Contacts of the helix formed by residues 874 - 889 (chain E) 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 LEU 874 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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872E PHE 5.9 0.2 - - - +
873E LEU* 1.3 73.8 - - - +
875E GLN* 1.3 63.4 + - - +
876E ALA 3.4 0.7 - - - -
877E PRO* 3.7 17.0 - - + -
878E LEU* 3.3 25.3 + - - +
56R GLN* 3.3 25.4 - - + +
57R VAL* 2.4 31.4 + - - +
58R LEU* 4.1 8.5 - - - +
59R THR* 4.8 15.3 - - + +
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Residues in contact with GLN 875 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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871E THR* 4.6 20.0 - - + +
873E LEU* 3.4 8.6 + - - +
874E LEU* 1.3 71.7 - - - +
876E ALA* 1.3 53.2 + - - +
878E LEU* 5.1 1.1 - - - -
879E GLN* 2.7 61.6 + - + +
896E PRO* 4.8 22.0 + - - +
899E VAL* 5.8 7.6 - - + +
900E SER* 5.7 8.2 - - - +
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Residues in contact with ALA 876 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875E GLN* 1.3 79.9 - - - +
877E PRO* 1.4 64.2 - - + +
879E GLN* 3.7 7.0 - - - +
880E ARG* 2.9 48.8 + - - +
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Residues in contact with PRO 877 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874E LEU* 3.7 29.6 - - + +
876E ALA* 1.4 93.2 - - + +
878E LEU* 1.3 58.0 + - - +
880E ARG* 3.3 28.8 + - - +
881E ARG* 3.0 34.5 + - - +
55R ASN 4.7 12.8 - - - +
56R GLN 4.0 8.7 - - - +
57R VAL* 3.9 15.5 - - + -
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Residues in contact with LEU 878 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873E LEU* 3.7 36.1 - - + -
874E LEU 3.3 15.5 + - - +
875E GLN* 4.3 1.1 - - - +
876E ALA 3.4 0.4 - - - -
877E PRO* 1.3 81.0 - - - +
879E GLN* 1.3 57.9 + - - +
881E ARG* 3.1 17.3 + - + +
882E ILE* 2.8 49.6 + - + +
899E VAL* 5.9 2.9 - - + -
902E VAL* 6.2 3.1 - - + -
903E SER* 6.0 0.9 - - - -
57R VAL* 3.5 29.5 - - + +
92R ILE* 4.0 24.5 - - + -
96R VAL* 5.5 2.5 - - + -
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Residues in contact with GLN 879 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875E GLN* 2.7 47.7 + - + +
876E ALA* 3.7 6.6 - - - +
878E LEU* 1.3 76.2 - - - +
880E ARG* 1.3 57.6 + - + +
882E ILE* 3.3 11.2 + - + +
883E LEU* 2.9 40.5 + - + +
894E LEU* 3.5 38.1 - - + +
896E PRO* 5.2 5.8 - - - +
899E VAL* 5.1 7.8 - - + +
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Residues in contact with ARG 880 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876E ALA* 2.9 36.0 + - - +
877E PRO* 3.4 36.1 - - - +
878E LEU 3.2 0.2 - - - -
879E GLN* 1.3 77.5 - - + +
881E ARG* 1.3 58.2 + - + +
883E LEU* 3.8 5.9 - - - +
884E GLU* 2.8 31.2 + - - +
55R ASN 5.8 1.2 - - - +
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Residues in contact with ARG 881 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877E PRO* 3.0 23.6 + - - +
878E LEU* 3.1 16.1 + - + +
880E ARG* 1.3 74.4 - - + +
882E ILE* 1.3 60.5 + - + +
884E GLU* 3.3 18.8 + - - +
885E ILE* 3.0 42.9 + - + +
55R ASN 4.1 17.9 + - - -
57R VAL* 4.5 17.5 - - - +
93R GLU* 4.6 14.1 + - - +
96R VAL* 5.7 0.4 - - - -
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Residues in contact with ILE 882 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878E LEU* 2.8 41.0 + - + +
879E GLN* 3.5 6.3 - - - +
881E ARG* 1.3 77.8 - - + +
883E LEU* 1.3 60.0 + - + +
885E ILE* 3.9 1.2 - - - +
886E GLY* 2.9 26.7 + - - -
894E LEU* 3.8 20.6 - - + -
899E VAL* 3.8 29.4 - - + -
902E VAL* 5.7 6.5 - - + -
92R ILE* 6.2 0.2 - - + -
96R VAL* 3.8 35.2 - - + +
100R CYS* 5.1 1.9 - - - -
111R LEU* 6.1 4.5 - - + -
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Residues in contact with LEU 883 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879E GLN* 2.9 32.0 + - + +
880E ARG* 4.1 5.2 - - + +
882E ILE* 1.3 73.1 - - + +
884E GLU* 1.3 59.2 + - - +
886E GLY* 4.5 1.6 - - - +
887E LYS* 2.9 49.1 + - - +
891E ILE* 4.9 1.6 - - + +
892E THR 3.4 22.7 - - - +
893E GLU* 3.6 26.0 - - - +
894E LEU* 3.7 24.5 - - + +
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Residues in contact with GLU 884 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880E ARG* 2.8 17.1 + - - +
881E ARG* 3.3 29.9 + - - +
882E ILE 3.2 0.2 - - - -
883E LEU* 1.3 75.8 - - - +
885E ILE* 1.3 65.3 + - + +
887E LYS* 3.8 5.2 - - - +
888E LYS* 3.0 47.9 + - + +
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Residues in contact with ILE 885 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881E ARG* 3.0 26.0 + - + +
882E ILE 4.2 1.6 - - - +
884E GLU* 1.3 86.9 - - + +
886E GLY* 1.3 57.5 + - - +
888E LYS* 3.2 7.8 + - + -
889E HIS* 2.7 56.8 + - + +
93R GLU* 3.7 33.9 - - - +
96R VAL* 4.2 14.1 - - + -
97R THR* 6.4 0.4 - - - -
100R CYS* 4.4 11.0 - - - -
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Residues in contact with GLY 886 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882E ILE 2.9 17.4 + - - -
883E LEU* 3.9 0.7 - - - -
885E ILE* 1.3 78.5 - - - +
887E LYS* 1.3 49.3 + - - +
889E HIS* 2.9 4.1 + - - -
890E GLY 2.6 15.8 + - - -
891E ILE* 2.4 47.0 + - - +
100R CYS* 4.0 14.5 - - - -
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Residues in contact with LYS 887 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883E LEU* 2.9 33.0 + - - +
884E GLU* 3.8 5.2 - - - +
886E GLY* 1.3 72.9 - - - +
888E LYS* 1.3 67.6 + - - +
889E HIS 3.4 0.3 + - - -
890E GLY* 3.5 8.1 + - - -
891E ILE 3.0 16.8 + - - +
892E THR* 2.8 46.3 + - - +
893E GLU* 5.5 0.2 - - - +
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Residues in contact with LYS 888 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884E GLU* 3.0 39.5 + - + +
885E ILE* 3.2 14.1 + - + +
887E LYS* 1.3 79.5 - - - +
889E HIS* 1.3 73.7 + - + +
890E GLY 3.6 0.2 - - - -
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Residues in contact with HIS 889 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885E ILE* 2.7 43.8 + - + +
886E GLY* 2.9 9.9 + - - +
888E LYS* 1.3 89.9 + - + +
890E GLY* 1.3 57.6 + - - +
891E ILE* 3.6 5.3 + - + +
100R CYS* 4.9 16.5 - - + +
104R ARG* 4.5 27.8 + - + +
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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