Contacts of the helix formed by residues 137 - 145 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11Y ASP* 4.2 6.1 - - - +
12Y ASN 4.1 13.2 + - - +
74Y GLY* 5.0 5.9 + - - -
106Y THR* 3.8 22.5 + - - +
107Y GLU* 3.0 33.8 + - - +
108Y ALA* 3.4 11.7 - - - +
109Y PRO* 4.8 6.8 - - + +
136Y ILE* 1.3 71.8 - - - +
138Y ALA* 1.3 57.8 + - - +
140Y LEU* 2.9 23.8 + - - +
141Y SER* 3.1 11.8 + - - -
154Y ASP* 4.0 15.9 - - - +
339Y VAL* 4.0 21.1 - - + +
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Residues in contact with ALA 138 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Y PRO* 5.0 2.9 - - + +
136Y ILE* 3.6 3.3 - - + +
137Y GLN* 1.3 76.3 - - - +
139Y VAL* 1.3 62.5 + - + +
141Y SER* 3.2 3.3 + - - -
142Y LEU* 2.9 21.1 + - - +
152Y VAL* 3.3 32.3 - - + +
154Y ASP* 4.1 9.3 + - + +
163Y VAL* 3.4 44.4 - - + -
165Y ILE* 3.7 2.9 - - + -
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Residues in contact with VAL 139 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135Y ALA* 6.1 0.9 - - + -
136Y ILE* 3.3 39.5 - - + +
137Y GLN 3.1 0.2 - - - -
138Y ALA* 1.3 78.2 - - + +
140Y LEU* 1.3 62.2 + - + +
142Y LEU* 3.5 2.5 + - - +
143Y TYR* 3.3 25.0 + - + +
165Y ILE* 3.5 27.1 - - + -
168Y GLY* 4.2 19.3 - - - +
170Y ALA* 3.9 15.7 - - + -
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Residues in contact with LEU 140 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y VAL* 6.0 0.2 - - + -
104Y LEU* 4.4 1.1 - - + -
106Y THR* 3.4 33.0 - - + -
135Y ALA* 3.6 24.2 - - + -
136Y ILE 3.2 12.8 + - - +
137Y GLN 2.9 6.2 + - - +
139Y VAL* 1.3 74.4 - - + +
141Y SER* 1.3 67.3 + - - +
143Y TYR* 4.4 5.6 - - + -
144Y ALA* 3.0 25.1 + - - +
338Y SER 3.8 0.8 - - - +
339Y VAL* 3.3 28.0 - - + +
342Y GLY* 3.4 7.8 - - - +
343Y GLY* 3.8 21.3 - - - +
346Y LEU* 3.7 23.8 - - + -
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Residues in contact with SER 141 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Y GLN 3.1 7.4 + - - -
138Y ALA* 3.2 11.4 + - - -
140Y LEU* 1.3 80.8 - - - +
142Y LEU* 1.3 62.4 + - - +
144Y ALA* 3.3 10.7 + - - +
145Y SER* 3.4 11.3 + - - -
152Y VAL* 4.3 5.8 - - - -
298Y VAL* 4.5 6.3 - - - +
300Y SER* 3.0 31.5 + - - -
338Y SER* 3.2 14.3 + - - -
339Y VAL* 3.1 27.9 + - - +
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Residues in contact with LEU 142 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Y ALA 2.9 16.5 + - - +
139Y VAL* 3.8 5.6 - - - +
141Y SER* 1.3 75.8 - - - +
143Y TYR* 1.3 59.8 + - - +
145Y SER* 2.9 26.2 + - - -
147Y ARG* 3.4 27.6 + - + +
148Y THR* 3.6 33.2 - - - +
149Y THR 3.8 2.9 - - - +
150Y GLY* 3.8 24.7 - - - +
152Y VAL* 3.8 16.3 - - + +
165Y ILE* 3.9 20.6 - - + -
298Y VAL* 3.7 29.6 - - + -
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Residues in contact with TYR 143 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139Y VAL* 3.3 17.0 - - + +
140Y LEU* 3.9 5.8 - - + +
142Y LEU* 1.3 79.0 - - - +
144Y ALA* 1.3 59.2 + - - +
145Y SER 3.0 0.2 - - - -
146Y GLY* 2.9 28.0 + - - -
147Y ARG 3.4 13.9 - - - +
148Y THR* 5.0 10.5 - - + -
342Y GLY* 3.7 15.9 - - - -
345Y ILE* 3.5 34.0 - - + +
346Y LEU* 3.8 30.7 - - + +
349Y LEU* 4.2 17.7 - - - +
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Residues in contact with ALA 144 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140Y LEU 3.0 18.6 + - - +
141Y SER 3.4 6.3 - - - +
143Y TYR* 1.3 77.4 - - - +
145Y SER* 1.3 55.7 + - - +
146Y GLY 3.2 3.1 + - - -
334Y GLU* 5.2 8.0 - - - +
338Y SER* 3.5 17.0 - - - +
341Y ILE* 4.3 11.1 - - + +
342Y GLY* 3.5 21.3 - - - +
345Y ILE* 4.4 13.2 - - - +
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Residues in contact with SER 145 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141Y SER 3.4 8.4 + - - -
142Y LEU 2.9 12.2 + - - -
144Y ALA* 1.3 74.6 - - - +
146Y GLY* 1.3 54.5 + - - +
147Y ARG* 3.0 45.4 + - - -
298Y VAL* 3.5 21.9 - - - +
330Y ILE* 4.9 2.9 - - - +
332Y 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