Contacts of the helix formed by residues 126 - 143 (chain A) in PDB entry 5MQI
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 SER 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 5.4 0.7 - - - +
70A THR* 5.5 0.9 - - - +
123A ALA 4.0 11.6 + - - -
124A PHE 2.5 14.2 + - - +
125A ALA* 1.3 76.5 - - - +
127A GLU* 1.3 63.9 + - - +
128A LYS* 3.2 4.6 + - - +
129A ALA* 3.2 31.2 + - - +
130A PHE* 3.3 12.5 + - - -
192A ALA* 4.2 6.8 - - - +
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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
----------------------------------------------------------
126A SER* 1.3 72.9 - - - +
128A LYS* 1.3 53.9 + - - +
130A PHE* 4.3 1.5 - - - +
131A GLY* 2.7 30.5 + - - -
192A ALA* 4.3 13.7 - - + +
195A LEU* 3.6 51.7 - - + +
196A SER* 4.3 10.7 - - - +
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Residues in contact with LYS 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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70A THR* 3.3 35.8 + - + -
71A GLN* 5.3 1.4 - - - +
73A HIS* 4.6 7.9 - - - -
126A SER* 3.1 4.6 - - - +
127A GLU* 1.3 76.9 - - - +
129A ALA* 1.3 59.8 - - - +
131A GLY* 4.1 2.2 - - - +
132A VAL* 2.9 53.9 + - - +
135A GLU* 5.4 6.7 - - - +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.9 26.2 - - + -
69A LEU* 4.4 4.3 - - + +
70A THR* 3.9 13.7 - - + +
124A PHE* 4.3 20.0 - - + +
126A SER* 3.2 22.8 + - - +
128A LYS* 1.3 79.0 - - - +
130A PHE* 1.3 58.0 + - + +
132A VAL* 3.3 3.5 + - - +
133A LEU* 3.1 31.8 + - - +
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Residues in contact with PHE 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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124A PHE* 3.5 36.6 - + + -
126A SER 3.3 6.4 + - - +
127A GLU 4.3 1.1 - - - +
129A ALA* 1.3 77.3 - - + +
131A GLY* 1.3 56.6 + - - +
133A LEU* 3.7 12.8 - - + +
134A SER* 2.7 37.8 + - - -
163A VAL* 4.1 20.2 - - + -
166A ILE* 4.8 11.2 - - + -
167A LEU* 6.0 1.1 - - + -
189A LEU* 3.7 23.1 - - + -
192A ALA* 3.7 24.7 - - + +
193A ILE* 3.8 25.4 - - + -
196A SER* 3.7 17.7 + - - +
198A LEU* 3.6 27.5 - - + +
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Residues in contact with GLY 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 2.7 24.9 + - - -
128A LYS* 3.6 5.2 - - - -
129A ALA 3.2 0.4 - - - -
130A PHE* 1.3 74.1 - - - +
132A VAL* 1.3 56.7 + - - +
134A SER* 3.3 1.7 + - - -
135A GLU* 2.9 43.6 + - - +
196A SER* 3.7 13.0 - - - -
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Residues in contact with VAL 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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69A LEU* 3.6 15.3 - - + +
70A THR* 4.0 12.1 - - - -
73A HIS* 3.9 26.0 - - + +
79A PHE* 3.5 31.2 - - + -
128A LYS* 2.9 43.7 + - - +
129A ALA* 3.7 4.9 - - - +
131A GLY* 1.3 71.8 - - - +
133A LEU* 1.3 65.5 + - - +
135A GLU* 3.9 9.6 - - - +
136A THR* 2.8 32.3 + - - +
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Residues in contact with LEU 133 (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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69A LEU* 4.5 9.9 - - + -
79A PHE* 4.7 4.7 - - + -
83A ILE* 3.8 29.6 - - + -
124A PHE* 4.6 11.9 - - + -
129A ALA 3.1 18.8 + - - +
130A PHE* 3.8 18.4 - - + +
132A VAL* 1.3 76.1 - - - +
134A SER* 1.3 58.6 + - - +
136A THR* 3.7 4.6 - - - -
137A LEU* 2.9 31.5 + - - +
159A ILE* 4.2 25.9 - - + +
162A LEU* 4.2 20.6 - - + -
163A VAL* 4.3 20.4 - - + -
198A LEU* 5.5 3.6 - - + -
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Residues in contact with SER 134 (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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130A PHE 2.7 21.9 + - - -
131A GLY 3.8 2.5 - - - -
133A LEU* 1.3 71.8 - - - +
135A GLU* 1.3 59.0 + - - +
137A LEU* 4.4 0.7 - - - -
138A TYR* 2.7 33.0 + - - +
196A SER* 3.1 26.7 + - - -
197A GLY* 3.6 1.9 - - - -
198A LEU* 3.5 20.0 + - - +
201A LEU* 3.3 23.1 - - - +
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Residues in contact with GLU 135 (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 HIS* 4.3 17.5 + - - -
128A LYS* 5.4 6.5 - - - +
131A GLY* 2.9 31.5 + - - +
132A VAL* 3.9 13.1 - - - +
134A SER* 1.3 71.9 - - - +
136A THR* 1.3 64.1 + - - +
138A TYR* 3.2 7.1 + - - +
139A GLU* 2.9 36.8 + - + +
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Residues in contact with THR 136 (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 HIS* 5.5 3.3 - - - +
79A PHE* 3.6 28.6 - - + -
132A VAL* 2.8 22.3 + - - +
133A LEU 3.7 3.1 - - - -
135A GLU* 1.3 76.7 - - - +
137A LEU* 1.3 63.2 + - - +
139A GLU* 3.3 14.3 + - - +
140A LEU* 2.9 34.7 + - + +
155A LEU* 4.1 7.2 - - + -
159A ILE* 3.9 19.7 - - + -
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Residues in contact with LEU 137 (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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133A LEU 2.9 18.2 + - - +
134A SER 3.8 2.9 - - - +
136A THR* 1.3 77.6 - - - +
138A TYR* 1.3 63.2 + - - +
140A LEU* 3.3 5.9 + - - +
141A LEU* 2.9 43.4 + - + +
156A ILE* 4.1 39.9 - - + +
159A ILE* 4.2 17.9 - - + +
160A LEU* 4.3 20.2 - - + -
198A LEU* 3.8 25.6 - - + -
201A LEU* 3.9 14.6 - - + -
202A LEU* 5.9 0.4 - - + -
205A LEU* 4.5 8.5 - - + -
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Residues in contact with TYR 138 (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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134A SER* 2.7 22.3 + - - +
135A GLU* 3.3 9.0 - - - +
137A LEU* 1.3 71.2 - - - +
139A GLU* 1.3 73.0 + - + +
141A LEU* 3.2 5.2 + - - +
142A GLN* 3.0 63.9 + - + +
201A LEU* 3.8 27.0 - - + +
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Residues in contact with GLU 139 (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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135A GLU* 2.9 30.6 + - - +
136A THR* 3.6 13.1 + - - +
138A TYR* 1.3 81.9 - - + +
140A LEU* 1.3 65.3 + - + +
141A LEU 3.1 0.9 + - - -
142A GLN* 3.1 20.2 + - - +
143A LEU* 3.6 12.5 + - - +
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Residues in contact with LEU 140 (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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136A THR* 2.9 28.4 + - + +
137A LEU* 3.3 5.8 + - - +
139A GLU* 1.3 76.2 - - + +
141A LEU* 1.3 59.2 + - - +
143A LEU* 3.4 23.6 - - + +
148A ARG* 3.5 15.4 + - - -
152A ASP* 3.5 42.0 - - + +
155A LEU* 3.7 38.1 - - + -
156A ILE* 3.9 27.1 - - + +
159A ILE* 4.2 7.4 - - + -
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Residues in contact with LEU 141 (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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137A LEU* 2.9 38.9 + - + +
138A TYR* 3.2 4.2 + - - +
139A GLU 3.1 0.2 - - - -
140A LEU* 1.3 73.6 - - - +
142A GLN* 1.3 64.4 + - - +
143A LEU 2.8 16.7 - - - +
148A ARG* 3.7 17.1 + - - +
156A ILE* 4.1 18.8 - - + -
201A LEU* 4.5 14.1 - - + -
204A PHE* 4.1 23.8 - - + -
205A LEU* 3.9 37.7 - - + -
211A GLU* 4.0 14.3 - - - +
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Residues in contact with GLN 142 (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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138A TYR* 3.0 65.0 + - + +
139A GLU* 3.1 10.5 + - - +
141A LEU* 1.3 78.3 - - - +
143A LEU* 1.3 65.0 + - + +
144A GLY* 3.3 2.8 + - - -
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Residues in contact with LEU 143 (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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139A GLU 3.8 10.8 - - - +
140A LEU* 3.4 24.0 - - + +
141A LEU 2.8 19.3 - - - +
142A GLN* 1.3 78.0 - - + +
144A GLY* 1.3 71.6 + - - +
147A GLU* 5.0 4.9 - - + +
148A ARG* 3.2 23.1 + - + +
152A ASP* 3.6 31.4 - - + +
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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