Contacts of the helix formed by residues 936 - 949 (chain C) 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 LYS 936 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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802C ASN* 6.0 1.1 - - - +
805C GLU* 3.0 37.8 + - - -
870C GLN* 4.4 17.7 + - - +
873C VAL* 4.7 0.9 - - - -
934C ARG 4.7 3.1 - - - +
935C PRO* 1.3 76.3 - - - +
937C PHE* 1.3 59.5 + - - +
938C ARG* 3.7 32.5 - - - +
939C GLU* 2.9 27.3 + - + +
940C LEU* 2.8 29.6 + - - +
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Residues in contact with PHE 937 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798C ALA* 4.0 11.4 - - + +
801C MET* 3.4 53.6 - - + -
802C ASN* 3.9 22.9 - - + +
805C GLU* 3.8 16.8 + - + +
869C HIS* 3.8 14.8 - - + -
872C ASP* 3.7 25.8 - - + -
873C VAL* 3.7 18.6 - - + +
876C TYR* 3.7 26.5 - + + -
935C PRO 4.2 0.4 + - - -
936C LYS* 1.3 74.5 - - - +
938C ARG* 1.3 52.9 + - - +
940C LEU* 2.9 15.3 + - + +
941C ILE* 2.8 40.5 + - - +
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Residues in contact with ARG 938 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802C ASN* 4.1 15.9 - - - +
936C LYS* 3.1 33.9 - - + +
937C PHE* 1.3 75.7 - - - +
939C GLU* 1.3 102.7 + - - +
941C ILE* 3.6 12.5 + - - +
942C ILE* 3.3 36.9 + - + +
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Residues in contact with GLU 939 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925C LYS* 3.6 22.0 + - - -
934C ARG 4.8 0.9 - - - +
935C PRO* 3.7 10.2 - - + +
936C LYS* 2.9 32.3 + - - +
938C ARG* 1.3 111.7 + - - +
940C LEU* 1.3 58.4 + - - +
942C ILE* 3.3 10.2 + - - +
943C GLU* 2.9 31.9 + - - +
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Residues in contact with LEU 940 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798C ALA* 4.3 10.9 - - + +
873C VAL* 4.3 9.6 - - + -
876C TYR* 3.7 32.3 - - + -
922C ILE* 3.6 31.9 - - + -
926C CYS* 4.3 10.5 - - - -
935C PRO* 3.9 20.0 - - + -
936C LYS 2.8 16.4 + - - +
937C PHE* 2.9 26.7 + - + +
939C GLU* 1.3 75.1 - - + +
941C ILE* 1.3 64.7 + - - +
943C GLU* 4.6 3.4 - - + +
944C PHE* 3.1 35.1 + - + +
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Residues in contact with ILE 941 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795C VAL* 4.5 4.4 - - + +
798C ALA* 3.8 21.3 - - + -
799C LYS* 3.8 34.8 - - + +
802C ASN* 3.5 37.5 - - + +
937C PHE 2.8 21.1 + - - +
938C ARG* 3.7 9.2 - - - +
939C GLU 3.3 0.2 - - - -
940C LEU* 1.3 71.8 - - - +
942C ILE* 1.3 59.5 + - + +
944C PHE* 4.0 1.8 - - - +
945C SER* 2.3 47.0 + - - +
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Residues in contact with ILE 942 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938C ARG* 3.3 31.4 + - + +
939C GLU* 3.3 12.1 + - - +
941C ILE* 1.3 84.5 - - + +
943C GLU* 1.3 65.6 + - + +
945C SER* 3.3 6.1 + - - -
946C LYS* 3.1 23.3 + - + +
949C ARG* 4.5 2.9 + - - +
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Residues in contact with GLU 943 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922C ILE* 3.9 25.6 - - + -
939C GLU 2.9 20.4 + - - +
940C LEU* 4.1 6.1 - - + +
942C ILE* 1.3 76.3 - - + +
944C PHE* 1.3 62.5 + - - +
946C LYS* 3.3 12.6 + - - +
947C MET* 3.2 26.6 + - + +
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Residues in contact with PHE 944 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791C LEU* 3.7 26.4 - - + +
794C CYS* 3.5 33.0 - - + -
795C VAL* 3.5 19.9 - - + +
876C TYR* 3.5 28.3 - + - -
880C VAL* 4.4 12.8 - - + -
884C MET* 4.6 4.3 - - + -
919C VAL* 4.7 8.5 - - + -
922C ILE* 3.9 34.5 - - + -
923C MET* 5.8 1.1 - - + -
940C LEU* 3.1 28.1 + - + +
943C GLU* 1.3 76.2 - - + +
945C SER* 1.3 56.0 + - - +
946C LYS 3.1 0.7 - - - -
947C MET* 3.7 13.2 - - - +
948C ALA* 2.7 36.6 + - - +
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Residues in contact with SER 945 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795C VAL* 3.4 24.2 - - - +
799C LYS* 4.9 1.0 - - - -
941C ILE* 2.3 33.4 + - - +
942C ILE* 3.5 6.5 - - - -
944C PHE* 1.3 77.2 - - - +
946C LYS* 1.3 62.6 + - - +
948C ALA* 3.7 4.4 + - - +
949C ARG* 3.3 37.1 + - - +
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Residues in contact with LYS 946 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942C ILE* 3.1 12.9 + - + +
943C GLU* 3.4 13.9 - - - +
944C PHE 3.1 0.2 - - - -
945C SER* 1.3 74.6 - - - +
947C MET* 1.3 71.5 - - + +
949C ARG* 3.2 41.7 + - - +
950C ASP* 3.9 3.1 + - - +
954C TYR* 3.6 28.9 + - - +
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Residues in contact with MET 947 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791C LEU* 4.3 11.0 - - + -
918C ASP* 3.7 33.9 - - + +
919C VAL* 3.9 16.6 - - + -
922C ILE* 4.1 14.8 - - + -
943C GLU* 3.2 15.9 + - + +
944C PHE* 3.3 21.5 + - - +
946C LYS* 1.3 79.4 - - + +
948C ALA* 1.3 53.3 + - - +
949C ARG 2.9 5.2 - - - -
950C ASP 2.7 38.3 + - - -
951C PRO* 3.0 1.7 - - - +
954C TYR* 3.0 53.2 - - + -
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Residues in contact with ALA 948 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C GLN* 2.8 28.4 + - - +
791C LEU* 4.1 19.6 - - + +
792C ASN* 3.4 23.8 - - - +
795C VAL* 4.2 9.6 - - + -
944C PHE 2.7 21.9 + - - +
945C SER* 3.9 6.7 - - - +
946C LYS 3.4 0.2 - - - -
947C MET* 1.3 72.7 - - - +
949C ARG* 1.3 58.8 + - - +
950C ASP 3.1 1.0 + - - -
951C PRO* 3.4 5.6 - - - +
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Residues in contact with ARG 949 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C GLN* 5.7 0.2 - - - -
942C ILE* 4.5 2.8 + - - +
945C SER* 3.3 19.8 + - - +
946C LYS* 3.2 59.8 + - - +
947C MET 2.8 1.2 + - - -
948C ALA* 1.3 76.2 - - - +
950C ASP* 1.3 59.9 + - + +
951C PRO* 3.9 2.3 - - - +
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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