Contacts of the helix formed by residues 137 - 145 (chain X) in PDB entry 1MVW
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 137 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11X ASP* 4.2 6.1 - - - +
12X ASN 4.1 13.4 + - - +
74X GLY* 5.0 5.1 + - - -
106X THR* 3.8 23.6 + - - +
107X GLU* 3.0 34.2 + - - +
108X ALA* 3.4 11.5 - - - +
109X PRO* 4.8 6.7 - - + +
136X ILE* 1.3 72.4 - - - +
138X ALA* 1.3 58.6 + - - +
140X LEU* 2.9 23.6 + - - +
141X SER* 3.1 11.3 + - - -
154X ASP* 4.0 17.3 - - - +
339X VAL* 4.0 20.7 - - + +
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Residues in contact with ALA 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X PRO* 5.0 2.3 - - + +
136X ILE* 3.6 3.7 - - + +
137X GLN* 1.3 75.2 - - - +
139X VAL* 1.3 63.1 + - + +
141X SER* 3.2 3.7 + - - -
142X LEU* 2.9 20.8 + - - +
152X VAL* 3.3 31.9 - - + +
154X ASP* 4.1 9.1 + - + +
163X VAL* 3.4 44.4 - - + -
165X ILE* 3.7 3.1 - - + +
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Residues in contact with VAL 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135X ALA* 6.1 1.1 - - + -
136X ILE* 3.3 39.3 - - + +
137X GLN 3.1 0.2 - - - -
138X ALA* 1.3 79.0 - - - +
140X LEU* 1.3 61.2 + - + +
142X LEU* 3.5 2.7 + - - +
143X TYR* 3.3 24.3 + - + +
165X ILE* 3.5 27.4 - - + -
168X GLY* 4.2 18.6 - - - +
170X ALA* 3.9 15.9 - - + -
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Residues in contact with LEU 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X VAL* 6.0 0.4 - - + -
104X LEU* 4.4 0.9 - - + -
106X THR* 3.4 33.0 - - + -
135X ALA* 3.6 28.9 - - + -
136X ILE 3.2 8.6 + - - +
137X GLN 2.9 6.8 + - - +
139X VAL* 1.3 73.9 - - + +
141X SER* 1.3 67.8 + - - +
143X TYR* 4.4 5.2 - - + -
144X ALA* 3.1 24.8 + - - +
338X SER 4.3 0.9 - - - -
339X VAL* 3.3 27.6 - - + +
342X GLY* 3.4 7.5 - - - -
343X GLY* 3.8 21.3 - - - +
346X LEU* 3.7 23.8 - - + -
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Residues in contact with SER 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X GLN 3.1 7.6 + - - -
138X ALA* 3.2 11.6 + - - -
140X LEU* 1.3 80.6 - - - +
142X LEU* 1.3 61.2 + - - +
144X ALA* 3.2 10.2 + - - +
145X SER* 3.4 10.7 + - - -
152X VAL* 4.3 6.1 - - - -
298X VAL* 4.5 6.7 - - - +
300X SER* 3.0 30.7 + - - -
338X SER* 3.2 14.1 + - - -
339X VAL* 3.1 27.5 + - - +
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Residues in contact with LEU 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138X ALA 2.9 16.5 + - - +
139X VAL* 3.8 5.2 - - - +
141X SER* 1.3 75.8 - - - +
143X TYR* 1.3 59.2 + - - +
145X SER* 2.9 26.0 + - - -
147X ARG* 3.4 27.5 + - + +
148X THR* 3.6 33.0 - - - +
149X THR 3.8 3.1 - - - +
150X GLY* 3.8 24.0 - - - +
152X VAL* 3.8 16.3 - - + +
165X ILE* 3.9 21.3 - - + -
298X VAL* 3.7 29.8 - - + -
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Residues in contact with TYR 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139X VAL* 3.3 17.0 - - + +
140X LEU* 3.9 6.3 - - + +
142X LEU* 1.3 78.8 - - - +
144X ALA* 1.3 59.9 + - - +
145X SER 3.0 0.4 - - - -
146X GLY* 2.9 28.4 + - - -
147X ARG 3.4 13.9 - - - +
148X THR* 5.0 10.5 - - + -
342X GLY* 3.7 15.3 - - - -
345X ILE* 3.5 33.9 - - + +
346X LEU* 3.8 30.5 - - + +
349X LEU* 4.2 17.8 - - - +
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Residues in contact with ALA 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140X LEU 3.1 19.3 + - - +
141X SER 3.4 6.3 - - - +
143X TYR* 1.3 76.8 - - - +
145X SER* 1.3 55.9 + - - +
146X GLY 3.2 2.7 + - - -
334X GLU* 5.2 8.4 - - - +
338X SER* 3.5 16.8 - - - +
341X ILE* 4.3 11.0 - - + +
342X GLY* 3.5 21.3 - - - +
345X ILE* 4.4 13.0 - - - +
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Residues in contact with SER 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141X SER 3.4 8.0 + - - -
142X LEU 2.9 12.1 + - - -
144X ALA* 1.3 74.4 - - - +
146X GLY* 1.3 54.2 + - - +
147X ARG* 3.0 44.7 + - - -
298X VAL* 3.5 22.4 - - - +
330X ILE* 4.9 2.9 - - - +
332X PRO* 4.7 17.5 - - - -
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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