Contacts of the helix formed by residues 845 - 850 (chain B) in PDB entry 1M8X
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 GLN 845 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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894A VAL* 3.1 31.2 + - - +
895A ASP* 5.2 0.9 - - - -
896A VAL 5.3 0.5 + - - -
931A GLN* 2.9 31.3 - - - +
933A TYR* 4.1 11.6 - - - -
843B ASN* 4.7 9.6 + - - +
844B LEU* 1.3 80.4 - - - +
846B LEU* 1.3 56.2 + - - +
847B ARG* 4.4 12.6 - - - +
848B GLU* 2.7 54.8 + - + +
849B ILE 3.8 0.2 + - - -
865B PHE* 3.9 6.7 - - - -
869B LYS* 4.1 11.4 - - - +
877B GLU* 5.7 1.6 - - - +
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Residues in contact with LEU 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845B GLN* 1.3 71.6 - - - +
847B ARG* 1.3 61.4 + - - +
848B GLU 3.0 1.4 + - - -
849B ILE* 3.1 35.7 + - + +
850B ALA* 3.9 2.8 + - - -
853B ILE* 4.7 2.9 - - - +
865B PHE* 3.9 19.3 - - + -
866B ILE* 4.3 13.0 - - + -
869B LYS* 3.4 46.1 - - + +
870B LEU* 4.6 2.2 - - + -
873B ALA* 4.2 6.1 - - + -
877B GLU* 4.2 35.2 - - + +
880B LEU* 6.0 2.6 - - + +
881B VAL* 4.0 29.6 - - + +
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Residues in contact with ARG 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896A VAL* 3.6 38.0 - - - +
897A PHE* 5.1 6.9 - - - -
932A MET* 4.5 12.4 - - + +
933A TYR* 3.3 27.5 + - - +
845B GLN* 3.0 15.9 + - + +
846B LEU* 1.3 77.6 - - - +
848B GLU* 1.3 59.8 + - - +
849B ILE 3.3 0.7 + - - -
850B ALA* 3.6 18.5 - - - +
874B THR* 5.2 2.2 - - - +
876B ALA* 3.9 24.5 - - - +
877B GLU* 4.4 22.3 + - + +
880B LEU* 3.9 31.8 - - + +
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Residues in contact with GLU 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930A LEU 5.6 0.2 - - - +
931A GLN* 3.2 30.0 + - - +
932A MET* 4.1 23.4 - - + +
832B LEU* 3.4 17.9 - - + +
841B TYR* 5.9 3.0 - - - -
843B ASN 3.8 3.2 - - - +
844B LEU* 3.3 24.5 - - + +
845B GLN* 2.7 52.5 + - + +
847B ARG* 1.3 78.9 - - - +
849B ILE* 1.3 58.4 + - - -
850B ALA 3.3 4.6 + - - +
852B HIS* 4.8 1.0 - - - -
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Residues in contact with ILE 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832B LEU* 4.0 9.9 - - + -
844B LEU* 3.5 29.8 - - + -
846B LEU* 3.1 19.5 + - + +
848B GLU* 1.3 78.4 - - - +
850B ALA* 1.3 54.7 + - - +
851B GLY 3.2 0.3 + - - -
852B HIS* 2.8 36.3 + - + +
853B ILE* 3.4 28.0 + - + +
856B PHE* 3.6 36.1 - - + -
865B PHE* 4.1 9.4 - - + -
866B ILE* 4.0 26.0 - - + -
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Residues in contact with ALA 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846B LEU 3.9 3.0 + - - +
847B ARG* 3.6 17.8 + - - +
848B GLU 3.3 4.1 - - - +
849B ILE* 1.3 77.1 - - - +
851B GLY* 1.3 59.2 - - - +
852B HIS* 3.5 10.4 + - - -
853B ILE* 4.8 2.7 - - - -
880B LEU* 6.3 7.0 - - + -
884B GLU* 3.6 8.3 - - - +
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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