Contacts of the helix formed by residues 119 - 129 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.7 33.4 - - + -
86A LYS* 4.7 10.3 - - + -
90A ASP 4.0 10.1 - - - +
91A LEU* 3.0 27.5 + - + +
93A GLN* 3.4 29.1 + - - +
95A ILE* 3.7 17.0 - - + +
118A THR* 1.3 69.6 - - - +
120A LYS* 1.3 66.9 + - - +
122A LEU* 3.1 11.4 + - + +
123A ALA* 2.8 23.1 + - - +
138A ILE* 4.4 15.7 - - + -
141A GLN* 4.0 19.1 - - + +
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE* 5.2 9.2 - - - -
91A LEU* 2.6 32.2 + - + +
92A ASN* 4.3 14.6 - - - +
118A THR* 2.8 6.5 + - - +
119A LEU* 1.3 74.1 - - - +
121A GLU* 1.3 66.5 + - + +
123A ALA* 3.0 8.7 + - - +
124A ASP* 2.9 23.2 + - + +
206A LEU* 4.5 29.0 - - - +
210A TRP* 3.8 21.4 - - + +
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ARG* 4.7 4.7 + - - -
112A HIS* 5.8 4.2 + - - -
116A GLY 5.0 0.3 - - - +
117A MET* 3.5 33.0 - - + +
118A THR* 2.3 54.4 + - - +
120A LYS* 1.3 70.5 - - + +
122A LEU* 1.3 53.2 - - - +
124A ASP* 3.5 7.1 - - - +
125A ALA* 3.1 22.3 + - - +
205B GLU* 5.4 3.1 - - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 3.5 41.1 - - + -
97A TYR* 5.2 2.2 - - + -
109A THR* 4.3 3.8 - - - +
117A MET* 3.9 32.3 - - + +
118A THR 3.0 8.1 + - - +
119A LEU* 3.5 13.9 - - + +
121A GLU* 1.3 71.7 - - - +
123A ALA* 1.3 66.1 + - - +
125A ALA* 4.6 0.7 - - - +
126A SER* 3.2 23.9 + - - -
134A ALA* 3.8 26.6 - - + +
137A LEU* 4.3 26.0 - - + -
138A ILE* 3.9 15.0 - - + +
141A GLN* 6.4 0.4 - - + -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL* 4.3 12.6 - - + -
80A LEU* 4.9 7.4 - - + -
91A LEU* 5.7 0.9 - - + -
119A LEU 2.8 16.0 + - - +
120A LYS* 3.4 6.1 - - - +
122A LEU* 1.3 66.6 - - - +
124A ASP* 1.3 65.5 + - - +
126A SER* 3.4 0.7 + - - -
127A LEU* 3.0 32.5 + - - +
138A ILE* 3.8 14.7 - - + +
210A TRP* 3.2 38.6 - - + -
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Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LYS* 2.9 13.7 + - + +
121A GLU* 3.5 9.2 - - - +
123A ALA* 1.3 75.5 - - - +
125A ALA* 1.4 57.5 + - - +
127A LEU 3.1 0.9 + - - -
128A ARG* 2.7 78.3 + - - +
129A TYR* 4.9 1.0 - - - -
210A TRP* 2.9 33.9 + - - +
213A ARG* 3.7 8.5 + - - -
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ILE* 3.7 37.0 - - + -
109A THR* 5.7 0.2 - - - +
117A MET* 4.6 4.5 - - + -
121A GLU 3.1 17.5 + - - +
122A LEU 4.0 3.6 - - - +
123A ALA 3.5 0.2 - - - -
124A ASP* 1.4 77.0 + - - +
126A SER* 1.3 56.9 + - - +
129A TYR* 3.1 14.2 - - - +
130A SER 3.1 19.8 + - - -
131A ASP* 3.2 14.5 + - + +
134A ALA* 4.4 4.9 - - + -
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LYS* 3.3 31.9 + - - +
77A VAL* 5.6 1.3 - - - -
122A LEU 3.2 16.1 + - - -
123A ALA 3.7 4.7 - - - -
124A ASP 3.1 0.8 - - - -
125A ALA* 1.3 80.4 - - - +
127A LEU* 1.3 63.7 - - - +
130A SER* 3.2 17.5 - - - -
131A ASP 3.6 14.2 + - - +
134A ALA* 4.1 7.0 - - - -
135A GLN* 3.6 12.3 + - - +
138A ILE* 4.4 9.6 - - - +
234A LYS* 3.7 1.4 - - - -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LYS 3.6 26.9 - - - +
74A ALA* 3.8 17.3 - - + +
77A VAL* 4.0 13.9 - - + -
123A ALA 3.0 20.6 + - - +
124A ASP 4.0 0.4 - - - +
126A SER* 1.3 84.7 - - - +
128A ARG* 1.3 61.5 + - - +
129A TYR 3.4 0.7 - - - -
130A SER 4.2 0.6 + - - -
207A LEU* 4.0 14.1 - - + -
210A TRP* 3.4 49.4 - - + +
211A MET* 5.0 9.4 - - + +
214A ASN* 3.2 15.8 - - - +
216A THR* 4.8 0.2 + - - -
233A ASP 4.8 1.4 - - - +
234A LYS* 3.4 23.5 + - + +
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASP* 2.7 53.4 + - - +
127A LEU* 1.3 74.1 - - - +
129A TYR* 1.3 84.3 + - + +
210A TRP* 3.4 28.3 - - + +
213A ARG* 2.9 51.2 + - - +
214A ASN* 3.2 11.5 - - - +
215A THR* 2.7 46.4 + - - +
216A THR* 3.7 1.4 - - - +
209B ASP* 3.1 25.9 + - - +
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Residues in contact with TYR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TYR* 3.8 18.1 + - - -
107A PRO* 4.3 15.3 - - + -
108A ILE* 3.5 34.5 - - + -
124A ASP* 4.9 0.7 - - - -
125A ALA* 3.1 18.5 + - - +
128A ARG* 1.3 117.6 + - + +
130A SER* 1.3 64.3 + - - +
215A THR* 4.1 24.3 - - + +
216A THR* 3.5 12.9 - - - +
209B ASP* 5.4 1.4 + - - -
212B LYS* 4.2 13.3 + - - +
230B GLU* 3.2 39.4 + - - -
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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