Contacts of the helix formed by residues 921 - 932 (chain D) 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 THR 921 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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916D GLN* 3.8 2.9 - - - +
919D ILE 4.1 0.2 + - - -
920D CYS* 1.3 77.6 - - - +
922D ILE* 1.3 66.0 + - - +
923D ASP* 3.9 20.5 + - - +
924D VAL* 3.2 6.2 + - - +
925D TYR* 3.1 17.5 + - - +
958D ARG 3.8 18.4 - - - +
959D TYR* 3.1 26.4 + - - +
961D VAL* 4.5 16.4 - - + -
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Residues in contact with ILE 922 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916D GLN* 3.8 23.3 - - - +
921D THR* 1.3 71.8 - - - +
923D ASP* 1.3 68.1 + - - +
925D TYR* 3.7 22.9 - - + -
926D MET* 2.8 45.1 + - + +
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Residues in contact with ASP 923 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921D THR* 3.1 13.1 + - - +
922D ILE* 1.3 86.2 - - - +
924D VAL* 1.3 62.2 + - - +
926D MET* 3.5 10.5 + - - +
927D VAL* 3.3 18.2 + - - +
951D ARG* 5.4 3.9 + - - -
952D MET* 4.1 8.8 - - + +
958D ARG 5.7 0.2 - - - +
959D TYR* 3.9 28.0 - - + -
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Residues in contact with VAL 924 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796D LEU* 4.7 2.5 - - + -
889D MET* 3.9 22.0 - - + -
920D CYS* 3.9 22.0 - - + -
921D THR* 3.2 8.3 + - - +
923D ASP* 1.3 75.9 - - - +
925D TYR* 1.3 66.4 + - - +
927D VAL* 3.2 19.2 + - - +
928D MET* 3.2 17.9 + - + +
949D PHE* 4.2 13.8 - - + -
952D MET* 3.7 25.6 - - + -
959D TYR* 3.6 27.8 - - + +
960D LEU* 4.4 4.9 - - + -
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Residues in contact with TYR 925 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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913D ARG* 4.8 6.2 - - - +
914D LEU 2.9 29.3 + - - -
915D PRO* 3.7 3.6 - - - +
916D GLN* 3.4 47.0 + - + -
917D PRO* 4.1 0.9 - - + -
920D CYS* 4.7 2.0 - - - -
921D THR 3.1 15.7 + - - +
922D ILE* 3.8 26.2 - - + +
924D VAL* 1.3 75.5 - - - +
926D MET* 1.3 61.9 + - + +
928D MET* 3.0 28.2 + - + +
929D VAL* 2.9 49.8 + - + +
932D TRP* 4.8 1.6 - + - -
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Residues in contact with MET 926 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922D ILE* 2.8 36.4 + - + +
923D ASP* 3.6 8.1 - - - +
925D TYR* 1.3 77.1 - - - +
927D VAL* 1.3 58.2 + - + +
929D VAL* 3.2 18.1 + - + +
930D LYS* 2.8 63.4 + - + +
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Residues in contact with VAL 927 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885D ILE* 5.3 0.7 - - + -
923D ASP 3.3 17.7 - - - +
924D VAL* 3.2 12.9 + - - +
926D MET* 1.3 75.8 - - + +
928D MET* 1.3 62.0 + - - +
930D LYS* 3.5 12.9 + - + +
931D CYS* 3.2 27.9 + - - -
940D PRO* 4.8 2.2 - - + +
945D LEU* 3.6 28.5 - - + -
948D GLU* 4.3 24.2 - - + +
949D PHE* 3.6 23.1 - - + -
952D MET* 4.6 4.3 - - + -
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Residues in contact with MET 928 (chain D).
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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882D GLY* 3.8 11.9 - - - +
885D ILE* 3.8 23.3 - - + -
886D TRP* 3.0 50.3 - - + -
889D MET* 4.8 3.6 - - - -
917D PRO* 3.6 24.5 - - + -
920D CYS* 4.7 0.7 - - - -
924D VAL* 3.2 20.5 + - - +
925D TYR* 3.0 23.5 + - + +
927D VAL* 1.3 79.3 - - - +
929D VAL* 1.3 62.2 + - - +
931D CYS* 3.0 23.9 + - - +
932D TRP* 3.4 25.8 - - + -
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Residues in contact with VAL 929 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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913D ARG* 5.3 13.0 + - + +
925D TYR* 2.9 51.9 + - + +
926D MET* 3.6 21.3 - - + +
928D MET* 1.3 73.5 - - - +
930D LYS* 1.3 59.8 + - + +
932D TRP* 2.8 38.9 + - + +
933D MET* 3.6 5.1 + - + +
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Residues in contact with LYS 930 (chain D).
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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926D MET* 2.8 51.1 + - + +
927D VAL* 3.7 13.1 - - + +
928D MET 3.3 0.2 - - - -
929D VAL* 1.3 73.1 - - + +
931D CYS* 1.3 60.3 + - - +
932D TRP 3.3 0.5 + - - -
933D MET* 3.4 29.5 - - - +
938D SER 5.7 1.3 - - - +
939D ARG* 3.5 5.5 - - - +
940D PRO* 3.3 30.9 - - + +
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Residues in contact with CYS 931 (chain D).
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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878D VAL* 3.4 35.0 - - - +
879D TRP* 3.3 19.9 + - - -
881D TYR* 4.4 2.0 - - - -
882D GLY* 3.9 19.7 - - - -
885D ILE* 5.6 0.9 - - - -
927D VAL* 3.2 23.0 + - - -
928D MET* 3.0 12.8 + - - +
930D LYS* 1.3 76.6 - - - +
932D TRP* 1.3 58.1 + - + +
933D MET 3.5 0.2 - - - -
939D ARG* 3.4 15.6 + - - -
940D PRO* 4.2 2.2 - - - -
945D LEU* 3.8 27.4 - - - -
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Residues in contact with TRP 932 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879D TRP* 3.2 54.7 + + + -
882D GLY* 3.4 25.2 - - - -
883D VAL* 3.4 12.2 - - + +
886D TRP* 4.0 0.9 - + + -
896D TYR* 5.6 2.2 - - - -
913D ARG* 2.9 58.6 + - + +
914D LEU* 3.7 54.7 - - + -
925D TYR* 4.8 2.9 - + - -
928D MET* 3.4 45.1 - - + -
929D VAL* 2.8 15.9 + - + +
931D CYS* 1.3 85.7 - - - +
933D MET* 1.3 61.3 + - - +
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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