Contacts of the helix formed by residues 100 - 113 (chain B) in PDB entry 3MI9
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 LYS 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLU* 3.0 18.4 - - - +
99B LYS* 1.3 76.7 - - - +
101B LEU* 1.3 64.7 + - - +
102B GLU* 3.2 9.6 - - + +
103B HIS* 3.2 24.4 + - + +
104B VAL* 3.3 11.6 + - - +
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Residues in contact with LEU 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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56A LYS* 2.8 32.3 - - - +
57A GLU* 3.2 20.6 + - - +
58A GLY 4.5 2.9 - - - +
89B PHE* 3.6 20.1 - - + -
99B LYS 3.6 0.8 + - - -
100B LYS* 1.3 73.2 - - - +
102B GLU* 1.3 58.9 + - - +
104B VAL* 3.6 1.3 + - + +
105B ILE* 3.0 43.9 + - + +
130B VAL* 3.6 20.9 - - + +
133B LEU* 3.4 41.5 - - + -
134B VAL* 3.8 17.0 - - + -
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Residues in contact with GLU 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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56A LYS* 3.8 26.6 + - + +
100B LYS* 3.2 6.6 - - + +
101B LEU* 1.3 74.4 - - - +
103B HIS* 1.3 67.3 + - - +
105B ILE* 3.2 3.4 + - - +
106B LYS* 2.9 24.3 + - - +
121B THR* 4.5 14.6 - - - +
126B TYR* 3.1 30.3 + - + +
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Residues in contact with HIS 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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51B ARG 5.2 2.0 + - - -
52B LEU* 3.5 33.8 - - + +
99B LYS* 4.1 20.1 - - + +
100B LYS* 3.2 23.8 + - + +
102B GLU* 1.3 77.8 - - - +
104B VAL* 1.3 61.8 + - - +
106B LYS* 3.1 17.8 + - + +
107B VAL* 3.0 28.6 + - + +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B MET* 5.1 3.2 - - - +
52B LEU* 3.9 29.2 - - + -
85B PRO* 3.8 29.4 - - + +
88B LEU* 5.5 3.1 - - + -
89B PHE* 4.0 27.6 - - + +
92B ALA* 6.2 0.7 - - + -
99B LYS* 4.0 11.7 - - + -
100B LYS 3.3 11.7 + - - +
101B LEU 3.9 7.2 - - - +
103B HIS* 1.3 80.0 - - - +
105B ILE* 1.3 58.3 + - - +
107B VAL* 3.5 1.6 + - - +
108B ALA* 2.9 28.7 + - + +
133B LEU* 4.2 15.5 - - + -
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Residues in contact with ILE 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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56A LYS* 5.3 0.2 - - - +
101B LEU* 3.0 41.1 + - + +
102B GLU* 3.2 6.0 + - - +
104B VAL* 1.3 73.8 - - - +
106B LYS* 1.3 65.8 + - - +
108B ALA* 3.8 6.1 - - + +
109B HIS* 3.1 22.1 + - + +
126B TYR* 3.9 15.9 - - + +
129B GLN* 2.9 35.2 + - + +
130B VAL* 3.4 38.4 - - + +
133B LEU* 3.6 20.6 - - + -
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Residues in contact with LYS 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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102B GLU 2.9 12.8 + - - +
103B HIS* 3.4 21.7 + - + +
105B ILE* 1.3 75.8 - - - +
107B VAL* 1.3 72.3 + - + +
109B HIS* 2.8 17.8 + - - +
110B THR* 2.9 25.7 + - - +
118B LEU* 3.7 32.9 - - + +
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Residues in contact with VAL 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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48B MET* 3.5 29.4 - - + +
51B ARG* 3.5 35.7 - - + -
52B LEU* 3.4 30.5 - - + +
103B HIS* 3.0 17.7 + - + +
104B VAL 3.9 3.4 - - - +
106B LYS* 1.3 84.2 - - + +
108B ALA* 1.3 63.6 + - - +
110B THR* 3.2 9.1 + - - -
111B CYS* 3.0 23.3 + - - -
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Residues in contact with ALA 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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48B MET* 3.9 25.1 - - - -
85B PRO* 4.0 20.2 - - + -
104B VAL 2.9 20.6 + - - +
105B ILE* 3.8 7.0 - - - +
107B VAL* 1.3 78.2 - - - +
109B HIS* 1.3 56.4 + - - +
111B CYS* 3.3 1.9 + - - +
112B LEU* 2.9 39.1 + - + +
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Residues in contact with HIS 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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105B ILE* 3.1 15.8 + - + +
106B LYS* 2.8 10.5 + - - +
108B ALA* 1.3 72.5 - - - +
110B THR* 1.3 61.6 + - - +
113B HIS* 2.6 80.5 + + + +
116B GLU* 3.8 16.1 + - - +
117B SER 3.6 31.4 + - - -
118B LEU* 3.9 13.5 + - + +
119B PRO* 3.9 23.7 - - + +
129B GLN* 5.5 7.9 - - - +
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Residues in contact with THR 110 (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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51B ARG* 4.7 22.6 + - - +
106B LYS* 2.9 27.4 + - - +
107B VAL* 3.5 12.5 - - - -
109B HIS* 1.3 80.2 + - - +
111B CYS* 1.3 63.1 + - - +
113B HIS 4.4 2.9 - - - -
114B PRO* 3.2 29.2 - - + +
118B LEU* 5.4 5.5 - - - +
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Residues in contact with CYS 111 (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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44B LEU* 4.0 10.3 - - + -
47B ASP* 3.7 7.2 - - - -
48B MET* 3.9 18.4 - - + -
51B ARG* 3.6 34.1 - - - +
107B VAL 3.0 19.1 + - - +
108B ALA 3.6 4.3 - - - +
109B HIS 3.2 0.2 - - - -
110B THR* 1.3 79.9 - - - +
112B LEU* 1.3 61.2 + - - +
113B HIS 3.5 0.2 + - - -
114B PRO* 3.6 12.1 - - - +
47C TYR* 3.3 41.2 + - + +
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Residues in contact with LEU 112 (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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44B LEU* 4.2 11.4 - - + -
81B ASN* 3.0 59.2 - - + +
85B PRO* 5.2 4.3 - - + -
108B ALA* 2.9 26.4 + - + +
111B CYS* 1.3 72.4 - - - +
113B HIS* 1.3 90.3 + - + +
114B PRO* 3.7 3.9 - - - +
47C TYR* 3.9 18.6 - - + +
48C GLY* 5.9 1.8 - - - -
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Residues in contact with HIS 113 (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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109B HIS* 2.6 62.4 + + + +
110B THR* 4.4 1.2 - - - -
112B LEU* 1.3 105.9 + - + +
114B PRO* 1.3 67.7 - - - +
115B GLN* 3.1 4.7 + - - +
116B GLU* 3.5 39.3 + - + +
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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