Contacts of the helix formed by residues 87 - 101 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295G GLU* 3.3 8.7 - - - +
607G ARG* 6.0 0.2 - - - -
85M SER 3.9 2.4 - - - -
86M PRO* 1.3 73.4 - - - +
88M PRO* 1.3 53.4 - - - +
89M ARG* 4.3 4.9 - - + +
90M ASP* 3.0 26.3 + - + +
91M PHE* 2.7 32.3 + - - +
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Residues in contact with PRO 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295G GLU* 3.3 18.6 - - + +
299G ASP* 3.4 27.8 - - - +
607G ARG* 6.2 1.6 - - + -
86M PRO 4.6 0.2 - - - +
87M PRO* 1.3 69.9 - - - +
89M ARG* 1.3 61.6 + - - +
91M PHE* 3.3 11.0 - - + +
92M LEU* 2.9 28.2 + - - +
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Residues in contact with ARG 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M PRO* 3.2 4.7 - - + -
88M PRO* 1.3 79.2 - - - +
90M ASP* 1.3 57.6 + - - +
92M LEU* 3.3 6.3 + - - +
93M LEU* 2.9 28.6 + - - +
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Residues in contact with ASP 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M PRO* 6.4 0.2 - - + -
87M PRO* 3.0 26.0 + - + +
89M ARG* 1.3 74.3 - - - +
91M PHE* 1.3 60.3 + - - +
93M LEU* 3.7 7.8 - - - +
94M ASP* 2.9 30.7 + - - +
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Residues in contact with PHE 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607G ARG* 5.6 10.1 - - + -
608G VAL* 5.6 2.5 - - + -
622G ILE* 5.7 0.9 - - - -
624G ALA* 3.9 31.9 - - + +
86M PRO* 6.1 1.3 - - + -
87M PRO 2.7 16.2 + - - +
88M PRO* 3.3 15.3 - - + +
89M ARG 3.2 0.2 - - - -
90M ASP* 1.3 74.9 - - - +
92M LEU* 1.3 56.3 + - - +
94M ASP* 3.4 6.1 + - - +
95M ILE* 2.8 28.8 + - - +
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Residues in contact with LEU 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624G ALA 6.0 0.4 - - - -
88M PRO 2.9 16.1 + - - +
89M ARG* 3.8 5.8 - - - +
91M PHE* 1.3 76.3 - - - +
93M LEU* 1.3 57.9 + - - +
95M ILE* 3.3 8.8 + - - +
96M ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M ARG 2.9 17.4 + - - +
90M ASP* 3.7 8.7 - - - +
91M PHE 3.3 0.2 - - - -
92M LEU* 1.3 73.7 - - - +
94M ASP* 1.3 59.8 + - - +
96M ALA* 3.2 7.0 + - - +
97M ARG* 2.9 28.5 + - - +
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Residues in contact with ASP 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622G ILE* 3.7 21.9 - - + +
90M ASP 2.9 17.2 + - - +
91M PHE* 3.8 4.9 - - - +
93M LEU* 1.3 73.3 - - - +
95M ILE* 1.3 59.9 + - - +
97M ARG* 3.6 6.8 - - - +
98M GLN* 2.9 34.1 + - - +
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Residues in contact with ILE 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622G ILE* 3.7 15.9 - - + +
624G ALA* 5.4 10.8 - - + +
91M PHE 2.8 17.1 + - - +
92M LEU* 3.3 11.7 - - - +
94M ASP* 1.3 77.5 - - - +
96M ALA* 1.3 57.4 + - - +
99M ARG* 2.8 40.8 + - + +
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Residues in contact with ALA 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92M LEU 2.9 14.0 + - - +
93M LEU* 3.6 10.1 - - - +
95M ILE* 1.3 74.9 - - - +
97M ARG* 1.3 52.3 + - - +
99M ARG 5.4 0.2 - - - -
100M ASN* 2.6 40.9 + - - +
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Residues in contact with ARG 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93M LEU 2.9 16.8 + - - +
94M ASP* 3.6 8.7 - - - +
95M ILE 3.2 0.2 - - - -
96M ALA* 1.3 79.1 - - - +
98M GLN* 1.3 63.2 + - + +
100M ASN* 3.3 12.7 - - - +
101M GLN* 3.4 7.1 + - - +
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Residues in contact with GLN 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619G PRO* 4.8 11.9 - - + +
620G LEU 4.6 2.8 - - - +
621G ARG* 4.1 11.9 + - - -
622G ILE* 4.1 20.2 - - + +
94M ASP 2.9 16.9 + - - +
97M ARG* 1.3 73.0 - - + +
99M ARG* 1.3 61.8 + - - +
101M GLN* 2.9 34.6 + - - +
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Residues in contact with ARG 99 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621G ARG* 3.9 12.9 - - - +
622G ILE* 4.6 8.3 - - - +
657G LEU 5.0 0.7 - - - +
658G ASN* 3.3 35.8 - - - +
659G GLY* 5.2 3.1 - - - -
660G ASN* 5.6 0.4 - - - +
95M ILE* 2.8 23.8 + - + +
96M ALA* 5.1 0.4 - - - -
98M GLN* 1.3 73.9 - - - +
100M ASN* 1.3 62.8 + - - +
101M GLN 4.1 3.5 - - - +
102M THR* 5.3 0.9 - - - -
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Residues in contact with ASN 100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96M ALA* 2.6 25.4 + - - +
97M ARG* 3.3 7.0 - - - +
98M GLN 3.1 0.2 - - - -
99M ARG* 1.3 80.0 - - - +
101M GLN* 1.3 59.1 + - - +
102M THR* 3.4 6.4 + - - -
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Residues in contact with GLN 101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620G LEU 4.7 3.1 - - - +
621G ARG* 3.6 15.1 + - - -
97M ARG 3.4 7.9 + - - +
98M GLN* 2.9 27.8 + - - +
99M ARG 4.1 1.3 - - - +
100M ASN* 1.3 78.8 - - - +
102M THR* 1.3 60.3 + - - +
103M PRO* 3.6 7.1 - - + -
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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