VAL* 5.1 0.2 - - - +
937E GLY 3.0 14.4 + - - -
938E TYR 3.2 4.4 + - - -
940E PHE* 1.3 76.0 - - - +
942E VAL* 1.3 61.8 + - - +
944E ARG* 3.2 3.1 + - - +
945E ILE* 3.0 28.8 + - - +
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Residues in contact with VAL 942 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804E LEU* 5.7 0.4 - - + -
809E ILE* 4.0 18.0 - - + +
811E ILE* 4.0 27.1 - - + -
840E CYS* 4.5 13.0 - - + +
843E ALA* 3.8 13.7 - - + +
844E ALA* 3.6 32.8 - - - +
847E HIS* 5.0 3.1 - - + -
851E VAL* 5.0 0.7 - - + -
877E VAL* 4.4 7.6 - - + -
938E TYR 2.9 18.4 + - - +
939E VAL 3.6 5.8 - - - +
941E GLY* 1.3 75.0 - - - +
943E GLU* 1.3 65.8 + - - +
945E ILE* 3.4 3.0 + - - +
946E ALA* 3.0 23.1 + - + +
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Residues in contact with GLU 943 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843E ALA* 5.6 1.5 - - + +
847E HIS* 3.9 28.3 + - + +
939E VAL* 2.8 41.3 + - + +
940E PHE* 3.5 9.6 - - - +
942E VAL* 1.3 76.5 - - + +
944E ARG* 1.3 62.1 + - - +
946E ALA* 3.5 7.4 + - - +
947E ALA 3.1 16.3 + - - -
2336L GLN* 3.4 14.3 + - - +
2340L PHE* 3.4 18.9 - - + -
2343L GLU* 2.6 36.8 - - - +
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Residues in contact with ARG 944 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903E VAL* 3.8 21.8 - - + -
927E ASP* 6.2 1.2 - - + +
928E GLY* 6.0 1.1 - - - +
940E PHE 2.9 17.5 + - - +
941E GLY 3.2 4.2 + - - +
943E GLU* 1.3 76.9 - - - +
945E ILE* 1.3 64.5 + - - +
947E ALA* 3.0 9.8 + - - +
948E LEU* 2.9 55.8 + - + +
2332L GLY 4.6 4.2 + - - -
2333L CYS* 3.1 50.7 + - - +
2334L GLY* 3.8 7.3 - - - +
2336L GLN* 2.8 34.7 + - - +
2340L PHE* 3.9 7.5 - - + -
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Residues in contact with ILE 945 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804E LEU* 4.4 0.7 - - + -
809E ILE* 4.0 29.8 - - + -
874E CYS* 4.3 11.9 - - - +
875E GLY* 4.1 15.3 - - - -
876E ILE 3.8 13.0 - - - +
877E VAL* 3.8 16.4 - - + -
901E PRO* 3.6 36.1 - - + +
903E VAL* 4.0 15.7 - - + -
941E GLY 3.0 19.8 + - - +
942E VAL 3.8 3.6 - - - +
944E ARG* 1.3 76.0 - - - +
946E ALA* 1.3 55.0 + - - +
948E LEU* 3.8 4.4 - - + +
949E ALA* 2.7 33.9 + - + +
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Residues in contact with ALA 946 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804E LEU* 3.5 30.4 - - + +
847E HIS* 3.9 25.1 - - + +
942E VAL* 3.0 18.0 + - + +
943E GLU 3.7 5.6 - - - +
945E ILE* 1.3 76.8 - - - +
947E ALA* 1.3 62.8 + - - +
950E GLY* 3.0 24.6 + - - -
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Residues in contact with ALA 947 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943E GLU 3.1 9.9 + - - +
944E ARG* 3.0 12.3 + - - +
946E ALA* 1.3 76.9 - - - +
948E LEU* 1.3 60.9 + - + +
950E GLY 3.1 14.5 - - - +
2336L GLN* 3.3 31.9 - - - +
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Residues in contact with LEU 948 (chain E).
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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901E PRO* 3.6 32.3 - - + +
902E VAL 5.5 0.2 - - - +
903E VAL* 5.6 0.7 - - + -
927E ASP* 4.9 15.5 - - + -
944E ARG* 2.9 60.8 + - + +
945E ILE* 3.8 3.6 - - + +
947E ALA* 1.3 78.7 - - + +
949E ALA* 1.3 66.8 + - - +
950E GLY 3.5 2.3 - - - +
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Residues in contact with ALA 949 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802E ARG 4.1 18.5 - - - +
803E SER* 4.9 8.8 - - - -
804E LEU* 3.6 19.5 - - + +
874E CYS* 4.2 14.6 - - + +
901E PRO* 4.7 5.2 - - + -
945E ILE* 2.7 23.5 + - + +
948E LEU* 1.3 73.4 - - - +
950E GLY* 1.3 68.4 + - - +
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Residues in contact with GLY 950 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803E SER* 5.5 4.0 - - - -
804E LEU* 4.3 11.8 - - - +
946E ALA 3.0 18.9 + - - -
947E ALA* 3.1 18.1 - - - +
948E LEU 3.5 3.1 - - - +
949E ALA* 1.3 91.1 - - - +
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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