Contacts of the helix formed by residues 877 - 883 (chain M) in PDB entry 2DFS
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 TRP 877 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873M HIS* 3.7 13.6 + + - -
874M VAL* 3.0 51.4 + - + +
875M ARG* 3.2 0.4 - - - -
876M GLY* 1.3 75.4 - - - +
878M LEU* 1.3 57.3 + - - +
879M ALA* 3.1 2.0 - - - -
880M ARG* 2.9 72.3 + - - +
881M VAL* 3.3 10.0 + - - +
123R GLU* 6.1 4.7 - - + -
124R MET* 4.4 19.7 - - + -
145R MET* 3.0 38.2 + - + +
146R THR* 4.7 2.7 - - - +
148R LYS* 6.0 3.8 - - + -
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Residues in contact with LEU 878 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875M ARG* 3.3 28.0 + - + +
876M GLY 3.1 0.4 - - - -
877M TRP* 1.3 75.0 - - - +
879M ALA* 1.3 50.3 + - - +
881M VAL* 3.0 14.2 + - + +
882M HIS* 2.7 62.1 + - + +
34R THR* 3.8 30.5 - - + -
37R ARG* 3.5 35.4 - - + +
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Residues in contact with ALA 879 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876M GLY 3.1 18.9 + - - +
877M TRP* 4.3 1.1 - - - -
878M LEU* 1.3 73.2 - - - +
880M ARG* 1.3 56.4 + - - +
882M HIS* 4.2 5.3 + - - -
883M TYR* 2.9 61.1 + - + +
884M HIS 3.5 2.1 + - - -
37R ARG 3.4 11.3 + - - +
38R SER* 4.9 4.9 - - - +
40R GLY 6.2 0.2 - - - +
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Residues in contact with ARG 880 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877M TRP* 2.9 78.8 + - + +
879M ALA* 1.3 74.8 - - - +
881M VAL* 1.3 57.4 + - + +
884M HIS* 3.1 34.6 + - + +
885M ARG* 2.8 34.7 + - + +
145R MET 3.2 13.7 + - - -
146R THR 4.3 2.6 + - - -
148R LYS* 2.8 50.5 + - - +
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Residues in contact with VAL 881 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877M TRP 3.8 11.0 - - - +
878M LEU* 3.0 16.3 + - + +
880M ARG* 1.3 76.3 - - + +
882M HIS* 1.3 60.1 + - + +
885M ARG* 3.6 8.9 - - + -
886M THR* 2.7 48.0 + - + +
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Residues in contact with HIS 882 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878M LEU* 2.7 46.6 + - + +
879M ALA* 4.0 4.3 - - - +
881M VAL* 1.3 83.0 - - + +
883M TYR* 1.3 61.0 + - + +
886M THR* 2.8 17.4 + - - -
887M LEU* 3.0 19.9 + - - +
19R PHE* 3.5 32.4 - + - -
34R THR* 3.7 16.4 - - - -
38R SER* 2.8 28.4 + - - +
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Residues in contact with TYR 883 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879M ALA* 2.9 47.4 + - + +
882M HIS* 1.3 77.0 - - + +
884M HIS* 1.3 77.1 + + + +
885M ARG 3.3 2.2 + - - -
886M THR 4.2 1.1 - - - -
887M LEU* 4.0 14.1 + - + +
888M LYS* 3.3 38.1 + - + +
38R SER* 5.3 9.2 - - - -
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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