Contacts of the helix formed by residues 848 - 859 (chain B) in PDB entry 1M2V
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 PHE 848 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759B LEU 4.1 14.4 - - - -
760B HIS* 5.6 2.5 - - - -
762B MET* 3.9 20.6 - - + -
799B LEU* 4.6 13.0 - - + -
819B ALA 5.5 0.9 - - - -
822B PHE* 3.6 47.8 - + + -
849B ASN* 1.3 60.3 + - - +
850B GLN* 2.9 8.5 - - - +
851B ARG* 2.6 62.2 + - - +
852B VAL* 3.3 27.2 + - + -
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Residues in contact with ASN 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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821B VAL 4.9 3.0 + - - -
822B PHE* 2.8 30.9 + - - +
848B PHE* 1.3 81.0 - - - +
850B GLN* 1.3 62.7 + - - +
852B VAL* 3.6 5.9 + - - +
853B ARG* 3.0 62.2 + - - +
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Residues in contact with GLN 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848B PHE 2.9 5.7 + - - +
849B ASN* 1.3 80.2 - - - +
851B ARG* 1.3 51.8 + - + +
853B ARG* 2.6 45.2 + - - +
854B ASN* 2.6 58.2 + - - +
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Residues in contact with ARG 851 (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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762B MET* 4.0 24.0 + - - +
763B ALA 2.8 22.6 + - - -
764B ASP* 2.5 55.1 + - - +
766B ALA* 4.9 1.1 - - - -
767B GLY* 4.0 24.2 - - - +
848B PHE* 2.6 46.8 + - + +
850B GLN* 1.3 70.2 - - + +
852B VAL* 1.3 55.5 + - - +
854B ASN* 2.7 26.5 + - - +
855B ILE* 2.7 23.9 + - + +
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Residues in contact with VAL 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759B LEU* 4.2 24.7 - - + -
762B MET* 4.8 1.6 - - + -
799B LEU* 4.3 8.3 - - + -
810B LEU* 4.6 23.1 - - + -
822B PHE 6.0 0.7 - - - +
848B PHE* 3.3 39.5 + - + +
849B ASN* 4.1 7.2 - - - +
851B ARG* 1.3 78.1 - - - +
853B ARG* 1.3 65.7 + - + +
855B ILE* 3.4 10.0 + - - +
856B ILE* 3.2 31.3 + - + +
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Residues in contact with ARG 853 (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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849B ASN* 3.0 41.3 + - - +
850B GLN* 2.6 43.9 + - - +
852B VAL* 1.3 80.0 - - + +
854B ASN* 1.3 59.4 + - - +
856B ILE* 3.7 7.1 + - - +
857B ASN* 2.6 42.4 + - - +
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Residues in contact with ASN 854 (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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767B GLY 3.0 26.0 + - - +
768B LEU* 3.7 13.9 - - - +
781B ILE* 2.9 40.1 - - + +
850B GLN* 2.6 49.3 + - - +
851B ARG* 2.7 10.0 + - - +
853B ARG* 1.3 77.8 + - - +
855B ILE* 1.3 62.6 + - - +
857B ASN* 3.1 9.2 + - - +
858B GLN 3.0 10.9 + - - -
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Residues in contact with ILE 855 (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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757B TYR* 5.6 2.7 - - + -
759B LEU* 3.8 29.6 - - + -
762B MET* 4.1 20.6 - - + -
766B ALA* 5.3 1.8 - - + -
767B GLY 5.5 2.2 - - - +
781B ILE* 4.3 8.7 - - + -
782B VAL 4.7 3.4 - - - +
783B LEU* 3.7 23.3 - - + -
784B PRO* 4.2 12.8 - - + -
801B LEU* 3.7 24.5 - - + -
851B ARG* 2.7 25.1 + - + +
852B VAL* 3.7 5.2 - - - +
854B ASN* 1.3 71.8 - - + +
856B ILE* 1.3 55.8 + - - +
858B GLN* 2.6 36.3 + - - +
859B LEU* 3.0 11.6 + - + -
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Residues in contact with ILE 856 (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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801B LEU* 4.2 23.1 - - + -
808B LEU* 4.4 7.4 - - + +
810B LEU* 4.8 5.4 - - + -
852B VAL* 3.2 26.2 + - + +
853B ARG* 4.0 7.0 - - - +
855B ILE* 1.3 78.6 - - - +
857B ASN* 1.3 66.5 + - - +
858B GLN 3.2 0.2 + - - -
859B LEU* 3.5 8.4 + - - +
860B ARG* 3.4 55.1 + - - +
871B LEU* 3.2 37.9 - - + -
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Residues in contact with ASN 857 (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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781B ILE* 4.8 4.5 - - + +
853B ARG* 2.6 34.8 + - - +
854B ASN* 3.1 13.6 + - - +
855B ILE 3.1 0.8 - - - -
856B ILE* 1.3 78.6 - - - +
858B GLN* 1.3 62.6 + - - +
860B ARG* 3.3 14.8 + - - +
861B ASN* 2.9 42.3 + - - +
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Residues in contact with GLN 858 (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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780B THR* 3.9 15.7 - - - +
781B ILE* 3.1 43.0 + - + +
783B LEU* 3.9 29.2 - - + -
854B ASN 3.0 10.2 + - - +
855B ILE* 2.6 24.0 + - - +
857B ASN* 1.3 69.2 - - - +
859B LEU* 1.3 52.0 + - + +
860B ARG 2.6 15.9 + - - -
861B ASN* 3.2 26.3 + - - +
862B HIS* 4.4 3.5 - - - -
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Residues in contact with LEU 859 (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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750B LYS* 4.6 1.6 + - - +
757B TYR* 3.6 34.3 - - + +
783B LEU* 3.6 23.6 - - + -
801B LEU* 3.6 32.1 - - + -
803B ASP* 4.2 15.5 - - + +
808B LEU* 4.0 24.9 - - + -
855B ILE* 3.0 12.9 + - + +
856B ILE* 3.5 7.3 + - - +
858B GLN* 1.3 76.5 - - - +
860B ARG* 1.3 57.8 + - - +
862B HIS* 3.0 23.7 + - + -
869B GLN* 3.5 17.5 + - - +
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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