Contacts of the helix formed by residues 852 - 862 (chain A) in PDB entry 5M64
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 ASP 852 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849A THR* 2.9 30.2 + - - +
851A VAL* 1.3 77.0 - - + +
853A THR* 1.3 65.7 + - - +
854A GLY 3.2 2.2 - - - -
855A ARG* 3.3 24.5 + - - +
856A GLU* 3.0 26.2 + - - +
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Residues in contact with THR 853 (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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849A THR 3.9 8.5 + - - -
850A SER* 4.4 8.2 - - - -
851A VAL 3.5 0.4 - - - -
852A ASP* 1.3 85.3 + - - +
854A GLY* 1.3 60.8 + - - +
856A GLU* 3.1 11.9 + - + +
857A ALA 2.9 24.6 + - - -
899A LYS* 3.2 42.8 + - + +
900A VAL* 5.8 1.1 - - + -
903A ILE* 4.7 19.3 - - + +
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Residues in contact with GLY 854 (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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850A SER 4.5 1.0 + - - -
851A VAL 4.1 4.7 + - - -
852A ASP 3.2 0.6 - - - -
853A THR* 1.3 78.9 - - - +
855A ARG* 1.3 58.3 + - - +
857A ALA* 3.3 18.1 + - - +
858A ALA* 3.7 6.2 + - - +
896A THR* 5.8 1.6 - - - -
899A LYS* 4.4 4.9 - - - +
975A ASP* 4.0 12.4 + - - -
976A ALA* 3.5 37.5 - - - +
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Residues in contact with ARG 855 (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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851A VAL 4.4 3.4 + - - +
852A ASP* 3.3 27.5 + - - +
854A GLY* 1.3 73.1 - - - +
856A GLU* 1.3 70.2 + - - +
858A ALA* 3.5 3.8 + - - +
859A ALA* 2.9 33.2 + - + +
865A ASP 5.3 2.0 + - - -
866A LYS* 5.8 0.2 - - - +
867A ASP* 5.1 4.6 - - - +
868A THR 2.6 44.5 + - - +
869A PRO* 4.3 14.3 - - - +
870A ALA* 4.9 2.5 - - - +
974A THR* 3.9 35.2 - - - +
975A ASP* 4.1 3.6 - - - +
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Residues in contact with GLU 856 (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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852A ASP 3.0 13.7 + - - +
853A THR* 3.1 19.0 + - + +
855A ARG* 1.3 83.8 + - - +
857A ALA* 1.3 59.0 + - - +
859A ALA* 4.0 2.8 - - - +
860A GLU* 2.8 31.8 + - + +
865A ASP* 3.5 35.0 - - - +
866A LYS* 4.9 6.4 - - - +
899A LYS* 4.9 2.7 - - + -
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Residues in contact with ALA 857 (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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853A THR 2.9 6.2 + - - -
854A GLY 3.4 11.7 - - - +
855A ARG 3.1 0.4 - - - -
856A GLU* 1.3 73.6 - - - +
858A ALA* 1.3 65.7 + - - +
860A GLU* 3.1 14.0 + - - +
861A VAL* 3.1 21.4 + - - +
892A LEU* 6.2 0.4 - - - -
895A VAL* 6.0 2.2 - - + -
896A THR* 3.3 31.9 - - + +
899A LYS* 3.5 26.7 - - - +
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Residues in contact with ALA 858 (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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854A GLY 3.7 5.6 + - - +
855A ARG* 3.5 6.3 + - + +
857A ALA* 1.3 79.1 - - - +
859A ALA* 1.3 62.3 + - - +
861A VAL* 3.3 12.1 - - + +
862A THR* 3.1 28.6 + - - +
875A LEU* 5.6 4.0 - - + -
879A LEU* 5.6 8.5 - - + -
892A LEU* 6.3 0.4 - - - -
974A THR* 4.6 23.6 - - + -
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Residues in contact with ALA 859 (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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855A ARG* 2.9 28.3 + - + +
856A GLU* 3.8 9.4 - - - +
858A ALA* 1.3 77.7 - - - +
860A GLU* 1.3 59.6 + - - +
862A THR* 3.3 11.4 - - - +
864A LEU 2.8 41.4 + - - +
865A ASP* 3.3 18.6 + - - +
868A THR* 5.3 4.5 - - - +
875A LEU* 5.4 3.4 - - + -
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Residues in contact with GLU 860 (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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856A GLU* 2.8 23.7 + - + +
857A ALA* 3.1 6.0 + - - +
859A ALA* 1.3 77.9 - - - +
861A VAL* 1.3 74.4 + - - +
862A THR 3.5 0.2 + - - -
863A ASN* 3.6 13.0 + - - -
865A ASP* 3.7 17.8 - - - +
895A VAL* 4.3 20.6 - - + +
899A LYS* 6.4 0.4 - - - -
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Residues in contact with VAL 861 (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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857A ALA 3.1 13.9 + - - +
858A ALA* 3.3 21.1 - - - +
860A GLU* 1.3 89.4 - - - +
862A THR* 1.3 58.8 + - - +
863A ASN* 3.3 10.5 + - - +
882A ILE* 4.4 15.2 - - + +
891A ILE* 4.7 12.2 - - + +
892A LEU* 3.7 46.0 - - + -
895A VAL* 4.1 9.0 - - + -
896A THR* 5.5 0.2 - - - +
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Residues in contact with THR 862 (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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858A ALA 3.1 20.1 + - - +
859A ALA* 3.3 19.1 - - - +
861A VAL* 1.3 77.9 - - - +
863A ASN* 1.3 68.3 + - - +
864A LEU* 3.2 25.2 + - + +
875A LEU* 3.7 24.9 - - + +
878A ARG* 3.2 39.4 + - - +
879A LEU* 5.9 0.7 - - - -
882A ILE* 6.1 2.9 - - - -
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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