Contacts of the helix formed by residues 127 - 142 (chain A) in PDB entry 3MOS
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 GLN 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A SER 5.5 0.2 + - - -
121A ALA 5.4 4.0 + - - +
122A THR* 5.6 2.5 - - + -
124A SER* 3.2 34.4 + - - +
125A LEU 3.3 4.9 - - - +
126A GLY* 1.3 81.7 - - - +
128A GLY* 1.3 66.4 + - - +
129A LEU 3.3 2.5 - - - -
130A GLY* 3.3 6.4 + - - +
131A ALA* 3.2 18.5 + - - +
162A SER* 5.1 0.4 - - - +
371A SER* 3.9 9.5 + - - +
398A ASP* 3.3 23.9 - - - +
399A GLN* 3.5 31.2 + - - +
402A MET* 3.4 26.4 - - - +
619A EDO 2.7 34.7 + - - +
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Residues in contact with GLY 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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72A VAL* 3.6 21.9 - - - +
74A SER* 3.1 16.7 + - - -
120A VAL* 5.4 0.2 - - - -
122A THR* 4.0 12.8 - - - +
127A GLN* 1.3 76.2 - - - +
129A LEU* 1.4 59.4 + - - +
131A ALA* 3.3 4.9 + - - +
132A ALA* 2.9 29.6 + - - +
151A CYS* 3.7 7.4 - - - -
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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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74A SER* 3.8 3.2 + - - -
126A GLY 5.0 0.6 - - - +
127A GLN 3.3 1.4 - - - +
128A GLY* 1.4 77.5 - - - +
130A GLY* 1.3 56.4 + - - +
132A ALA* 3.3 2.6 + - + +
133A CYS* 2.9 29.4 + - - -
151A CYS* 3.6 31.0 - - + -
153A LEU* 4.2 17.9 - - + +
163A VAL* 3.9 18.2 - - + +
166A ALA* 3.6 21.5 - - + -
167A MET* 3.6 33.0 - - + +
178A LEU* 4.3 12.1 - - + -
180A ALA* 4.2 15.3 - - + -
211A TRP* 4.3 11.0 - - + -
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Residues in contact with GLY 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 GLY 5.3 1.6 + - - -
127A GLN* 3.3 5.8 + - - +
129A LEU* 1.3 77.1 - - - +
131A ALA* 1.3 63.2 + - - +
133A CYS* 3.2 6.2 + - - +
134A GLY 3.1 16.8 + - - -
162A SER 5.6 0.4 + - - -
166A ALA* 3.7 6.1 - - - +
368A ASN* 3.5 27.6 - - - -
371A SER* 3.7 17.2 - - - +
372A ILE* 3.4 6.4 - - - +
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Residues in contact with ALA 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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72A VAL* 5.2 0.2 - - + -
120A VAL* 4.0 36.1 - - + -
127A GLN 3.2 11.1 + - - +
128A GLY* 3.3 7.6 + - - +
130A GLY* 1.3 77.3 - - - +
132A ALA* 1.3 57.5 + - - +
134A GLY 3.0 2.9 + - - -
135A MET* 3.0 27.4 + - + +
371A SER* 3.4 18.1 - - - +
374A VAL* 5.0 0.2 - - + -
375A GLY* 3.4 12.2 - - - +
619A EDO 4.4 9.0 - - - -
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Residues in contact with ALA 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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72A VAL* 4.0 7.0 - - + +
128A GLY 2.9 20.0 + - - +
129A LEU* 3.5 5.6 - - - +
131A ALA* 1.3 68.2 - - - +
133A CYS* 1.4 61.1 + - - +
135A MET* 3.1 8.5 + - - +
136A ALA* 2.8 31.0 + - - +
149A VAL* 3.7 24.6 - - + +
151A CYS* 3.8 23.8 - - + -
178A LEU* 4.0 8.5 - - + -
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Residues in contact with CYS 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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129A LEU* 2.9 20.3 + - - -
130A GLY 3.2 3.3 + - - +
132A ALA* 1.4 75.1 - - - +
134A GLY* 1.3 54.5 + - - +
136A ALA 4.5 0.4 - - - +
137A TYR* 2.8 35.0 + - - +
166A ALA* 3.6 33.0 - - - -
169A PHE* 3.7 14.7 - - + -
170A ALA* 4.1 3.1 - - - -
175A LEU* 3.8 9.5 - - + +
178A LEU* 3.7 22.4 - - - -
372A ILE* 3.3 23.3 - - + -
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Residues in contact with GLY 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 GLY 3.1 8.4 + - - -
131A ALA 3.0 8.6 + - - -
133A CYS* 1.3 74.1 - - - +
135A MET* 1.3 60.8 + - - +
137A TYR* 3.8 0.8 - - - +
138A THR* 3.0 30.1 + - - -
372A ILE* 3.5 31.8 - - - +
375A GLY 3.9 6.5 - - - -
376A CYS* 3.6 7.8 - - - -
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Residues in contact with MET 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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70A ARG* 3.7 33.2 - - + +
71A PHE 5.8 0.2 - - - +
72A VAL* 3.7 32.5 - - + -
119A ASP* 3.9 29.4 - - + +
120A VAL* 4.0 19.3 - - + -
131A ALA* 3.0 19.4 + - + +
132A ALA* 3.1 6.9 + - - +
134A GLY* 1.3 78.9 - - - +
136A ALA* 1.3 56.6 + - - +
138A THR* 3.4 6.2 + - - -
139A GLY* 2.9 24.8 + - - -
147A TYR* 3.8 7.7 + - + -
149A VAL* 4.1 11.2 - - + -
375A GLY 3.7 16.6 - - - +
378A THR* 3.7 11.2 - - + +
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Residues in contact with ALA 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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132A ALA 2.8 20.5 + - - +
133A CYS 4.0 2.5 - - - +
135A MET* 1.3 70.9 - - - +
137A TYR* 1.3 65.0 + - - +
139A GLY* 4.9 0.2 - - - -
140A LYS* 2.9 23.2 + - - +
149A VAL* 3.7 14.3 - - + +
175A LEU* 4.2 9.0 - - + -
177A ASN* 3.1 33.1 + - - +
178A LEU* 3.9 20.0 - - + -
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Residues in contact with TYR 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 CYS 2.8 21.9 + - - +
134A GLY* 3.8 6.1 - - - +
136A ALA* 1.3 71.1 - - - +
138A THR* 1.3 58.2 + - - +
141A TYR* 2.8 58.6 + + + +
142A PHE* 3.5 34.5 - + - -
169A PHE* 3.8 20.9 - + + -
173A TYR* 3.7 34.4 - + + -
175A LEU* 3.8 10.4 - - + +
357A ASP 5.1 3.6 + - - -
359A PHE 4.1 9.4 + - - -
360A ILE* 3.5 39.0 - - + +
376A CYS* 5.1 2.0 - - - -
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Residues in contact with THR 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 GLY 3.0 19.3 + - - -
135A MET* 3.5 6.1 - - - -
137A TYR* 1.3 77.6 - - - +
139A GLY* 1.3 56.1 + - - +
142A PHE* 2.9 30.4 + - + -
143A ASP* 2.7 53.0 + - - +
147A TYR* 3.7 4.0 - - - +
375A GLY 5.4 0.7 - - - +
376A CYS* 3.4 26.2 + - - +
381A ARG* 3.9 24.0 - - + -
382A THR* 4.4 1.1 - - + +
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Residues in contact with GLY 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 MET 2.9 11.1 + - - -
136A ALA 3.3 2.6 + - - -
138A THR* 1.3 78.2 - - - +
140A LYS* 1.3 56.0 + - - +
143A ASP* 4.1 2.7 - - - -
144A LYS* 3.0 6.8 + - - -
145A ALA 2.9 33.1 + - - +
147A TYR* 3.2 34.0 + - - -
177A ASN* 4.2 5.2 - - - -
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Residues in contact with LYS 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 ALA 2.9 16.8 + - - +
137A TYR 4.1 1.6 - - - +
139A GLY* 1.3 79.3 - - - +
141A TYR* 1.3 99.4 + - + +
144A LYS* 3.7 15.9 - - - +
145A ALA 5.2 1.6 - - - -
174A LYS* 2.6 36.0 + - - +
175A LEU* 4.8 1.6 - - + -
176A ASP* 3.2 24.7 + - - +
177A ASN* 3.7 16.3 - - + +
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Residues in contact with TYR 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 TYR* 2.8 72.0 + + + +
140A LYS* 1.3 112.5 + - + +
142A PHE* 1.3 66.6 + - + +
144A LYS* 3.3 23.6 - - - +
173A TYR* 2.6 34.0 + + + -
174A LYS* 4.2 3.6 - - - +
175A LEU* 4.0 5.2 - - + -
357A ASP 5.7 1.8 - - - +
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Residues in contact with PHE 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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137A TYR* 3.5 34.5 - + - -
138A THR* 2.9 36.2 + - + +
141A TYR* 1.3 84.3 - - + +
143A ASP* 1.3 64.9 + - - +
144A LYS* 3.2 11.2 - - - +
294A PRO* 5.0 2.9 - - - +
336A ILE* 3.8 41.1 - - + -
357A ASP 3.5 24.9 - - - -
358A ARG* 4.3 8.3 - - + -
360A ILE* 4.1 11.2 - - + -
376A CYS* 4.3 0.7 - - - -
382A THR* 3.8 17.7 - - + -
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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