Contacts of the helix formed by residues 1242 - 1244 (chain A) in PDB entry 3MP1
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 THR1242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1224A THR* 3.9 13.6 - - - +
1241A VAL* 1.3 78.1 - - + +
1243A ARG* 1.3 60.5 + - - +
1244A ARG* 3.5 20.4 + - + +
1245A LEU* 2.8 52.6 + - + -
1246A VAL* 3.8 1.2 - - - +
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Residues in contact with ARG1243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119A TYR* 3.0 27.5 + - - +
1120A ASN* 3.1 22.6 + - - +
1187A PRO* 6.1 0.6 - - - +
1191A PRO* 3.4 34.2 - - + +
1192A THR* 5.4 0.8 - - - +
1193A LYS 3.0 25.3 + - - +
1194A ASN* 4.3 9.7 - - - +
1195A TYR* 3.2 25.8 + - - -
1223A GLY* 4.0 20.9 - - - +
1224A THR* 4.2 5.9 - - - +
1225A CYS* 3.6 27.4 - - - -
1241A VAL 3.4 2.8 + - - -
1242A THR* 1.3 73.1 + - - +
1244A ARG* 1.3 64.1 + - - +
1245A LEU 2.9 1.6 + - - -
1246A VAL* 2.9 24.1 + - - -
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Residues in contact with ARG1244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A ARG* 4.1 14.3 - - - +
1186A ILE* 3.6 23.3 - - + +
1187A PRO* 4.3 13.7 + - - +
1188A PRO 2.6 31.7 + - - -
1189A GLY* 3.2 16.4 + - - +
1190A PHE* 3.6 34.8 - - - +
1191A PRO* 4.0 20.4 - - + +
1242A THR* 3.0 14.1 + - + +
1243A ARG* 1.3 79.9 - - - +
1245A LEU* 1.3 63.9 + - + +
1246A VAL 3.5 0.4 - - - -
1247A LEU* 4.8 4.9 - - - +
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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