Contacts of the helix formed by residues 144 - 154 (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 GLY 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B LEU* 2.7 36.1 + - - +
140B LYS* 4.6 2.2 - - - -
142B ILE* 3.2 2.0 - - - +
143B GLY* 1.4 70.9 - - - +
145B PRO* 1.4 68.4 - - - +
146B GLU 3.5 2.5 - - - -
147B SER* 3.0 17.7 - - - -
148B LEU* 3.1 9.4 + - - +
165B PHE* 5.0 3.8 - - - -
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Residues in contact with PRO 145 (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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139B LEU* 4.1 14.1 - - + -
144B GLY* 1.4 79.5 - - - +
146B GLU* 1.3 62.7 + - - +
147B SER 3.1 1.8 - - - -
148B LEU* 3.5 8.5 - - + +
149B LYS* 2.8 27.0 + - - +
162B PRO* 3.7 20.1 - - + +
163B GLU* 3.7 35.4 - - - +
164B ARG 3.9 17.3 - - - +
165B PHE* 4.4 10.1 - - + -
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Residues in contact with GLU 146 (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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144B GLY 3.5 0.8 - - - -
145B PRO* 1.3 82.4 - - - +
147B SER* 1.3 63.4 + - - +
149B LYS* 3.6 35.1 + - + +
150B LYS* 3.3 23.9 + - + +
162B PRO 4.6 1.0 - - - +
163B GLU* 4.5 12.3 - - - +
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Residues in contact with SER 147 (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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142B ILE* 3.0 25.3 + - - -
143B GLY* 3.4 18.0 + - - -
144B GLY 3.0 14.1 - - - -
146B GLU* 1.3 82.0 - - - +
148B LEU* 1.3 56.0 + - - +
150B LYS* 3.5 12.1 + - - +
151B GLU* 2.8 31.1 + - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 4.2 19.7 - - + -
75B LEU 4.3 1.6 - - - +
76B THR* 3.8 32.3 - - + +
79B VAL* 3.3 39.5 - - + -
135B GLN* 5.3 0.7 - - - +
139B LEU* 4.7 7.4 - - + -
142B ILE* 4.5 12.3 - - + -
144B GLY 3.1 12.8 + - - +
145B PRO* 3.3 7.6 + - + +
146B GLU 3.3 0.4 - - - -
147B SER* 1.3 73.6 - - - +
149B LYS* 1.3 70.7 + - - +
150B LYS 3.1 0.9 - - - -
151B GLU* 3.1 10.6 + - - +
152B LEU* 3.1 24.9 + - + +
162B PRO* 4.0 19.1 - - + -
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Residues in contact with LYS 149 (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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145B PRO 2.8 18.8 + - - +
146B GLU* 3.6 36.6 + - + +
148B LEU* 1.3 78.5 - - - +
150B LYS* 1.3 59.8 + - - +
151B GLU 2.8 6.8 + - - -
152B LEU* 3.1 3.0 + - - +
153B ARG* 3.0 67.3 + - + +
161B ASN* 4.7 7.9 + - - +
162B PRO* 3.7 24.7 + - + +
163B GLU* 3.1 26.9 + - - -
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Residues in contact with LYS 150 (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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146B GLU* 3.3 18.0 + - + +
147B SER* 3.5 13.4 + - - +
148B LEU 3.1 0.8 - - - -
149B LYS* 1.3 82.3 - - + +
151B GLU* 1.3 71.2 + - + +
152B LEU 3.4 0.2 - - - -
153B ARG* 4.0 8.0 - - - +
154B LYS* 3.3 48.1 + - + +
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Residues in contact with GLU 151 (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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79B VAL* 4.2 28.5 - - + +
82B GLN* 4.0 16.8 + - - +
83B GLN* 4.3 14.6 - - - +
142B ILE* 6.4 0.2 - - + -
147B SER* 2.8 27.2 + - - +
148B LEU 3.8 4.3 - - - +
149B LYS 2.9 0.6 - - - -
150B LYS* 1.3 91.0 + - + +
152B LEU* 1.3 66.0 + - - +
153B ARG 3.4 0.2 - - - -
154B LYS* 3.3 33.9 + - - +
155B ILE* 3.3 24.8 + - - +
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Residues in contact with LEU 152 (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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72B ILE* 4.4 4.5 - - + -
75B LEU* 4.1 22.4 - - + -
79B VAL* 4.4 1.6 - - + -
148B LEU* 3.1 42.5 + - + +
149B LYS* 3.6 4.5 - - - +
151B GLU* 1.3 81.2 - - - +
153B ARG* 1.3 62.7 + - - +
154B LYS 3.0 0.9 - - - -
155B ILE* 2.8 27.7 + - + +
157B ASP* 3.1 29.4 + - + +
160B THR* 3.7 34.8 - - + +
162B PRO* 4.6 5.6 - - + -
189B SER* 5.4 0.9 - - - +
193B PHE* 4.4 22.2 - - + -
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Residues in contact with ARG 153 (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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149B LYS* 3.0 55.4 + - + +
150B LYS* 4.1 7.0 - - - +
152B LEU* 1.3 79.2 - - - +
154B LYS* 1.3 60.4 + - - +
155B ILE 3.1 1.4 + - - -
156B GLY* 3.3 12.6 + - - -
157B ASP 2.3 41.3 + - - -
158B GLU* 3.2 47.7 + - - +
159B VAL 4.2 0.8 + - - -
160B THR* 3.0 31.7 + - - +
161B ASN* 3.5 13.5 - - - +
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Residues in contact with LYS 154 (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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82B GLN* 6.1 0.4 - - - +
150B LYS* 3.3 45.2 + - + +
151B GLU* 3.3 35.3 + - - +
152B LEU 3.0 0.6 - - - -
153B ARG* 1.3 79.0 - - - +
155B ILE* 1.3 61.6 + - + +
156B GLY 3.4 1.1 + - - -
198B LYS* 5.0 3.3 + - - -
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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