Contacts of the helix formed by residues 141 - 147 (chain Q) 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 PRO 141 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137Q TRP* 3.6 9.4 - - - +
139Q ALA* 2.5 18.4 - - - +
140Q PHE* 1.1 112.5 - - + +
142Q PRO* 1.4 70.0 - - + -
143Q ASP* 3.7 1.3 - - + +
144Q VAL* 4.1 13.7 - - + -
145Q ALA* 2.4 30.6 + - - +
162Q ASP* 5.8 3.6 - - - +
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Residues in contact with PRO 142 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Q TRP* 1.5 55.8 - - + -
141Q PRO* 1.4 89.5 - - + -
143Q ASP* 1.3 69.3 + - + +
146Q GLY* 2.3 0.3 + - - -
148Q VAL* 5.6 0.2 - - - +
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Residues in contact with ASP 143 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141Q PRO* 6.0 0.2 - - + -
142Q PRO* 1.3 93.6 - - + +
144Q VAL* 1.3 57.5 + - + +
146Q GLY* 4.9 0.2 - - - -
147Q ASN* 2.8 29.6 + - - -
148Q VAL* 3.0 21.7 + - - +
149Q ASP* 3.5 30.6 + - + +
152Q ASN* 6.1 0.2 - - - +
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Residues in contact with VAL 144 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Q LEU* 5.0 0.2 - - - +
140Q PHE* 3.1 36.6 - - + +
141Q PRO* 3.7 19.2 + - + -
142Q PRO 3.2 0.2 - - - -
143Q ASP* 1.3 86.1 - - + +
145Q ALA* 1.3 63.6 + - - +
147Q ASN* 3.2 12.8 + - - +
149Q ASP* 4.8 7.4 - - + -
152Q ASN* 4.4 21.1 - - + +
153Q ILE* 2.0 74.4 - - + +
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Residues in contact with ALA 145 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Q MET* 4.3 5.5 - - - +
137Q TRP* 1.2 116.7 + - + +
140Q PHE 3.0 2.2 + - - -
141Q PRO 2.4 21.3 + - - +
144Q VAL* 1.3 74.4 - - - +
146Q GLY* 1.3 51.7 - - - -
147Q ASN* 3.3 10.7 + - - +
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Residues in contact with GLY 146 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Q LYS* 1.8 53.6 + - - -
137Q TRP* 0.8 137.0 - - - -
142Q PRO 2.3 1.5 + - - -
143Q ASP 3.8 0.7 - - - -
145Q ALA* 1.3 41.2 - - - +
147Q ASN* 1.3 60.1 + - - +
148Q VAL* 3.5 6.1 - - - -
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Residues in contact with ASN 147 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Q ILE* 1.7 50.9 + - - +
113Q LYS 3.0 7.4 - - - +
114Q LYS 2.4 18.2 + - - -
117Q LEU* 1.7 70.9 - - + +
118Q GLU* 3.7 3.8 - - - +
143Q ASP 2.8 9.6 + - - -
144Q VAL 3.7 8.1 - - - +
145Q ALA 3.2 13.5 + - - +
146Q GLY* 1.3 92.5 + - - +
148Q VAL* 1.3 52.1 + - - +
149Q ASP 3.7 6.4 - - - +
150Q TYR* 5.4 0.2 - - - -
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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