Contacts of the helix formed by residues 132 - 136 (chain P) 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 LEU 132 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P TYR* 4.4 16.2 - - + -
113P TRP* 4.4 19.3 - - + +
115P ILE* 4.4 29.4 - - + -
128P PRO* 3.6 26.0 - - + +
130P MLY 3.7 15.9 + - + +
131P TRP* 1.3 119.4 + - - +
133P PRO* 1.3 69.7 - - + +
134P VAL* 2.8 32.2 + - + +
135P TYR* 4.0 14.0 + - + +
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Residues in contact with PRO 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P GLU* 4.0 13.9 - - + +
13P ALA* 3.5 17.6 - - - +
16P TYR* 3.2 42.0 - - + -
131P TRP* 3.5 16.8 - - + +
132P LEU* 1.3 85.8 - - + +
134P VAL* 1.3 56.5 + - - -
135P TYR 3.4 1.6 - - - -
136P ASN* 2.8 44.5 - - - +
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Residues in contact with VAL 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P ALA* 4.6 5.8 - - + -
16P TYR* 4.2 17.9 - - + +
17P LEU* 4.3 13.5 - - + -
115P ILE* 5.1 2.2 - - + -
116P TYR* 3.9 11.0 - - + -
132P LEU* 2.8 30.8 + - + -
133P PRO* 1.3 75.0 - - - +
135P TYR* 1.3 79.3 + - + +
136P ASN 2.8 9.0 + - - -
139P VAL* 3.7 9.2 - - + +
154P HIS* 3.0 44.4 - - + +
156P PHE* 3.6 3.8 - - - -
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Residues in contact with TYR 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P ILE* 4.3 12.2 - - + +
116P TYR* 2.7 28.5 + - - -
125P THR* 5.7 1.0 - - - +
128P PRO* 5.6 5.2 - - + +
131P TRP* 6.3 1.8 - - + +
132P LEU* 4.0 12.2 + - + +
133P PRO 3.4 0.4 - - - -
134P VAL* 1.3 96.7 - - + +
136P ASN* 1.3 63.3 - - - +
137P PRO* 3.5 3.9 - - - +
140P VAL* 4.4 8.7 - - - +
154P HIS* 4.9 1.3 - - - -
155P ILE* 6.3 0.7 - - + -
156P PHE* 4.3 15.1 - + + -
187P VAL* 5.1 8.3 - - + +
188P ASN* 3.9 14.2 + - - -
191P ARG* 3.1 49.6 - - + -
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Residues in contact with ASN 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P GLU* 5.2 2.8 - - - +
13P ALA* 5.1 1.4 - - + +
131P TRP* 3.9 16.2 - - - -
133P PRO* 2.8 42.9 + - - +
134P VAL 2.8 2.0 - - - -
135P TYR* 1.3 78.8 - - - +
137P PRO* 1.3 75.3 - - + +
138P MLY 2.5 31.7 + - + +
139P VAL* 2.5 47.3 + - + +
140P VAL* 3.3 3.9 + - - -
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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