Contacts of the helix formed by residues 108 - 115 (chain B) in PDB entry 3M18
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 TRP 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B TRP* 3.7 25.4 - + - -
31B ALA* 4.9 3.4 - - + -
35B GLU* 3.3 29.2 - - + +
56B LEU* 2.7 42.1 + - + +
57B GLN 4.9 3.3 + - - -
58B ILE* 4.8 1.6 - - + +
95B ALA* 3.7 38.1 - - + -
98B ILE* 3.7 34.0 - - + +
99B VAL* 4.1 5.2 - - + -
104B GLY 4.4 0.7 - - - -
105B MET* 3.0 45.6 + - + +
106B ASN 4.0 0.7 - - - -
107B ALA* 1.3 78.1 - - + +
109B VAL* 1.3 59.2 + - - +
111B TRP* 3.4 15.2 - - + +
112B ARG* 2.9 28.2 + - - +
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Residues in contact with VAL 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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67A TYR* 3.9 16.4 - - + +
91A ASN* 3.3 32.1 - - - +
115A GLY* 4.0 16.8 - - - +
139A THR* 4.0 7.4 - - + -
35B GLU* 3.3 4.3 + - - +
107B ALA 3.3 11.8 + - - +
108B TRP* 1.3 69.2 - - - +
110B ALA* 1.3 60.1 + - - +
112B ARG* 3.3 30.7 + - - +
113B ASN* 2.9 28.3 + - + +
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Residues in contact with ALA 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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139A THR* 3.8 24.9 - - + +
163A THR* 4.5 2.5 - - + -
34B PHE* 3.4 38.8 - - + +
35B GLU* 2.7 21.8 + - - +
109B VAL* 1.3 71.4 - - - +
111B TRP* 1.3 58.8 + - - +
113B ASN* 3.6 0.7 - - - +
114B ARG* 2.8 34.1 + - - +
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Residues in contact with TRP 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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23B TYR* 3.7 24.9 - + - -
27B ASN* 2.9 55.0 + - - +
31B ALA* 3.8 12.0 - - + +
35B GLU* 3.2 7.5 + - - +
105B MET* 3.1 50.9 - - + -
106B ASN* 3.7 19.5 - - - -
108B TRP* 3.4 20.9 - - + +
109B VAL 3.4 0.2 - - - -
110B ALA* 1.3 75.8 - - - +
112B ARG* 1.3 72.0 + - + +
115B CYS* 2.8 53.1 + - + +
116B LYS* 2.8 47.7 + - + -
117B GLY 5.4 0.2 - - - -
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Residues in contact with ARG 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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67A TYR* 5.8 4.6 - - - -
91A ASN* 5.0 8.3 + - - +
92A ASN 5.8 1.6 + - - -
115A GLY 5.3 4.2 + - - -
117A GLN* 6.0 2.4 - - - +
106B ASN* 2.7 62.3 + - - +
107B ALA 4.8 0.2 + - - -
108B TRP 2.9 16.8 + - - +
109B VAL* 3.6 37.9 - - - +
111B TRP* 1.3 86.1 - - + +
113B ASN* 1.3 62.4 + - - +
116B LYS* 3.7 26.8 + - + +
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Residues in contact with ASN 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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116A ASN 4.5 4.8 + - - -
117A GLN* 5.5 5.1 + - - +
139A THR* 3.4 32.8 + - + +
140A ASN* 3.0 27.8 + - - +
141A GLN* 4.7 11.5 + - - +
163A THR* 3.7 7.1 - - - +
165A GLN* 5.3 1.0 + - - -
109B VAL* 2.9 17.3 + - + +
110B ALA 3.6 4.3 - - - +
112B ARG* 1.3 79.9 - - - +
114B ARG* 1.3 79.3 + - - +
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Residues in contact with ARG 114 (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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140A ASN 4.9 0.8 + - - -
163A THR* 3.4 13.1 - - + +
164A ASN* 2.6 41.6 + - - +
165A GLN* 3.3 23.7 - - - +
187A GLY 2.9 18.4 + - - -
188A ASN 4.7 0.8 + - - -
189A GLN* 3.6 9.8 - - - +
30B CYS* 4.7 1.6 - - - -
34B PHE* 3.3 47.1 - - + -
110B ALA 2.8 18.5 + - - +
113B ASN* 1.3 85.0 + - - +
115B CYS* 1.3 57.8 + - - +
116B LYS 5.2 0.4 - - - -
118B THR* 3.5 18.4 + - - +
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Residues in contact with CYS 115 (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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30B CYS* 2.1 65.1 - - + -
31B ALA 3.6 2.2 - - - -
34B PHE* 3.8 8.5 - - - -
111B TRP* 2.8 40.9 + - + +
114B ARG* 1.3 72.0 - - - +
116B LYS* 1.3 65.0 - - - +
117B GLY 3.2 0.9 + - - -
118B THR* 2.5 27.9 + - - -
120B VAL* 3.3 10.7 - - + +
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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