Contacts of the helix formed by residues 119 - 129 (chain B) in PDB entry 3M2K
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 LEU 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B LEU* 4.4 28.0 - - + +
86B LYS* 4.5 14.8 - - + +
90B ASP 4.4 2.7 - - - +
91B LEU* 3.6 31.7 + - + +
93B GLN* 3.3 29.3 + - + +
95B ILE* 3.6 29.8 - - + -
118B THR* 1.4 73.1 - - - +
120B LYS* 1.3 60.6 + - - +
122B LEU* 3.5 13.0 + - + +
123B ALA* 3.3 20.3 + - - +
137B LEU 5.3 1.1 - - - +
138B ILE* 4.8 5.3 - - + +
141B GLN* 3.6 19.7 - - + -
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Residues in contact with LYS 120 (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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209A ASP* 4.5 15.6 + - - -
212A LYS* 5.7 5.8 - - - +
213A ARG* 5.8 4.5 - - - +
88B ILE* 5.8 7.9 - - + +
91B LEU* 3.1 33.2 + - + +
92B ASN* 4.6 11.9 - - - +
118B THR* 3.0 6.8 - - - +
119B LEU* 1.3 78.3 - - - +
121B GLU* 1.3 59.1 + - + +
123B ALA* 3.2 7.9 + - - +
124B ASP* 3.0 25.8 + - - +
206B LEU* 4.7 18.1 - - + +
210B TRP* 3.5 26.0 - - + +
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Residues in contact with GLU 121 (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 ARG* 4.2 6.8 + - - -
108B ILE* 5.3 0.5 - - - +
116B GLY 4.1 1.4 - - - +
117B MET* 2.9 38.2 - - + +
118B THR* 2.4 55.9 + - - +
120B LYS* 1.3 80.4 - - + +
122B LEU* 1.4 57.4 - - - +
124B ASP* 3.3 11.1 - - - +
125B ALA* 3.2 18.9 + - - +
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Residues in contact with LEU 122 (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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95B ILE* 3.6 34.8 - - + -
97B TYR* 4.6 3.1 - - + -
109B THR* 4.2 5.4 - - - +
117B MET* 3.8 31.0 - - + +
118B THR 3.2 15.0 + - - +
119B LEU* 3.8 15.7 - - + +
121B GLU* 1.4 73.6 - - - +
123B ALA* 1.3 59.0 + - - +
124B ASP 3.4 0.2 - - - -
125B ALA* 3.9 2.7 - - - -
126B SER* 3.1 28.4 + - - -
134B ALA* 3.5 24.1 - - + +
137B LEU* 4.2 27.8 - - + -
138B ILE* 3.8 15.1 - - + +
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Residues in contact with ALA 123 (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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77B VAL* 4.4 13.5 - - + -
80B LEU* 5.0 4.0 - - + -
91B LEU* 6.2 0.7 - - + -
119B LEU 3.3 11.4 + - - +
120B LYS* 3.2 11.2 + - - +
122B LEU* 1.3 76.6 - - - +
124B ASP* 1.3 60.3 + - - +
126B SER* 3.6 1.3 + - - -
127B LEU* 2.9 37.3 + - - +
138B ILE* 4.0 12.3 - - + -
210B TRP* 3.6 28.5 - - + -
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Residues in contact with ASP 124 (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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108B ILE* 5.4 2.1 - - - +
120B LYS 3.0 9.8 + - - +
121B GLU* 3.3 14.9 - - - +
123B ALA* 1.3 76.7 - - - +
125B ALA* 1.3 62.8 + - - +
127B LEU 3.2 0.7 + - - -
128B ARG* 2.8 69.2 + - - +
129B TYR* 4.3 7.4 - - - -
210B TRP* 3.5 28.2 + - - +
213B ARG* 4.2 4.9 + - - -
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Residues in contact with ALA 125 (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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108B ILE* 3.9 22.4 - - + -
109B THR* 5.4 0.4 - - - +
117B MET* 4.5 2.2 - - + -
121B GLU 3.2 13.4 + - - +
122B LEU* 3.8 7.4 - - - +
123B ALA 3.5 0.4 - - - -
124B ASP* 1.3 83.1 + - - +
126B SER* 1.3 57.8 + - - +
129B TYR* 3.0 40.0 + - - +
130B SER 3.3 2.1 + - - -
131B ASP* 3.3 17.4 - - + +
134B ALA* 4.1 4.9 - - + -
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Residues in contact with SER 126 (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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73B LYS* 3.3 37.0 + - - +
77B VAL* 5.3 2.2 - - - +
122B LEU 3.1 17.2 + - - -
123B ALA* 3.7 5.4 - - - -
125B ALA* 1.3 78.0 - - - +
127B LEU* 1.3 64.5 - - - +
130B SER* 3.3 12.5 + - - -
131B ASP 3.9 9.6 - - - +
134B ALA* 3.9 12.5 - - - +
135B GLN* 3.5 18.9 + - - +
138B ILE* 4.6 4.7 - - - +
234B LYS* 3.6 1.2 - - - -
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Residues in contact with LEU 127 (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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73B LYS* 3.7 27.4 - - + +
74B ALA* 4.0 13.5 - - + +
77B VAL* 4.1 12.6 - - + -
123B ALA 2.9 18.1 + - - +
124B ASP 4.1 0.9 - - - +
126B SER* 1.3 77.7 - - - +
128B ARG* 1.3 62.4 + - + +
129B TYR 3.4 0.2 - - - -
130B SER 4.6 0.2 + - - -
207B LEU* 3.8 25.8 - - + -
210B TRP* 3.7 45.7 - - + +
211B MET* 4.4 9.7 - - + +
214B ASN* 3.0 18.0 - - - +
233B ASP 5.0 0.5 - - - +
234B LYS* 3.4 23.8 - - + +
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Residues in contact with ARG 128 (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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222A ARG* 5.9 3.0 - - - +
124B ASP* 2.8 45.2 + - - +
127B LEU* 1.3 81.1 - - - +
129B TYR* 1.4 76.4 + - + +
210B TRP* 3.2 37.0 - - + +
213B ARG* 3.0 59.4 + - - +
214B ASN* 3.5 8.8 - - - +
215B THR* 2.7 55.8 + - - +
216B THR* 3.8 1.3 - - - +
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Residues in contact with TYR 129 (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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227A ASP* 3.0 37.1 + - - -
228A GLY 5.3 1.4 + - - -
1B CEF 5.4 0.2 - - - +
105B TYR* 3.4 19.2 + - - -
107B PRO* 4.0 17.3 - - + -
108B ILE* 3.3 33.4 - - + -
124B ASP* 4.3 3.8 - - - -
125B ALA* 3.0 18.6 + - - +
128B ARG* 1.4 108.6 + - + +
130B SER* 1.3 67.9 + - - +
131B ASP 3.2 0.2 - - - -
215B THR* 3.4 33.9 - - + +
216B THR* 4.0 9.4 - - + +
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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