Contacts of the helix formed by residues 1181 - 1185 (chain A) in PDB entry 1MUK
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 PRO1181 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A PRO* 4.0 26.9 - - + -
894A THR* 5.0 5.6 - - + +
897A LEU* 4.6 3.1 - - + -
1179A ALA 3.2 8.5 - - - +
1180A VAL* 1.3 85.6 - - + +
1182A ASP* 1.3 67.3 + - - +
1183A THR* 4.1 7.2 - - - +
1184A TRP* 2.8 73.6 + - + +
1185A MET* 3.6 3.8 + - - +
1224A PHE* 4.9 2.2 - - + -
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Residues in contact with ASP1182 (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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564A ILE* 3.3 26.9 - - + +
826A PHE* 6.4 1.8 - - + -
830A HIS* 3.7 19.1 + - - +
1180A VAL 3.5 2.0 + - - +
1181A PRO* 1.3 69.8 - - - +
1183A THR* 1.3 65.8 + - + +
1185A MET* 2.9 40.5 + - - +
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Residues in contact with THR1183 (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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826A PHE* 4.0 28.3 - - + -
829A VAL* 4.0 23.2 - - + +
830A HIS* 3.9 18.5 + - + +
890A TRP 4.0 8.8 + - - +
891A TYR* 3.5 39.2 + - - -
892A MET 4.7 3.4 + - - +
1181A PRO* 4.1 5.9 - - - +
1182A ASP* 1.3 77.7 - - + +
1184A TRP* 1.3 73.8 + - - +
1186A SER* 4.1 9.5 + - - -
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Residues in contact with TRP1184 (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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891A TYR* 2.7 29.9 + - + -
893A PRO* 3.7 20.6 - - + -
897A LEU* 5.0 3.8 - - + -
1180A VAL* 4.2 8.5 - - + -
1181A PRO* 2.8 40.1 + - + +
1183A THR* 1.3 86.9 - - - +
1185A MET* 1.3 53.5 + - - +
1186A SER 3.0 6.1 - - - -
1187A LEU* 2.8 43.6 + - + +
1189A PHE* 3.8 16.9 - - + -
1192A MET* 3.6 22.2 - - + -
1193A PHE* 4.1 14.4 - + - -
1224A PHE* 4.8 2.7 - + - -
1227A ALA* 3.7 32.3 - - + -
1228A GLY* 3.9 3.6 - - - -
1231A MET* 3.5 31.1 - - + +
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Residues in contact with MET1185 (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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564A ILE* 3.5 37.8 - - + +
1098A MET* 3.4 22.3 - - - +
1102A THR* 3.8 19.2 - - + +
1106A PHE* 3.5 37.7 - - + -
1180A VAL* 3.6 27.1 - - - +
1181A PRO 3.8 1.3 - - - +
1182A ASP* 2.9 42.5 + - - +
1184A TRP* 1.3 76.5 - - - +
1186A SER* 1.3 56.7 + - - +
1187A LEU 3.3 0.9 - - - -
1189A PHE* 4.3 7.9 - - - -
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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