Contacts of the helix formed by residues 930 - 943 (chain A) in PDB entry 6MZL
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 ALA 930 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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894A ALA* 5.4 1.6 - - + -
898A LEU* 4.5 9.4 - - + -
926A GLU 3.6 1.7 + - - +
927A VAL 3.3 16.5 + - - +
928A ARG 3.2 1.4 - - - -
929A THR* 1.3 81.6 + - - +
931A PRO* 1.3 68.0 - - + +
932A TRP* 3.2 38.1 - - + -
933A ASN* 3.0 6.9 + - - +
934A THR* 3.0 24.1 + - - +
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Residues in contact with PRO 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688A GLY 5.6 0.4 - - - +
689A PRO* 3.9 20.9 - - + +
791A VAL* 3.6 13.8 - - + +
890A SER* 3.4 28.0 - - - +
894A ALA* 3.7 28.0 - - + -
897A ARG* 5.1 4.5 - - - +
929A THR 3.7 3.6 - - - +
930A ALA* 1.3 87.1 - - + +
932A TRP* 1.3 57.0 + - + +
934A THR* 3.4 9.9 - - - +
935A THR* 2.6 38.1 + - - +
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Residues in contact with TRP 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A VAL* 3.6 14.2 - - - +
792A PRO 3.3 28.9 - - - +
793A GLY* 3.9 8.1 - - - -
794A PRO* 3.7 34.2 - - + +
891A MET* 4.1 21.1 - - + -
894A ALA* 4.5 5.2 - - + -
895A GLU* 4.5 7.6 - - - -
898A LEU* 3.6 24.5 - - + -
908A PHE* 3.7 36.1 - + + +
927A VAL* 4.8 1.6 - - + -
930A ALA* 3.6 17.3 - - + -
931A PRO* 1.3 86.3 - - + +
933A ASN* 1.3 82.8 + - - +
935A THR* 4.2 0.2 - - - -
936A ARG* 3.3 36.3 + - - +
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Residues in contact with ASN 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923A ILE* 3.9 20.5 - - - +
927A VAL* 2.3 35.8 + - - +
928A ARG* 3.5 15.0 - - - +
930A ALA* 3.0 8.4 + - - +
932A TRP* 1.3 106.4 + - - +
934A THR* 1.3 64.5 + - - +
935A THR 3.4 0.2 - - - -
936A ARG* 3.8 2.7 + - - +
937A ALA* 3.2 23.4 + - - +
965A TYR 4.0 2.5 - - - +
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Residues in contact with THR 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A PRO* 4.3 8.0 - - - +
787A PRO* 5.7 0.2 - - - +
928A ARG 3.6 15.0 - - - +
929A THR* 3.9 14.4 - - - +
930A ALA 3.0 11.8 + - - +
931A PRO* 3.4 16.6 + - - +
933A ASN* 1.3 77.5 - - - +
935A THR* 1.3 65.1 + - - +
937A ALA 3.3 1.0 + - - -
938A PHE* 2.9 25.3 + - - +
954A ALA* 4.8 8.5 - - + +
965A TYR* 3.4 42.4 - - + +
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Residues in contact with THR 935 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A PRO* 3.9 13.2 - - + -
690A LEU* 5.5 0.2 - - + -
787A PRO* 3.7 31.2 - - + -
789A PHE 4.3 6.7 - - - +
790A GLU* 4.4 0.8 - - - -
791A VAL* 3.4 39.5 + - + +
931A PRO 2.6 23.8 + - - +
932A TRP 4.1 0.3 + - - -
934A THR* 1.3 78.2 + - - +
936A ARG* 1.3 63.4 + - - +
938A PHE* 4.3 4.9 - - - +
939A ILE* 3.0 39.9 + - - +
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Residues in contact with ARG 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A GLU* 2.7 50.3 + - + +
791A VAL 4.7 4.5 - - - +
792A PRO 6.4 0.4 - - - -
932A TRP* 3.3 25.0 + - - +
933A ASN* 3.8 3.5 + - - +
934A THR 3.4 0.2 - - - -
935A THR* 1.3 81.5 + - - +
937A ALA* 1.3 62.8 + - - +
939A ILE* 5.1 2.5 - - - -
940A ALA* 3.4 16.6 + - - +
967A LYS* 3.3 29.4 + - - +
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Residues in contact with ALA 937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933A ASN 3.2 14.8 + - - +
934A THR 3.4 2.2 - - - +
935A THR 3.2 0.2 - - - -
936A ARG* 1.3 78.7 - - - +
938A PHE* 1.3 61.5 + - - +
941A ALA* 3.1 22.7 + - - +
946A CYS* 4.1 5.4 - - - -
948A LEU* 3.7 6.8 - - + +
965A TYR 3.3 33.7 - - - +
966A VAL* 4.0 2.5 - - - +
967A LYS* 3.7 28.2 - - + +
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Residues in contact with PHE 938 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730A PHE 6.5 0.2 - - - -
731A LEU* 3.6 29.6 - - + -
786A CYS* 3.6 23.6 - - + -
787A PRO* 3.2 44.6 - - + -
788A LEU* 5.3 1.1 - - + -
934A THR 2.9 16.8 + - - +
935A THR* 3.3 5.4 + - - +
937A ALA* 1.3 76.2 - - - +
939A ILE* 1.3 57.6 + - + +
941A ALA* 3.1 7.0 + - + +
942A MET* 2.7 53.1 + - + +
948A LEU* 4.0 10.5 - - + -
965A TYR* 3.8 30.3 - + + -
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Residues in contact with ILE 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787A PRO 3.8 18.8 - - - +
788A LEU 4.2 11.7 - - - +
789A PHE 3.9 9.2 - - - +
790A GLU* 3.9 37.9 - - + +
935A THR* 3.0 22.9 + - - +
936A ARG* 4.8 2.5 - - - +
938A PHE* 1.3 74.1 - - + +
940A ALA* 1.3 60.4 + - - +
942A MET* 3.1 13.9 + - + +
943A LYS* 2.9 54.1 + - + +
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Residues in contact with ALA 940 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936A ARG 3.4 18.9 + - - +
938A PHE 3.3 0.4 - - - -
939A ILE* 1.3 78.5 - - - +
941A ALA* 1.3 59.1 - - - +
943A LYS* 3.4 3.7 + - - +
944A GLY 3.2 3.5 + - - -
945A LYS* 2.8 54.0 + - + +
946A CYS* 3.9 18.2 - - - -
967A LYS* 4.0 11.4 - - - +
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Residues in contact with ALA 941 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937A ALA 3.1 18.9 + - - +
938A PHE* 3.1 6.1 + - + +
940A ALA* 1.3 74.1 - - - +
942A MET* 1.3 64.3 + - - +
944A GLY* 3.3 10.7 + - - -
946A CYS* 3.3 25.3 - - - +
947A LEU* 4.5 2.3 - - + +
948A LEU* 3.8 29.2 - - + -
1062A TYR* 4.8 3.6 - - - +
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Residues in contact with MET 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729A PRO 6.0 0.7 - - - +
749A ARG* 4.5 9.4 - - - +
787A PRO 5.0 1.3 - - - +
788A LEU* 3.9 31.4 - - + -
938A PHE* 2.7 39.1 + - + +
939A ILE* 3.1 17.0 + - - +
941A ALA* 1.3 75.2 - - - +
943A LYS* 1.3 61.2 + - + +
944A GLY 3.2 1.5 + - - -
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Residues in contact with LYS 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939A ILE* 2.9 39.8 + - + +
940A ALA* 3.4 4.7 + - - +
941A ALA 3.3 0.2 - - - -
942A MET* 1.3 78.5 - - + +
944A GLY* 1.3 60.9 + - - +
945A LYS* 3.3 20.7 + - + +
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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