Contacts of the helix formed by residues 102 - 113 (chain B) in PDB entry 3M5B
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 VAL 102 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 5.4 0.2 - - - +
50B VAL* 4.0 23.3 - - + -
51B SER* 4.3 4.3 - - - -
54B LEU* 4.1 20.9 - - + -
74B LEU* 4.2 19.5 - - + -
77B PHE* 5.2 1.6 - - + -
78B VAL* 4.5 12.3 - - + -
97B ALA* 2.9 17.2 + - - +
100B LEU* 4.1 12.1 - - + +
101B GLY* 1.3 77.0 - - - +
103B GLN* 1.3 61.3 - - - +
104B SER* 4.2 8.1 - - - +
105B LEU* 3.9 23.1 - - + +
106B GLU* 3.1 23.2 + - - +
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Residues in contact with GLN 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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50B VAL 4.7 1.4 + - - -
101B GLY 3.1 11.1 + - - +
102B VAL* 1.3 71.6 - - - +
104B SER* 1.3 63.4 + - - +
106B GLU* 3.4 10.1 + - - +
107B GLU* 3.0 50.9 + - + +
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 4.4 11.4 - - - -
12B TYR* 2.9 30.2 + - - -
77B PHE* 3.5 19.0 - - - -
102B VAL* 4.2 5.7 - - - +
103B GLN* 1.3 78.8 - - - +
105B LEU* 1.3 59.3 + - - +
107B GLU* 3.7 11.2 - - - +
108B ALA* 3.0 27.7 + - - +
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Residues in contact with LEU 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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8B LEU* 3.9 17.7 - - + -
74B LEU* 3.8 29.6 - - + +
77B PHE* 3.8 34.3 - - + -
93B LEU* 3.6 31.9 - - + -
97B ALA* 3.9 13.9 - - + -
102B VAL* 3.3 16.0 + - + +
103B GLN 3.3 0.2 - - - -
104B SER* 1.3 79.4 + - - +
106B GLU* 1.3 66.0 + - - +
108B ALA* 3.3 0.8 + - + +
109B CYS* 3.0 39.3 + - - -
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Residues in contact with GLU 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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94B GLN* 4.2 29.1 + - + +
97B ALA* 3.5 15.0 - - + +
98B ARG* 2.5 67.7 + - - +
101B GLY* 6.0 0.9 - - - -
102B VAL 3.1 12.5 + - - +
103B GLN* 3.7 12.9 - - + +
105B LEU* 1.3 76.9 - - - +
107B GLU* 1.3 62.8 + - + +
109B CYS* 3.3 2.5 + - - +
110B TRP* 3.0 24.8 + - + +
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Residues in contact with GLU 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 GLN* 3.0 50.5 + - + +
104B SER* 3.7 8.5 - - - +
106B GLU* 1.3 75.2 - - - +
108B ALA* 1.3 57.8 + - - +
110B TRP* 3.3 9.5 + - + +
111B ARG* 2.9 46.6 + - + +
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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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8B LEU* 4.0 20.5 - - + +
9B PRO* 4.9 6.3 - - + +
77B PHE* 4.4 21.3 - - + -
104B SER 3.0 17.7 + - - +
105B LEU 3.3 4.7 + - - +
107B GLU* 1.3 76.0 - - - +
109B CYS* 1.3 63.4 + - - +
111B ARG* 3.5 9.2 + - - +
112B ALA* 3.1 22.9 + - - +
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Residues in contact with CYS 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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8B LEU* 4.0 7.2 - - - -
90B LEU* 3.8 23.6 - - + +
93B LEU* 4.0 12.8 - - - -
94B GLN* 3.7 40.6 - - + +
105B LEU* 3.0 34.8 + - - -
106B GLU 3.7 4.0 - - - +
108B ALA* 1.3 74.7 - - - +
110B TRP* 1.3 65.8 + - - +
112B ALA* 3.0 14.6 + - - +
113B ARG* 3.2 17.8 + - - +
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Residues in contact with TRP 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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94B GLN* 3.9 23.4 + - - +
106B GLU* 3.0 17.5 + - + +
107B GLU* 3.6 9.4 - - + +
109B CYS* 1.3 73.9 - - - +
111B ARG* 1.3 110.3 + - + +
113B ARG* 3.1 27.8 + - + +
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Residues in contact with ARG 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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107B GLU* 2.9 32.4 + - + +
108B ALA* 3.7 8.3 - - - +
110B TRP* 1.3 102.3 - - + +
112B ALA* 1.3 61.0 + - - +
113B ARG 3.5 1.7 + - - -
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Residues in contact with ALA 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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6B ILE* 4.2 18.3 - - + +
8B LEU* 3.9 21.1 - - + -
90B LEU* 4.1 17.7 - - + +
108B ALA 3.1 11.9 + - - +
109B CYS 3.0 10.7 + - - +
111B ARG* 1.3 76.9 - - - +
113B ARG* 1.3 62.4 + - - +
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Residues in contact with ARG 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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90B LEU* 3.4 26.7 - - - +
91B ARG* 3.5 61.6 - - - +
94B GLN* 3.1 24.3 + - - +
109B CYS 3.2 13.7 - - - +
110B TRP* 3.1 23.6 + - + +
111B ARG 3.3 2.2 - - - -
112B ALA* 1.3 82.0 - - - +
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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