Contacts of the helix formed by residues 132 - 145 (chain A) in PDB entry 2XMS
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 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASP* 3.4 14.8 - - - -
131A VAL* 1.3 70.9 - - - +
133A ALA* 1.3 63.4 + - - -
135A ALA* 3.0 12.0 + - - +
136A TYR* 3.2 10.7 + - - +
155A ILE 2.8 18.2 + - - -
156A ASN* 3.8 18.5 - - - +
157A ILE* 4.7 2.3 - - - -
158A ASP 5.2 1.4 + - - -
186A HIS* 4.6 6.7 - - - -
223A TYR* 4.6 6.9 - - - -
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Residues in contact with ALA 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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56A ASP* 3.0 9.4 + - - +
57A VAL* 3.8 20.4 - - + -
107A LEU* 4.3 5.3 - - + +
132A GLY* 1.3 71.3 - - - -
134A GLY* 1.3 56.1 + - - +
136A TYR* 3.2 6.2 + - - +
137A ILE* 3.0 32.1 + - - +
219A TYR* 3.5 25.1 - - + +
223A TYR* 3.6 32.9 - - + -
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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
----------------------------------------------------------
54A TYR* 3.5 32.7 - - - +
55A HIS 3.5 10.9 + - - -
130A GLY* 3.8 7.0 - - - -
131A VAL 3.0 6.8 + - - -
133A ALA* 1.3 77.2 - - - +
135A ALA* 1.3 57.0 + - - +
137A ILE* 3.6 2.5 + - - +
138A LEU* 3.0 35.2 + - - +
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Residues in contact with ALA 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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130A GLY* 3.6 24.7 - - - +
131A VAL 3.6 5.5 - - - +
132A GLY 3.0 10.4 + - - +
134A GLY* 1.3 75.9 - - - +
136A TYR* 1.3 64.1 + - - +
138A LEU* 3.5 0.4 + - - -
139A ALA* 3.0 25.5 + - - +
154A LEU* 3.6 14.7 - - + +
155A ILE 3.6 20.4 - - - +
157A ILE* 3.7 17.4 - - + +
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Residues in contact with TYR 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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107A LEU* 3.5 32.5 - - + -
108A ASP* 3.7 17.1 + - - -
132A GLY 3.2 10.1 + - - +
133A ALA* 3.2 10.1 + - - +
135A ALA* 1.3 75.5 - - - +
137A ILE* 1.3 61.7 + - - +
139A ALA* 3.2 3.6 + - - +
140A ARG* 2.9 55.1 + - + +
157A ILE* 4.1 12.6 - - + +
158A ASP 3.9 11.4 - - - +
159A PRO 4.3 3.6 - - - -
223A TYR* 5.4 1.6 - - + -
226A ARG* 3.7 26.2 - - + -
227A ARG* 2.4 38.7 + - - +
229A LEU* 3.7 25.8 - - + +
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Residues in contact with ILE 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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54A TYR* 3.5 49.1 - - + -
107A LEU* 3.8 26.5 - - + +
110A LEU* 3.8 21.1 - - + -
111A ALA* 3.5 28.7 - - - +
114A ILE* 4.1 5.2 - - + -
133A ALA 3.0 18.7 + - - +
134A GLY* 3.7 5.2 - - - +
136A TYR* 1.3 79.1 - - - +
138A LEU* 1.3 57.6 + - - +
140A ARG* 3.3 3.2 + - - -
141A TYR* 2.8 28.2 + - - +
219A TYR* 3.8 9.0 - - - +
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Residues in contact with LEU 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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52A LEU* 3.7 26.7 - - + +
54A TYR* 4.0 13.7 - - + +
114A ILE* 3.8 19.3 - - + -
126A ILE* 4.7 7.6 - - + -
128A GLY* 3.9 8.1 - - - -
129A VAL 3.4 45.1 - - - +
130A GLY* 3.6 4.9 - - - +
134A GLY 3.0 18.7 + - - +
135A ALA 4.1 3.1 - - - +
136A TYR 3.3 0.2 - - - -
137A ILE* 1.3 76.1 - - - +
139A ALA* 1.3 57.5 + - - +
141A TYR* 3.6 6.6 - - + +
142A ALA* 2.9 28.8 + - - +
152A LEU* 3.9 18.0 - - + +
154A LEU* 4.6 3.6 - - + -
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Residues in contact with ALA 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 ALA 3.0 18.3 + - - +
136A TYR 3.5 4.0 - - - +
138A LEU* 1.3 73.3 - - - +
140A ARG* 1.3 64.4 + - - +
142A ALA* 3.2 3.1 + - - +
143A LEU* 3.0 27.4 + - - +
152A LEU* 4.3 10.5 - - - -
154A LEU* 4.2 10.4 - - + +
157A ILE* 3.8 9.4 - - + -
229A LEU* 3.7 23.6 - - + -
231A PHE* 4.2 11.4 - - + -
239A LEU* 3.8 3.1 - - + +
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Residues in contact with ARG 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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108A ASP* 3.1 24.3 + - - +
111A ALA* 3.8 17.0 - - + -
136A TYR* 2.9 41.0 + - + +
137A ILE* 3.6 4.7 - - - +
139A ALA* 1.3 71.8 - - - +
141A TYR* 1.3 68.6 + - - +
143A LEU* 3.0 35.7 + - - +
144A ASN* 3.1 33.5 + - - +
227A ARG* 3.3 36.4 - - - +
228A ASP 2.9 27.5 + - - -
229A LEU* 3.4 22.5 - - + +
230A ASN 5.2 1.4 - - - +
237A ILE* 5.8 1.2 - - - +
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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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111A ALA* 3.5 24.2 - - - +
114A ILE* 3.7 33.4 - - + -
115A PRO* 3.7 16.0 - - + +
118A LEU* 3.2 20.4 - - + +
126A ILE* 4.1 20.4 - - + -
137A ILE 2.8 20.9 + - - +
138A LEU* 3.6 7.9 - - + +
140A ARG* 1.3 73.2 - - - +
142A ALA* 1.3 53.8 + - - +
144A ASN* 3.0 6.7 + - - +
145A HIS* 2.8 58.0 + + + +
148A THR* 2.8 34.9 + - - +
149A VAL* 3.6 17.5 - - + -
152A LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 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 LEU 2.9 17.6 + - - +
139A ALA 3.6 4.9 - - - +
140A ARG 3.2 0.2 - - - -
141A TYR* 1.3 75.8 - - - +
143A LEU* 1.3 61.2 + - - +
146A PRO* 3.2 28.3 - - + +
149A VAL* 3.8 28.0 - - + -
152A LEU* 3.6 23.8 - - + -
239A LEU* 3.7 9.6 - - + +
241A CYS* 5.1 2.0 - - - -
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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 ALA 3.0 14.6 + - - +
140A ARG* 3.0 30.5 + - - +
142A ALA* 1.3 77.0 - - - +
144A ASN* 1.3 65.9 - - - +
146A PRO* 3.7 10.3 - - - +
229A LEU* 3.8 20.2 - - + -
230A ASN 5.0 0.7 - - - +
231A PHE* 4.3 9.6 - - + -
237A ILE* 4.1 29.4 - - + -
238A THR 3.7 31.6 - - - +
239A LEU* 4.2 11.4 - - + -
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Residues in contact with ASN 144 (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 ASP* 5.4 1.2 + - - +
111A ALA* 5.1 4.0 - - - +
112A ASP* 5.0 10.9 + - - +
140A ARG* 3.1 38.1 + - - +
141A TYR* 3.0 5.4 + - - +
143A LEU* 1.3 81.6 - - - +
145A HIS* 1.3 89.0 + - + +
146A PRO* 3.5 5.9 - - - +
227A ARG* 5.6 1.7 + - - -
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Residues in contact with HIS 145 (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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111A ALA 5.7 0.2 + - - -
112A ASP* 5.0 7.7 + - - -
115A PRO* 3.8 23.8 - - + +
141A TYR* 2.8 40.2 + + + +
142A ALA 3.6 2.7 - - - -
144A ASN* 1.3 102.8 + - + +
146A PRO* 1.3 64.6 - - - +
147A ASP 3.3 2.5 - - - -
148A THR* 2.7 43.7 + - + +
149A VAL* 3.8 6.2 - - - +
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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