Contacts of the helix formed by residues 868 - 885 (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 868 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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810D VAL* 3.7 19.1 - - - +
860D GLU* 5.0 2.6 + - - -
866D ILE* 4.0 20.7 - - + +
867D TYR* 1.3 81.0 - - - +
869D HIS* 1.3 65.3 + - - +
870D GLN* 3.1 19.9 + - - +
871D SER* 2.7 27.5 + - - -
872D ASP* 3.1 6.8 + - - +
931D ALA* 5.3 1.4 - - - +
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Residues in contact with HIS 869 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724C ARG* 4.1 7.0 + - - -
805D GLU* 3.6 61.4 + - + +
808D ARG* 4.0 7.4 - - - +
809D LEU 3.1 39.2 + - - -
810D VAL* 3.7 15.0 - - + +
868D THR* 1.3 76.2 - - - +
870D GLN* 1.3 62.0 + - - +
872D ASP* 3.2 13.3 + - - +
873D VAL* 3.1 28.4 + - - +
937D PHE* 3.8 5.5 - - + -
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Residues in contact with GLN 870 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805D GLU* 5.1 1.4 - - - +
868D THR* 3.1 11.2 + - - +
869D HIS* 1.3 84.7 - - - +
871D SER* 1.3 63.9 + - - +
873D VAL* 3.2 18.2 + - - +
874D TRP 3.3 7.3 + - - -
931D ALA* 3.1 40.9 + - + +
932D ASP* 4.2 10.9 - - - +
934D ARG* 3.1 47.6 + - - +
935D PRO 3.1 16.5 + - - +
936D LYS* 4.3 19.5 + - - +
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Residues in contact with SER 871 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810D VAL* 4.8 0.2 - - - +
858D ALA* 4.0 19.5 + - - +
860D GLU* 4.0 8.0 + - - -
861D SER* 4.5 5.8 - - - -
866D ILE 4.3 11.0 - - - -
867D TYR* 3.5 11.0 - - - +
868D THR* 2.7 38.6 + - - -
870D GLN* 1.3 74.8 - - - +
872D ASP* 1.3 66.4 + - - +
874D TRP* 3.2 12.5 + - - +
875D SER* 3.2 16.8 + - - -
934D ARG* 3.9 8.6 - - - +
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Residues in contact with ASP 872 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801D MET* 3.7 24.6 - - + +
809D LEU 4.6 1.4 - - - +
810D VAL* 3.4 11.8 - - - +
811D HIS* 2.8 29.3 + - - +
812D ARG* 3.1 25.6 + - - -
814D LEU* 4.0 6.2 - - + +
868D THR 3.1 12.1 + - - +
869D HIS* 3.2 14.5 + - - +
871D SER* 1.3 75.4 + - - +
873D VAL* 1.3 61.2 + - - +
875D SER* 3.3 8.5 + - - -
876D TYR* 2.8 29.6 + - - +
937D PHE* 3.7 6.4 - - + -
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Residues in contact with VAL 873 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805D GLU* 5.9 0.2 - - - +
869D HIS 3.1 18.3 + - - +
870D GLN* 3.4 17.0 - - - +
871D SER 3.1 0.6 - - - -
872D ASP* 1.3 75.1 - - - +
874D TRP* 1.3 68.6 + - - +
876D TYR* 3.0 4.7 + - - +
877D GLY 3.0 15.4 + - - -
926D CYS* 3.7 31.4 - - + +
934D ARG* 4.1 8.5 - - + -
935D PRO* 3.2 30.5 - - + +
937D PHE* 3.7 32.5 - - + +
940D LEU* 4.3 5.2 - - + -
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Residues in contact with TRP 874 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855D LYS 5.5 0.8 + - - -
856D TRP 3.5 19.4 + - - -
857D MET 3.4 9.7 + - - -
858D ALA* 3.4 21.8 - - + -
859D LEU* 4.2 17.0 - - + -
870D GLN 3.3 5.7 + - - +
871D SER 3.2 12.0 + - - +
873D VAL* 1.3 78.2 - - - +
875D SER* 1.3 53.9 + - - +
877D GLY* 2.8 24.1 + - - -
878D VAL* 3.2 17.5 + - + +
891D TYR* 5.0 6.1 + - - -
903D LEU* 3.8 36.8 - - + +
908D ARG* 4.3 6.7 - - - -
926D CYS 3.4 12.1 + - - +
927D TRP* 3.1 59.6 + + + -
928D MET 3.6 3.4 - - - -
929D ILE* 4.6 4.3 - - + -
934D ARG* 3.4 35.0 - - - +
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Residues in contact with SER 875 (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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812D ARG 5.4 4.2 + - - -
813D ASP* 6.0 0.2 - - - -
814D LEU* 3.6 30.1 + - - +
856D TRP* 3.0 27.3 + - - +
857D MET* 4.6 3.8 - - - +
858D ALA 5.0 0.2 + - - -
871D SER 3.2 12.8 + - - -
872D ASP* 3.6 11.3 + - - -
874D TRP* 1.3 77.4 - - - +
876D TYR* 1.3 59.2 + - - +
878D VAL* 3.3 6.7 + - - +
879D THR* 2.8 30.9 + - - -
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Residues in contact with TYR 876 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794D CYS 2.7 34.0 + - - -
797D ILE* 3.8 29.4 - - + -
798D ALA* 3.8 16.9 - - + +
814D LEU* 3.6 14.6 - - + -
872D ASP 2.8 13.9 + - - +
873D VAL 3.0 10.7 + - - +
875D SER* 1.3 76.3 - - - +
877D GLY* 1.3 61.6 + - - +
879D THR* 3.1 4.9 + - - -
880D VAL* 2.9 49.1 + - + +
922D ILE* 5.9 0.4 - - + -
926D CYS* 4.2 4.3 - - - -
937D PHE* 3.7 18.2 - + + -
940D LEU* 3.7 27.6 - - + -
944D PHE* 3.6 24.8 - + - -
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Residues in contact with GLY 877 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873D VAL 3.0 6.3 + - - -
874D TRP 2.8 9.7 + - - -
876D TYR* 1.3 78.4 - - - +
878D VAL* 1.3 56.0 + - - +
880D VAL* 3.5 6.5 + - - +
881D TRP* 3.0 26.2 + - - +
923D MET* 3.9 7.0 - - - +
926D CYS* 4.0 19.1 - - - -
927D TRP* 3.5 19.4 - - - -
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Residues in contact with VAL 878 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855D LYS 3.8 15.5 - - - +
856D TRP* 3.4 31.0 - - + +
874D TRP* 3.2 23.4 + - + +
875D SER 3.6 6.1 - - - +
876D TYR 3.2 0.4 - - - -
877D GLY* 1.3 72.1 - - - +
879D THR* 1.3 61.7 + - - +
881D TRP* 3.0 9.3 + - - +
882D GLU* 2.8 27.6 + - + +
890D PRO* 3.8 24.7 - - + -
891D TYR* 5.4 1.8 - - - +
909D LEU* 4.2 15.5 - - + -
927D TRP* 3.7 16.4 - - - +
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Residues in contact with THR 879 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797D ILE* 4.1 25.6 - - + -
814D LEU* 3.6 12.7 + - + +
815D ALA* 3.4 19.8 - - - +
816D ALA* 3.7 25.4 - - + +
819D VAL* 4.7 2.5 - - + -
856D TRP* 4.4 0.2 - - - +
875D SER 2.8 15.8 + - - -
876D TYR* 3.3 12.1 - - + -
878D VAL* 1.3 76.2 - - - +
880D VAL* 1.3 64.0 + - + +
882D GLU* 3.1 15.9 + - - +
883D LEU* 3.0 23.6 + - + +
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Residues in contact with VAL 880 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794D CYS* 3.9 14.1 - - + -
797D ILE* 6.3 0.9 - - + -
876D TYR* 2.9 54.6 + - + +
877D GLY* 3.7 7.2 - - - +
879D THR* 1.3 75.2 - - + +
881D TRP* 1.3 58.5 + - - +
883D LEU* 3.0 12.1 + - + +
884D MET* 2.8 54.5 + - + +
919D VAL* 5.3 0.9 - - + -
923D MET* 4.0 19.5 - - + -
944D PHE* 4.4 9.6 - - + -
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Residues in contact with TRP 881 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877D GLY 3.0 10.1 + - - +
878D VAL* 3.0 14.9 + - - +
880D VAL* 1.3 73.5 - - - +
882D GLU* 1.3 69.7 + - - +
884D MET* 3.2 3.3 + - - +
885D THR* 3.0 42.5 + - + +
888D SER* 3.6 25.4 - - - -
889D LYS 3.5 15.5 - - - -
890D PRO* 3.3 34.8 - - + -
891D TYR 4.6 1.1 - - - -
909D LEU* 3.7 31.5 - - + +
910D PRO* 2.7 47.7 + - + -
912D PRO* 3.7 11.6 - - + +
923D MET* 3.0 37.4 - - + +
927D TRP* 4.4 0.4 - + - -
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Residues in contact with GLU 882 (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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775D LEU* 4.0 22.4 - - + +
778D VAL* 5.3 0.4 - - - -
815D ALA* 4.9 0.2 - - - +
816D ALA* 2.9 41.2 + - + +
817D ARG* 4.8 0.7 + - - +
856D TRP* 3.0 41.5 + - + +
878D VAL* 2.8 18.7 + - + +
879D THR* 3.3 13.4 - - - +
881D TRP* 1.3 80.5 - - + +
883D LEU* 1.3 61.1 + - - +
885D THR* 3.1 7.5 + - - -
886D PHE 3.0 3.6 + - - -
887D GLY* 2.7 29.9 + - - -
888D SER 4.2 15.7 - - - +
890D PRO* 4.6 0.8 - - + +
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Residues in contact with LEU 883 (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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774D LEU* 3.7 28.0 - - + -
778D VAL* 4.2 15.4 - - + +
790D LEU* 3.1 27.9 - - + +
793D TRP* 4.0 28.3 - - + -
794D CYS* 4.5 16.4 - - - -
797D ILE* 4.1 16.8 - - + -
816D ALA* 4.0 19.3 - - + -
879D THR* 3.0 14.9 + - + +
880D VAL* 3.0 9.6 + - + +
882D GLU* 1.3 81.2 - - - +
884D MET* 1.3 60.7 + - + +
886D PHE* 2.9 21.0 + - - -
887D GLY 4.8 0.9 - - - +
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Residues in contact with MET 884 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790D LEU* 4.3 19.3 - - + +
791D LEU* 4.7 2.2 - - + -
794D CYS* 3.4 33.7 - - - -
880D VAL* 2.8 31.5 + - + +
881D TRP* 3.2 4.9 + - - +
883D LEU* 1.3 74.0 - - + +
885D THR* 1.3 59.6 + - - +
886D PHE* 3.4 3.0 + - - -
912D PRO* 3.9 11.6 - - + +
913D PRO* 5.6 0.5 - - - +
914D ILE* 2.8 30.6 - - + +
915D CYS* 3.6 25.8 - - - -
919D VAL* 4.5 7.0 - - + -
923D MET* 4.8 1.3 - - - -
944D PHE* 4.5 8.7 - - + -
955D LEU* 3.7 36.6 - - + -
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Residues in contact with THR 885 (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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782D LYS* 5.5 0.2 - - - +
881D TRP* 3.0 45.9 + - + +
882D GLU* 3.1 10.6 + - - -
884D MET* 1.3 74.5 - - - +
886D PHE* 1.3 74.1 + - - +
888D SER* 3.1 36.7 + - - -
912D PRO* 3.7 22.2 - - + -
913D PRO* 5.5 4.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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