Contacts of the helix formed by residues 87 - 101 (chain L) 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 PRO 87 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295F GLU* 3.3 8.1 - - - +
607F ARG* 5.8 0.4 - - - -
85L SER 3.8 2.4 - - - +
86L PRO* 1.3 75.4 - - - +
88L PRO* 1.3 59.8 - - - +
89L ARG* 3.3 4.0 - - + +
90L ASP* 3.6 25.5 - - + +
91L PHE* 2.8 27.3 + - - +
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Residues in contact with PRO 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295F GLU* 3.2 24.4 - - + +
299F ASP* 3.6 23.3 - - - +
607F ARG* 5.9 2.5 - - + -
87L PRO* 1.3 69.9 - - - +
89L ARG* 1.3 60.7 + - - +
91L PHE* 3.4 9.6 - - + +
92L LEU* 2.9 27.9 + - - +
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Residues in contact with ARG 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L PRO* 3.3 4.2 - - + +
88L PRO* 1.3 75.7 - - - +
90L ASP* 1.3 59.0 + - - +
92L LEU* 3.3 6.7 + - - +
93L LEU* 2.9 27.1 + - - +
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Residues in contact with ASP 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87L PRO* 3.4 25.6 + - + +
88L PRO 3.4 0.4 - - - -
89L ARG* 1.3 75.4 - - - +
91L PHE* 1.3 59.3 + - - +
93L LEU* 3.7 7.7 - - - +
94L ASP* 2.9 30.5 + - - +
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Residues in contact with PHE 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606F ASP 5.7 0.2 - - - +
607F ARG* 5.3 12.1 - - + -
608F VAL* 5.2 7.0 - - + -
622F ILE* 6.1 0.2 - - - -
624F ALA* 3.8 25.5 - - + +
86L PRO* 6.2 1.6 - - + -
87L PRO 2.8 18.1 + - - +
88L PRO* 3.4 11.4 - - + +
90L ASP* 1.3 77.8 - - - +
92L LEU* 1.3 56.9 + - - +
94L ASP* 3.5 5.0 + - - +
95L ILE* 2.9 28.3 + - - +
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Residues in contact with LEU 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624F ALA 5.9 0.7 - - - -
88L PRO 2.9 16.5 + - - +
89L ARG* 3.3 7.4 + - - +
91L PHE* 1.3 73.4 - - - +
93L LEU* 1.3 60.9 + - - +
95L ILE* 3.4 7.8 - - - +
96L ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L ARG 2.9 17.4 + - - +
90L ASP* 3.7 9.2 - - - +
91L PHE 3.3 0.2 - - - -
92L LEU* 1.3 73.7 - - - +
94L ASP* 1.3 58.7 + - - +
96L ALA* 3.3 6.7 + - - +
97L ARG* 2.9 28.9 + - - +
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Residues in contact with ASP 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622F ILE* 3.5 27.6 - - + +
90L ASP 2.9 17.2 + - - +
91L PHE* 3.9 5.4 - - - +
93L LEU* 1.3 73.4 - - - +
95L ILE* 1.3 61.1 + - - +
97L ARG* 3.7 6.7 - - - +
98L GLN* 2.9 27.0 + - - +
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Residues in contact with ILE 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622F ILE* 3.7 15.7 - - + +
624F ALA* 4.6 15.5 - - + +
91L PHE 2.9 19.8 + - - +
92L LEU* 3.4 10.3 - - - +
94L ASP* 1.3 76.5 - - - +
96L ALA* 1.3 57.3 + - - +
99L ARG* 2.8 38.9 + - + +
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Residues in contact with ALA 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L LEU 2.9 17.5 + - - +
93L LEU* 3.3 6.5 + - - +
95L ILE* 1.3 74.4 - - - +
97L ARG* 1.3 58.0 + - - +
99L ARG* 4.9 0.9 - - - -
100L ASN* 2.8 35.4 + - - +
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Residues in contact with ARG 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L LEU 2.9 18.0 + - - +
94L ASP* 3.7 8.3 - - - +
96L ALA* 1.3 80.2 - - - +
98L GLN* 1.3 62.4 + - + +
100L ASN* 3.9 2.9 - - - +
101L GLN* 3.6 14.7 + - - +
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Residues in contact with GLN 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619F PRO* 4.7 12.1 - - + +
620F LEU 4.2 4.3 - - - +
621F ARG* 4.1 11.4 + - - -
622F ILE* 3.7 25.1 - - + +
94L ASP 2.9 19.4 + - - +
97L ARG* 1.3 72.5 - - - +
99L ARG* 1.3 60.1 + - - +
101L GLN* 2.9 29.7 + - - +
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Residues in contact with ARG 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621F ARG* 4.0 13.4 + - - +
622F ILE* 4.9 5.5 - - - +
657F LEU 4.9 1.6 - - - +
658F ASN* 3.3 33.1 - - - +
659F GLY* 4.8 5.6 - - - +
95L ILE* 2.8 22.7 + - + +
96L ALA* 4.9 1.1 - - - -
98L GLN* 1.3 74.6 - - - +
100L ASN* 1.3 64.4 + - - +
101L GLN 3.3 4.8 - - - +
102L THR* 5.2 0.9 - - - -
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Residues in contact with ASN 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L ALA 2.8 23.5 + - - +
97L ARG* 3.9 4.9 - - - +
98L GLN 3.2 0.2 - - - -
99L ARG* 1.3 77.0 - - - +
101L GLN* 1.3 60.7 + - - +
102L THR* 3.5 5.4 + - - -
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Residues in contact with GLN 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620F LEU 4.5 4.7 - - - +
621F ARG* 3.7 12.1 + - - -
97L ARG 3.6 8.9 + - - +
98L GLN* 2.9 23.4 + - - +
99L ARG 3.8 3.1 - - - +
100L ASN* 1.3 77.5 - - - +
102L THR* 1.3 60.0 + - - +
103L PRO* 3.6 7.5 - - + -
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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