Contacts of the helix formed by residues 936 - 949 (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 LYS 936 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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724C ARG* 5.2 1.4 - - - +
851C LYS* 6.3 3.9 - - + +
802D ASN* 6.0 0.7 - - - +
805D GLU* 3.0 37.2 + - - -
870D GLN* 4.3 16.1 + - - +
873D VAL* 4.7 1.6 - - - -
934D ARG 4.7 3.4 - - - +
935D PRO* 1.3 76.5 - - - +
937D PHE* 1.3 61.9 + - - +
938D ARG* 3.9 37.0 - - + +
939D GLU* 3.0 31.3 + - + +
940D LEU* 2.9 29.2 + - - +
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Residues in contact with PHE 937 (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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798D ALA* 4.1 10.7 - - - +
801D MET* 3.4 54.3 - - + -
802D ASN* 3.8 22.0 - - + +
805D GLU* 3.8 16.8 - - + +
869D HIS* 3.8 14.6 - - + -
872D ASP* 3.7 25.8 - - + -
873D VAL* 3.7 17.0 - - + +
876D TYR* 3.7 26.7 - + + -
935D PRO 4.2 0.6 + - - -
936D LYS* 1.3 75.3 - - - +
938D ARG* 1.3 53.1 + - - +
940D LEU* 2.9 16.6 + - + +
941D ILE* 2.8 40.5 + - - +
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Residues in contact with ARG 938 (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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696C SER* 4.0 26.4 + - - +
697C GLY* 3.3 26.1 - - - -
698C ALA* 3.4 33.7 + - - +
851C LYS* 6.0 0.8 - - - +
802D ASN* 4.0 14.6 - - - +
806D ASP* 6.2 0.2 - - - -
936D LYS* 3.9 40.9 - - + +
937D PHE* 1.3 78.5 - - - +
939D GLU* 1.3 71.9 + - + +
941D ILE* 3.4 11.4 + - - +
942D ILE* 3.2 32.2 + - + +
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Residues in contact with GLU 939 (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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925D LYS* 3.6 22.6 + - - -
934D ARG 4.8 1.0 - - - +
935D PRO* 3.7 9.5 - - + +
936D LYS* 3.0 43.7 + - + +
938D ARG* 1.3 91.2 + - - +
940D LEU* 1.3 57.6 + - - +
942D ILE* 3.3 11.2 + - - +
943D GLU* 2.9 31.6 + - - +
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Residues in contact with LEU 940 (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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798D ALA* 4.3 11.1 - - + +
873D VAL* 4.3 16.8 - - + -
876D TYR* 3.7 33.7 - - + +
922D ILE* 3.6 31.0 - - + -
926D CYS* 4.3 4.0 - - - -
935D PRO* 3.9 19.7 - - + -
936D LYS 2.9 17.7 + - - +
937D PHE* 2.9 26.2 + - + +
939D GLU* 1.3 74.1 - - - +
941D ILE* 1.3 65.0 + - - +
943D GLU* 4.6 2.2 - - + -
944D PHE* 3.1 34.8 + - + +
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Residues in contact with ILE 941 (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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696C SER* 5.3 4.7 - - - -
795D VAL* 4.4 5.8 - - + +
798D ALA* 3.8 22.2 - - + -
799D LYS* 3.8 35.4 - - + +
802D ASN* 3.4 38.6 - - + +
937D PHE 2.8 19.2 + - - +
938D ARG* 3.6 9.6 - - - +
940D LEU* 1.3 72.2 - - - +
942D ILE* 1.3 59.6 + - + +
944D PHE* 4.4 0.2 - - - +
945D SER* 2.7 47.0 + - - +
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Residues in contact with ILE 942 (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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696C SER 5.1 9.9 - - - +
779C ARG* 5.1 13.7 - - - +
938D ARG* 3.2 20.3 + - + +
939D GLU* 3.5 10.3 - - - +
941D ILE* 1.3 83.9 - - + +
943D GLU* 1.3 60.1 + - + +
945D SER* 3.2 7.0 - - - -
946D LYS* 3.0 30.6 + - + +
949D ARG* 4.5 2.9 + - - +
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Residues in contact with GLU 943 (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* 3.9 24.9 - - + -
939D GLU 2.9 20.6 + - - +
940D LEU* 4.1 5.8 - - + +
942D ILE* 1.3 74.3 - - - +
944D PHE* 1.3 58.4 + - + +
946D LYS* 3.4 10.1 + - - +
947D MET* 3.0 32.4 + - - +
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Residues in contact with PHE 944 (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* 3.4 29.1 - - + +
794D CYS* 3.5 31.2 - - + -
795D VAL* 3.5 19.5 - - + +
876D TYR* 3.6 27.4 - + - -
880D VAL* 4.4 13.2 - - + -
884D MET* 4.5 4.7 - - + -
919D VAL* 4.8 9.0 - - + -
922D ILE* 3.9 35.2 - - + -
923D MET* 5.8 0.9 - - + -
940D LEU* 3.1 29.4 + - + +
943D GLU* 1.3 75.3 - - - +
945D SER* 1.3 56.9 + - - +
947D MET* 3.6 11.0 - - - +
948D ALA* 2.7 37.2 + - - +
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Residues in contact with SER 945 (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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795D VAL* 3.5 20.9 - - - +
799D LYS* 4.9 2.3 + - - -
941D ILE* 2.7 30.7 + - - +
942D ILE* 3.2 8.7 - - - -
944D PHE* 1.3 77.3 - - - +
946D LYS* 1.3 61.1 + - - +
948D ALA* 3.3 4.8 + - - +
949D ARG* 3.2 38.8 + - - +
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Residues in contact with LYS 946 (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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782C LYS* 5.5 6.6 - - - +
942D ILE* 3.0 11.7 + - + +
943D GLU* 3.5 14.1 - - - +
945D SER* 1.3 79.6 - - - +
947D MET* 1.3 65.1 + - + +
949D ARG* 3.2 43.4 + - - +
950D ASP* 3.8 4.5 + - - +
954D TYR* 3.5 29.2 + - - +
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Residues in contact with MET 947 (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* 3.8 19.4 - - + +
918D ASP* 4.1 5.6 - - + +
919D VAL* 3.0 44.0 - - + +
922D ILE* 4.1 19.5 - - + -
943D GLU* 3.0 17.0 + - + +
944D PHE* 3.3 13.2 + - - +
946D LYS* 1.3 73.9 - - + +
948D ALA* 1.3 57.6 + - - +
949D ARG 3.1 5.4 - - - -
950D ASP 3.1 4.9 - - - +
951D PRO* 3.0 28.8 - - - +
954D TYR* 3.0 54.7 - - + -
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Residues in contact with ALA 948 (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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788D GLN* 2.8 29.4 + - - +
791D LEU* 4.1 21.5 - - + +
792D ASN* 3.5 22.7 - - - +
795D VAL* 4.3 4.9 - - + -
944D PHE 2.7 22.1 + - - +
945D SER* 3.3 6.0 + - - +
947D MET* 1.3 72.8 - - - +
949D ARG* 1.3 60.2 + - - +
950D ASP 3.2 0.4 - - - -
951D PRO* 3.6 5.9 - - - +
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Residues in contact with ARG 949 (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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780C GLU* 6.0 6.9 - - - +
788D GLN* 5.6 0.2 - - - -
942D ILE* 4.5 2.8 + - - +
945D SER* 3.2 19.6 + - - +
946D LYS* 3.2 58.8 + - - +
947D MET 3.1 0.4 - - - -
948D ALA* 1.3 80.3 - - - +
950D ASP* 1.3 59.6 + - + +
951D PRO* 3.6 2.9 - - - +
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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