Contacts of the helix formed by residues 948 - 959 (chain B) 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 948 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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904B TYR* 5.3 7.8 + - - +
946B ASN 4.7 0.2 - - - -
947B GLU* 1.3 82.1 - - + +
949B LEU* 1.3 65.4 + - - +
950B VAL 3.4 1.8 - - - -
951B ASP* 3.2 19.8 + - + +
952B GLN* 3.1 30.8 + - + +
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Residues in contact with LEU 949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904B TYR* 4.6 22.7 + - + +
907B LEU* 3.7 32.8 - - + -
908B GLN* 4.7 12.8 - - - +
911B LEU* 4.5 19.1 - - + -
936B PHE* 3.8 22.2 - - + -
944B LEU 5.0 1.3 - - - +
945B CYS* 3.2 33.0 + - - +
947B GLU* 6.1 0.2 - - + -
948B ALA* 1.3 76.4 - - - +
950B VAL* 1.3 60.5 + - - +
952B GLN* 3.4 7.8 + - - +
953B LEU* 2.9 42.9 + - + +
978B LEU* 6.4 0.4 - - + -
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Residues in contact with VAL 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 5.2 11.2 - - + +
945B CYS* 3.2 35.3 + - + +
946B ASN* 4.0 11.2 - - - +
948B ALA 5.2 0.2 - - - -
949B LEU* 1.3 75.0 - - - +
951B ASP* 1.3 62.9 + - - +
953B LEU* 4.3 1.6 - - - -
954B TRP* 2.8 15.1 + - + +
975B TYR* 2.5 36.8 + - + +
979B PHE* 3.7 23.1 - - + -
984B PRO* 4.0 24.5 - - + -
986B CYS* 4.4 6.5 - - - -
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Residues in contact with ASP 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 3.3 25.3 + - - +
946B ASN 5.6 1.7 - - - +
947B GLU 3.6 7.0 - - - +
948B ALA* 3.2 29.5 + - + +
949B LEU 3.1 0.2 - - - -
950B VAL* 1.3 82.6 - - - +
952B GLN* 1.3 59.6 + - + +
954B TRP* 3.2 8.2 + - - +
955B LYS* 2.9 42.5 + - - +
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Residues in contact with GLN 952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904B TYR* 5.4 3.3 + - - -
908B GLN* 2.9 40.3 + - - +
911B LEU* 5.1 8.7 - - + +
948B ALA* 3.1 19.9 + - + +
949B LEU* 4.0 12.1 - - + +
951B ASP* 1.3 80.2 - - + +
953B LEU* 1.3 58.6 + - - +
955B LYS* 3.3 20.3 + - + +
956B LEU* 2.9 34.5 + - + +
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Residues in contact with LEU 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911B LEU* 3.7 28.0 - - + -
945B CYS* 4.3 11.0 - - - -
949B LEU* 2.9 38.3 + - + +
950B VAL* 4.6 0.2 - - - -
952B GLN* 1.3 74.7 - - - +
954B TRP* 1.3 58.8 + - - +
956B LEU* 3.2 9.3 + - + +
957B MET* 2.9 32.3 + - + +
971B ALA* 5.4 2.1 - - + +
974B LEU* 4.1 26.2 - - + -
975B TYR* 3.2 29.8 - - + +
978B LEU* 4.5 15.9 - - + -
979B PHE* 4.6 0.2 - - + -
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Residues in contact with TRP 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B VAL* 4.9 3.6 - - + -
96B SER 4.8 8.0 + - - -
98B SER* 4.3 15.4 + - - -
100B GLN 3.6 9.2 - - - -
101B ARG* 3.6 64.0 - - + +
102B ASN 3.5 18.6 - - - -
105B TYR* 5.2 2.2 - + - -
106B PHE* 3.6 37.0 - + + -
950B VAL* 2.8 14.0 + - + +
951B ASP* 3.5 7.0 - - - +
953B LEU* 1.3 75.4 - - - +
955B LYS* 1.3 61.6 + - + +
957B MET* 3.3 10.6 + - + +
958B ASN* 3.0 49.2 + - - +
975B TYR* 2.7 35.3 + + - +
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Residues in contact with LYS 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951B ASP* 2.9 27.9 + - - +
952B GLN* 3.3 22.0 - - + +
954B TRP* 1.3 79.5 - - + +
956B LEU* 1.3 53.6 + - + +
958B ASN* 2.8 7.3 + - - +
959B SER* 2.3 49.4 + - - +
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Residues in contact with LEU 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911B LEU* 4.1 42.8 - - + +
914B ILE* 5.3 8.3 - - + -
915B GLN* 3.8 35.7 - - + +
952B GLN* 2.9 19.8 + - + +
953B LEU* 3.2 9.6 + - + +
955B LYS* 1.3 72.9 - - + +
957B MET* 1.3 61.5 + - - +
959B SER* 3.1 11.1 - - - +
960B GLY* 4.9 1.6 - - - +
961B THR* 2.2 37.3 + - + +
971B ALA* 4.7 6.3 - - + +
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Residues in contact with MET 957 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 5.9 2.2 - - + -
106B PHE* 3.5 42.0 - - + -
953B LEU* 2.9 19.1 + - + +
954B TRP* 3.5 15.3 - - + +
955B LYS 3.1 0.2 - - - -
956B LEU* 1.3 79.2 - - - +
958B ASN* 1.3 58.4 + - - +
968B ARG* 3.1 35.0 + - + +
971B ALA* 3.7 21.3 - - + +
972B VAL* 3.7 33.7 - - + +
975B TYR* 3.4 44.2 - - + -
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Residues in contact with ASN 958 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 5.1 3.1 - - - +
92B GLU* 3.5 52.2 + - - +
93B VAL* 3.6 11.9 + - - +
96B SER* 5.1 4.9 + - - +
106B PHE* 3.9 18.1 - - - -
954B TRP* 3.0 49.3 + - - +
955B LYS* 2.8 8.7 + - - +
957B MET* 1.3 76.8 - - - +
959B SER* 1.3 55.5 + - - +
968B ARG* 2.4 31.9 + - - +
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Residues in contact with SER 959 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 6.5 0.7 - - - -
92B GLU* 3.2 19.7 - - - -
955B LYS* 2.3 48.6 + - - +
956B LEU* 3.1 12.0 + - - +
958B ASN* 1.3 69.0 - - - +
960B GLY* 1.3 55.4 + - - +
961B THR* 2.4 30.2 + - - -
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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