Contacts of the helix formed by residues 916 - 927 (chain D) in PDB entry 3LZB
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 916 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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911D GLN* 3.7 2.0 + - - +
914D ILE 3.7 0.2 + - - -
915D CYS* 1.3 79.0 - - - +
917D ILE* 1.3 64.1 + - - +
918D ASP* 3.3 16.9 + - - -
919D VAL* 3.2 9.0 + - - +
920D TYR 3.2 15.1 + - - -
953D ARG 4.1 7.6 - - - +
954D TYR* 2.6 44.9 + - - +
955D LEU 4.1 0.2 - - - +
956D VAL* 3.9 22.0 - - + -
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Residues in contact with ILE 917 (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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894B ILE* 5.4 2.7 - - + -
898B GLU* 3.3 39.5 - - + +
901B SER* 4.4 19.3 - - - -
902B ILE* 4.0 19.1 - - + +
905B LYS* 5.7 5.4 - - + -
911D GLN* 3.9 4.7 - - - +
916D THR* 1.3 71.4 - - - +
918D ASP* 1.3 65.3 + - - +
920D TYR* 4.1 15.3 - - + -
921D MET* 2.6 66.4 + - + +
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Residues in contact with ASP 918 (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 THR* 3.3 17.7 + - - +
917D ILE* 1.3 80.4 + - - +
919D VAL* 1.3 59.9 + - - +
921D MET* 3.5 8.1 - - - +
922D ILE* 3.1 29.1 + - - +
947D MET* 4.1 15.3 - - + -
953D ARG* 5.2 3.2 + - - +
954D TYR* 3.9 20.4 - - + -
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Residues in contact with VAL 919 (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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791D LEU* 4.8 5.2 - - + -
880D VAL* 5.3 0.2 - - + -
884D MET* 4.5 17.3 - - + -
915D CYS* 3.9 25.1 - - + -
916D THR* 3.2 7.5 + - - +
917D ILE 3.2 0.4 - - - -
918D ASP* 1.3 74.3 - - - +
920D TYR* 1.3 67.1 + - - +
922D ILE* 2.9 18.6 + - - +
923D MET* 3.1 18.5 + - + +
944D PHE* 4.8 10.8 - - + -
947D MET* 3.0 33.2 - - + -
954D TYR* 3.3 25.4 - - + +
955D LEU* 5.1 2.9 - - + -
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Residues in contact with TYR 920 (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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893B GLY* 5.3 8.4 - - - -
894B ILE* 4.4 21.1 + - + +
895B PRO* 5.6 1.1 - - + -
898B GLU* 4.4 2.5 - - - -
908D ARG* 4.9 1.9 - - - +
909D LEU 2.6 26.0 + - - -
910D PRO* 3.8 3.4 - - - +
911D GLN* 3.5 67.9 + - + +
912D PRO* 4.2 7.2 - - + -
915D CYS* 4.4 3.0 - - + +
916D THR 3.2 3.0 + - - +
917D ILE* 3.7 18.4 - - + +
919D VAL* 1.3 77.8 - - - +
921D MET* 1.3 55.4 + - - +
923D MET* 3.0 15.8 + - + +
924D ARG* 2.7 56.7 + - + +
927D TRP* 4.3 14.8 - + - -
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Residues in contact with MET 921 (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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894B ILE* 4.7 11.0 - - + -
902B ILE* 3.9 27.4 - - + -
905B LYS* 6.1 3.4 - - + -
907B GLU* 4.2 31.9 - - + +
917D ILE* 2.6 50.2 + - + +
918D ASP* 3.5 10.5 - - - +
920D TYR* 1.3 75.7 - - - +
922D ILE* 1.3 55.6 + - + +
924D ARG* 3.4 18.4 + - + +
925D LYS* 3.0 28.6 + - - +
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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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876D TYR* 5.9 0.2 - - + -
918D ASP 3.1 17.9 - - - +
919D VAL* 2.9 8.5 + - - +
921D MET* 1.3 72.8 - - + +
923D MET* 1.3 68.1 + - - +
925D LYS* 3.0 18.1 + - - +
926D CYS* 3.2 13.6 + - - -
935D PRO* 4.7 2.6 - - + +
940D LEU* 3.6 28.5 - - + -
943D GLU* 3.9 26.5 - - + -
944D PHE* 3.9 21.1 - - + -
947D MET* 4.1 21.3 - - - -
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Residues in contact with MET 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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877D GLY* 3.9 4.9 - - - +
880D VAL* 4.0 24.2 - - + -
881D TRP* 3.0 59.0 - - + +
884D MET* 4.8 0.2 - - - -
912D PRO* 4.3 13.0 - - + -
915D CYS* 4.6 8.5 - - - -
919D VAL* 3.1 10.5 + - + +
920D TYR* 3.0 25.0 + - + +
922D ILE* 1.3 77.3 - - + +
924D ARG* 1.3 58.5 + - - +
926D CYS* 2.9 33.9 + - - +
927D TRP* 3.5 29.4 + - + -
944D PHE* 5.8 1.3 - - + -
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Residues in contact with ARG 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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892B ASP 5.8 2.3 + - - -
894B ILE* 5.4 11.4 - - + +
910B PRO* 5.2 14.5 - - - +
906D GLY 5.9 0.4 + - - -
908D ARG* 3.4 51.6 - - - +
920D TYR* 2.7 48.2 + - + +
921D MET* 3.5 22.1 - - + +
923D MET* 1.3 73.2 - - - +
925D LYS* 1.3 54.8 + - - +
927D TRP* 3.0 31.8 + - - +
928D MET* 3.8 14.2 + - - +
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Residues in contact with LYS 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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907B GLU* 6.1 0.7 - - - +
921D MET 3.0 14.0 + - - +
922D ILE* 3.0 12.3 + - - +
924D ARG* 1.3 75.4 - - - +
926D CYS* 1.3 60.3 - - - +
927D TRP 3.3 0.5 + - - -
928D MET* 3.5 30.7 + - + +
933D SER 3.3 22.3 + - - +
934D ARG* 3.4 11.2 + - - +
935D PRO* 3.0 42.4 - - + +
939D GLU* 3.6 22.2 + - - -
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Residues in contact with CYS 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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873D VAL* 3.7 34.8 - - - +
874D TRP* 3.4 13.0 - - - -
876D TYR* 4.2 11.0 - - - -
877D GLY* 4.0 20.2 - - - -
922D ILE* 3.2 18.1 + - - -
923D MET* 2.9 13.3 + - - +
925D LYS* 1.3 75.6 - - - +
927D TRP* 1.3 59.3 + - + +
928D MET 3.5 0.4 - - - -
934D ARG* 3.2 21.9 + - - -
935D PRO* 4.0 15.9 - - - -
940D LEU* 4.3 8.1 - - - -
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Residues in contact with TRP 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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874D TRP* 3.1 57.3 + + + -
877D GLY* 3.5 24.2 - - - -
878D VAL* 3.6 11.4 - - + +
881D TRP* 4.4 0.4 - + - -
891D TYR* 5.6 3.4 - - - -
908D ARG* 2.9 53.2 + - + +
909D LEU* 3.9 46.9 - - + -
920D TYR* 4.3 4.5 - + - -
923D MET* 3.5 47.6 - - + -
924D ARG* 3.0 25.0 + - - +
926D CYS* 1.3 85.9 - - - +
928D MET* 1.3 61.4 + - - +
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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