Contacts of the helix formed by residues 121 - 132 (chain A) in PDB entry 3MR3
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL* 2.8 25.9 + - + +
10A ALA* 4.1 13.7 - - + +
106A PHE 5.2 0.9 - - - +
107A ALA* 4.0 12.1 - - + -
119A VAL* 3.6 27.8 + - + +
120A ASP* 1.3 71.0 - - - +
122A THR* 1.3 65.5 + - - +
123A SER 3.3 2.5 - - - -
124A ALA* 3.2 12.9 + - + -
125A VAL* 2.9 28.8 + - + +
193A GLY* 3.8 15.9 - - - +
196A ILE* 3.9 23.3 - - + -
197A VAL* 3.6 31.0 - - + -
200A MET* 4.4 4.5 - - - -
216A ILE* 5.5 0.4 - - + -
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Residues in contact with THR 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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6A ASP 3.9 19.3 - - - +
7A ARG* 3.4 12.1 - - + +
8A VAL* 3.1 28.3 + - + +
120A ASP* 3.0 18.8 + - - -
121A LEU* 1.3 76.6 - - - +
123A SER* 1.3 61.2 + - - +
125A VAL* 3.4 3.8 + - - +
126A GLN* 2.9 42.9 + - + +
189A GLN* 6.0 2.2 - - - +
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Residues in contact with SER 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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120A ASP* 4.8 6.7 + - - -
122A THR* 1.3 76.4 - - - +
124A ALA* 1.3 66.5 + - - +
126A GLN* 3.2 11.6 + - - +
127A GLU* 3.0 22.9 + - - +
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Residues in contact with ALA 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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106A PHE 4.6 13.7 - - - +
107A ALA* 5.2 2.5 - - + -
121A LEU* 3.2 22.9 + - + +
123A SER* 1.3 80.7 + - - +
125A VAL* 1.3 57.5 + - - +
127A GLU* 3.4 8.0 + - - +
128A ARG* 2.9 29.3 + - - +
196A ILE* 3.8 21.0 - - + +
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Residues in contact with VAL 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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8A VAL* 4.2 9.4 - - + -
121A LEU* 2.9 23.6 + - + +
122A THR 3.5 5.6 - - - +
124A ALA* 1.3 75.2 - - - +
126A GLN* 1.3 68.8 + - - +
128A ARG* 3.2 1.4 + - - +
129A LEU* 2.9 33.0 + - + +
189A GLN* 3.7 36.6 - - + +
192A VAL* 4.0 14.8 - - + -
193A GLY* 3.6 33.2 - - - +
196A ILE* 4.2 4.9 - - + -
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Residues in contact with GLN 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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6A ASP 5.8 0.4 + - - -
122A THR* 2.9 34.8 - - + +
123A SER* 3.2 10.3 + - - +
125A VAL* 1.3 78.8 - - - +
127A GLU* 1.3 63.0 + - - +
129A LEU* 3.7 11.3 - - - +
130A GLN* 3.0 25.8 + - - +
183A LEU* 4.8 2.8 - - - +
189A GLN* 3.9 21.9 + - - +
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Residues in contact with GLU 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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123A SER 3.0 12.5 + - - +
124A ALA* 3.6 11.0 - - - +
126A GLN* 1.3 76.1 - - - +
128A ARG* 1.3 57.1 + - - +
130A GLN* 3.3 16.7 + - - +
131A LYS* 3.0 29.5 + - - +
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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 ALA 2.9 17.0 + - - +
125A VAL 3.2 0.4 + - - +
127A GLU* 1.3 75.8 - - - +
129A LEU* 1.3 56.4 + - - +
131A LYS* 3.2 29.8 + - - +
132A LEU* 2.8 64.2 + - + +
192A VAL* 3.7 26.5 - - + -
195A VAL* 3.9 14.5 - - + +
196A ILE* 4.1 17.2 - - + +
199A GLU* 2.8 43.4 + - - -
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Residues in contact with LEU 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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125A VAL* 2.9 33.1 + - + +
126A GLN* 3.7 10.5 - - - +
128A ARG* 1.3 76.8 - - - +
130A GLN* 1.3 59.9 + - - +
132A LEU* 2.8 32.2 - - + +
180A ILE* 5.8 3.1 - - + -
183A LEU* 3.5 50.5 - - + +
188A LEU* 3.8 25.4 - - + -
189A GLN* 4.3 9.0 - - + -
192A VAL* 3.5 27.1 - - + -
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Residues in contact with GLN 130 (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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126A GLN 3.0 15.9 + - - +
127A GLU* 3.6 16.7 - - - +
129A LEU* 1.3 76.7 - - - +
131A LYS* 1.3 63.7 + - + +
132A LEU 4.4 2.6 - - - -
183A LEU* 4.4 10.4 - - + +
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Residues in contact with LYS 131 (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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127A GLU 3.0 17.5 + - - +
128A ARG* 3.2 37.9 + - - +
130A GLN* 1.3 82.2 - - + +
132A LEU* 1.3 63.1 + - + +
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Residues in contact with LEU 132 (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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128A ARG* 2.8 56.7 + - + +
129A LEU* 2.8 24.3 - - + +
130A GLN 4.4 2.9 - - - -
131A LYS* 1.3 85.8 - - + +
135A GLN* 4.0 47.9 + - + +
136A PRO 5.0 3.4 - - - +
137A ILE* 4.8 17.0 - - + -
141A LEU* 5.5 10.1 - - + -
192A VAL* 5.7 5.2 - - + -
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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