Contacts of the helix formed by residues 99 - 109 (chain B) in PDB entry 1MQ0
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 CYS 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A CYS* 3.3 35.0 - - + -
62A LEU* 4.3 4.7 - - + -
65B CYS* 4.1 0.2 - - - -
67B GLU* 4.0 0.4 + - - -
97B SER 3.7 1.8 + - - -
98B PRO* 1.3 73.7 - - - +
100B GLY* 1.3 67.8 + - - +
101B ALA* 3.6 20.9 - - - -
102B CYS* 3.0 5.4 + - - +
103B ARG* 3.0 22.3 + - - -
147B ZN 2.3 39.1 - - - -
149B BRD 4.7 7.2 - - + +
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Residues in contact with GLY 100 (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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62A LEU* 5.1 4.2 - - - +
99B CYS* 1.3 73.0 - - - +
101B ALA* 1.3 62.1 + - - +
103B ARG* 3.2 15.1 + - - +
104B GLN* 3.1 22.2 + - - +
133B LEU* 5.2 4.6 - - - +
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Residues in contact with ALA 101 (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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62A LEU* 3.7 34.2 - - + +
68B ARG* 3.7 26.5 - - - +
99B CYS* 3.2 6.5 - - - -
100B GLY* 1.3 74.1 - - - +
102B CYS* 1.3 58.7 + - - +
104B GLN* 2.9 23.2 + - - +
105B VAL* 3.1 15.1 + - - +
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Residues in contact with CYS 102 (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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65B CYS* 3.2 14.8 - - - -
67B GLU* 3.6 34.8 - - + +
68B ARG* 3.2 28.7 - - - +
71B ILE* 4.9 0.7 - - - +
98B PRO* 4.3 3.8 - - + -
99B CYS* 3.0 8.2 + - - +
101B ALA* 1.3 78.6 - - - +
103B ARG* 1.3 57.5 + - - +
105B VAL* 3.3 1.9 + - - +
106B MET* 3.0 34.8 + - - +
147B ZN 2.4 32.3 - - - -
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Residues in contact with ARG 103 (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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97B SER* 3.1 17.6 + - - -
98B PRO* 2.9 45.5 + - + +
99B CYS 3.0 18.0 + - - +
100B GLY* 3.5 11.9 - - - +
101B ALA 3.2 0.2 - - - -
102B CYS* 1.3 75.8 - - - +
104B GLN* 1.3 57.2 + - - +
106B MET* 3.7 11.8 - - - +
107B ARG* 3.1 25.6 + - - +
129B VAL* 4.0 4.6 - - + +
132B LEU* 2.8 60.4 + - + +
133B LEU* 3.5 21.9 - - + +
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Residues in contact with GLN 104 (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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100B GLY 3.1 10.6 + - - +
101B ALA* 2.9 14.5 + - - +
103B ARG* 1.3 77.3 - - - +
105B VAL* 1.3 62.8 + - + +
107B ARG* 3.6 8.7 - - - +
108B GLU* 3.3 22.8 + - - +
133B LEU* 3.7 19.2 - - + +
137B PHE* 3.0 45.3 + - - +
138B GLY* 4.7 1.8 - - - -
139B PRO* 6.0 0.4 - - - +
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Residues in contact with VAL 105 (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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68B ARG* 3.4 37.7 - - + +
71B ILE* 3.8 32.3 - - + -
72B GLN* 5.2 6.5 - - + +
101B ALA 3.1 7.2 + - - +
102B CYS 3.3 6.7 + - - +
104B GLN* 1.3 75.3 - - + +
106B MET* 1.3 68.1 + - - +
108B GLU* 3.1 20.2 + - + +
109B PHE* 3.2 13.3 - - + -
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Residues in contact with MET 106 (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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67B GLU* 4.0 20.6 - - + -
71B ILE* 3.7 17.0 - - + -
85B ILE* 3.7 39.3 - - + -
98B PRO* 4.3 12.1 - - + -
102B CYS 3.0 25.0 + - - +
103B ARG* 3.7 19.7 - - - +
105B VAL* 1.3 77.4 - - - +
107B ARG* 1.3 57.3 + - - +
109B PHE* 2.9 20.5 + - - +
110B GLY 3.3 12.1 + - - +
113B TRP* 3.5 26.7 - - + -
115B VAL* 3.9 22.0 - - + -
129B VAL* 4.0 10.3 - - + -
132B LEU* 5.4 0.9 - - - -
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Residues in contact with ARG 107 (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 ARG 3.1 15.4 + - - +
104B GLN* 3.6 10.5 - - - +
106B MET* 1.3 79.8 - - - +
108B GLU* 1.3 64.4 + - - +
109B PHE 3.0 1.4 + - - -
110B GLY 3.3 15.4 + - - +
111B THR* 3.6 29.8 - - - +
129B VAL* 3.8 8.7 - - + +
130B GLN* 6.3 1.1 - - - +
133B LEU* 3.9 10.1 - - + -
136B SER* 2.8 28.3 + - - +
137B PHE 3.9 15.8 + - - +
138B GLY* 3.7 14.5 - - - +
139B PRO* 3.5 17.4 - - + +
140B GLU* 3.1 28.1 + - - -
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Residues in contact with GLU 108 (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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104B GLN* 3.3 13.5 + - - +
105B VAL* 3.1 18.9 + - + +
107B ARG* 1.3 80.5 + - - +
109B PHE* 1.3 79.5 + - + +
110B GLY 4.1 0.2 + - - -
139B PRO* 3.6 36.1 - - - +
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Residues in contact with PHE 109 (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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71B ILE* 3.9 22.9 - - + -
75B VAL* 3.7 29.6 - - + -
80B LYS* 3.7 50.1 - - + +
81B ASP* 5.3 0.7 - - - -
82B PHE* 3.8 19.7 + + + -
105B VAL* 3.2 25.4 - - + -
106B MET* 2.9 7.5 + - - +
108B GLU* 1.3 98.5 - - + +
110B GLY* 1.3 54.8 + - - +
113B TRP* 3.8 6.1 + - - -
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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