Contacts of the helix formed by residues 139 - 147 (chain I) 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 TYR 139 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I VAL* 4.1 15.8 - - + +
91I LEU* 3.3 45.3 - - + -
92I ARG* 3.0 43.9 + - - -
95I ASP* 2.8 40.0 + - - -
100I GLY* 2.9 34.9 + - - -
101I THR 3.5 0.7 - - - -
102I VAL* 3.2 23.6 - - + -
137I ILE* 3.2 3.8 + - + +
138I ASN* 1.3 69.6 - - - +
140I GLU* 1.3 65.5 + - + +
142I PHE* 3.5 16.8 - - + -
143I VAL* 2.9 30.8 + - - +
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Residues in contact with GLU 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I VAL* 5.3 11.9 - - + +
92I ARG* 3.8 23.5 + - - +
99I ASN* 4.5 5.2 + - - -
100I GLY* 3.3 18.5 + - - -
138I ASN* 3.0 27.9 + - - +
139I TYR* 1.3 84.8 - - + +
141I ALA* 1.3 61.0 + - - +
143I VAL* 4.4 1.0 - - - +
144I LYS* 3.3 26.5 + - - +
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Residues in contact with ALA 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I GLN* 5.5 1.1 - - + -
138I ASN* 3.1 14.8 + - + +
140I GLU* 1.3 77.7 - - - +
142I PHE* 1.3 60.1 + - - +
144I LYS* 3.3 14.4 + - + +
145I HIS* 2.9 54.5 + - + +
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Residues in contact with PHE 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797G PHE* 5.5 1.6 - + - -
91I LEU* 4.5 9.2 - - + -
107I LEU* 3.9 24.5 - - + -
111I LEU* 5.9 2.2 - - + -
126I LEU* 3.2 26.7 - - + -
127I MET* 3.7 25.1 - - + -
130I GLN* 3.6 31.1 - - + +
137I ILE* 4.2 7.6 - - + -
138I ASN 2.9 19.4 + - - +
139I TYR* 3.5 14.8 - - + -
140I GLU 3.4 0.4 - - - -
141I ALA* 1.3 76.4 - - - +
143I VAL* 1.3 71.2 + - + +
145I HIS* 3.2 4.2 + - - +
146I ILE* 3.0 49.2 + - + +
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Residues in contact with VAL 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I PHE* 5.4 0.2 - - + -
87I PHE* 4.2 16.4 - - + +
88I VAL* 4.0 26.9 - - + -
91I LEU* 3.8 27.8 - - + -
139I TYR* 2.9 22.2 + - + +
140I GLU 4.4 0.9 - - - +
142I PHE* 1.3 80.5 - - + +
144I LYS* 1.3 65.3 + - - +
146I ILE* 3.2 7.8 + - + +
147I MET* 3.0 45.7 + - + +
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Residues in contact with LYS 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I GLU 3.3 18.3 + - - +
141I ALA* 3.3 17.6 - - + +
143I VAL* 1.3 81.0 - - - +
145I HIS* 1.3 74.5 + - + +
147I MET* 3.2 6.6 + - - +
148I SER* 2.8 25.1 + - - +
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Residues in contact with HIS 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LYS* 5.7 5.2 + - - -
797G PHE* 4.7 0.7 - - - -
130I GLN* 4.0 26.6 - - + +
141I ALA* 2.9 38.0 + - + +
142I PHE 3.8 3.6 - - - +
144I LYS* 1.3 87.9 - - + +
146I ILE* 1.3 66.5 + - - +
148I SER* 3.1 25.3 + - - -
149I VAL* 3.9 5.9 + - - +
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Residues in contact with ILE 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793G ARG* 5.6 9.3 + - + -
794G CYS* 6.3 0.4 - - - -
797G PHE* 1.7 93.4 - - + -
800G ARG* 4.7 2.8 + - - -
126I LEU* 4.1 0.9 - - + -
130I GLN* 4.3 10.1 - - - +
142I PHE* 3.0 49.6 + - + +
143I VAL* 3.2 9.2 + - + +
145I HIS* 1.3 76.0 - - - +
147I MET* 1.3 62.5 + - + +
149I VAL* 3.1 25.1 - - - +
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Residues in contact with MET 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793G ARG* 4.5 27.8 - - + +
82I GLY 4.8 5.2 - - - +
84I PHE* 3.6 39.7 - - + +
87I PHE* 4.0 15.3 - - + -
143I VAL* 3.0 32.5 + - + +
144I LYS* 3.2 7.6 + - - +
146I ILE* 1.3 81.0 - - + +
148I SER* 1.3 58.2 + - - +
149I VAL 3.3 8.6 - - - +
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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