Contacts of the helix formed by residues 844 - 854 (chain A) in PDB entry 2XR9
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 SER 844 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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843A ARG* 1.3 77.5 - - - +
845A TYR* 1.3 62.5 + - - +
846A SER* 3.6 6.4 + - - -
847A GLU* 3.0 37.6 + - - +
848A ILE* 3.0 19.3 + - - +
1877A IOD 4.4 11.9 - - - -
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Residues in contact with TYR 845 (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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541A PRO* 3.7 37.0 - - + +
542A THR* 3.4 22.0 + - - -
543A MET* 3.6 50.7 - - + -
544A PRO* 3.6 11.8 - - - +
836A ASP* 4.9 3.0 + - - -
837A PHE 6.0 0.2 - - - -
838A TYR 5.8 0.7 - - - -
843A ARG 3.9 0.8 + - - -
844A SER* 1.3 73.2 - - - +
846A SER* 1.3 56.8 + - - +
848A ILE* 3.2 19.3 + - + -
849A LEU* 2.8 55.8 + - + +
852A LYS* 4.9 8.3 + - - -
1877A IOD 4.2 9.3 - - + +
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Residues in contact with SER 846 (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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528A GLY 3.5 22.2 + - - +
531A ASN* 3.7 17.4 + - - +
532A HIS 6.0 0.7 - - - -
541A PRO* 3.6 12.7 - - - +
844A SER* 3.2 4.8 + - - -
845A TYR* 1.3 78.8 - - - +
847A GLU* 1.3 62.1 + - - +
849A LEU* 3.1 7.1 + - - +
850A THR* 3.1 23.9 + - - -
1877A IOD 3.5 25.5 - - - +
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Residues in contact with GLU 847 (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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843A ARG* 3.0 45.2 + - + +
844A SER* 3.0 35.9 + - - +
846A SER* 1.3 74.7 - - - +
848A ILE* 1.3 59.0 + - - +
850A THR* 3.1 11.1 + - - -
851A LEU* 3.0 25.8 + - - +
1872A IOD 4.2 9.2 - - + +
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Residues in contact with ILE 848 (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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788A LEU* 4.6 2.7 - - + -
837A PHE 4.7 0.2 - - - +
838A TYR* 3.8 32.5 - - + +
841A THR* 3.7 33.2 - - + +
843A ARG* 3.7 17.3 - - + +
844A SER 3.0 18.8 + - - +
845A TYR* 3.2 21.3 + - + +
847A GLU* 1.3 74.3 - - - +
849A LEU* 1.3 65.4 + - - +
851A LEU* 3.1 20.6 + - + +
852A LYS* 2.9 40.2 + - + +
1872A IOD 4.5 2.7 - - + -
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Residues in contact with LEU 849 (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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526A THR* 3.7 20.2 - - + -
527A HIS 3.5 24.7 - - - +
528A GLY 4.1 5.6 - - - -
529A SER* 3.9 16.6 - - - +
541A PRO* 3.6 28.5 - - + -
827A ARG* 5.8 2.0 - - - +
845A TYR* 2.8 47.9 + - + +
846A SER* 3.1 7.4 + - - +
848A ILE* 1.3 73.3 - - - +
850A THR* 1.3 61.8 + - - +
852A LYS* 3.3 17.5 + - + +
853A THR* 3.2 27.2 + - - +
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Residues in contact with THR 850 (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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501A PRO* 5.0 14.6 - - + -
529A SER 2.8 22.5 + - - +
532A HIS* 3.4 27.1 + - + +
846A SER 3.1 12.0 + - - -
847A GLU* 3.1 13.3 + - - -
849A LEU* 1.3 74.3 - - - +
851A LEU* 1.3 63.6 + - - +
853A THR* 3.0 23.0 + - - +
854A TYR* 3.4 8.8 + - - +
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Residues in contact with LEU 851 (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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788A LEU* 3.8 48.2 - - + +
789A SER* 4.6 0.2 - - - -
790A VAL* 3.4 35.6 - - + +
826A VAL* 4.8 1.2 - - - +
838A TYR* 3.8 35.4 - - + +
847A GLU 3.0 12.5 + - - +
848A ILE* 3.1 17.4 + - + +
850A THR* 1.3 78.4 - - - +
852A LYS* 1.3 60.5 + - - +
854A TYR* 3.2 24.1 + - + +
1872A IOD 4.3 8.5 - - + -
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Residues in contact with LYS 852 (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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825A ARG* 3.6 0.9 - - - +
826A VAL* 3.3 21.7 + - + -
827A ARG* 2.9 40.3 + - + +
830A GLU* 2.5 38.7 + - - +
836A ASP* 2.8 22.4 + - - -
837A PHE* 3.1 28.5 + - - +
838A TYR* 4.1 15.9 - - + -
845A TYR* 4.9 10.3 + - - -
848A ILE* 2.9 32.9 + - + +
849A LEU* 3.3 18.5 + - + +
851A LEU* 1.3 77.0 - - - +
853A THR* 1.3 59.6 + - - +
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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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202A ARG* 5.0 1.4 + - - -
503A PHE* 6.1 1.2 - - - +
504A GLU* 4.9 8.7 - - - +
507A GLU* 3.9 14.0 - - - +
526A THR* 3.8 29.4 - - + +
529A SER* 4.1 10.0 + - - -
825A ARG* 3.2 36.3 - - - +
827A ARG* 4.6 2.9 - - - -
849A LEU 3.2 13.2 + - - +
850A THR* 3.0 19.1 + - - +
851A LEU 3.2 0.2 - - - -
852A LYS* 1.3 76.5 - - - +
854A TYR* 1.3 64.3 + - - +
855A LEU* 3.6 1.2 + - - +
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Residues in contact with TYR 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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501A PRO* 6.4 2.2 - - + -
502A PRO* 6.0 2.2 - - + -
790A VAL* 3.2 39.7 - - + +
791A SER* 5.4 0.7 - - - -
824A ALA 4.2 1.7 - - - +
825A ARG* 3.4 19.1 - - - -
826A VAL 4.5 1.0 + - - -
850A THR 3.4 9.0 + - - +
851A LEU* 3.2 23.3 + - + +
853A THR* 1.3 78.0 - - - +
855A LEU* 1.3 73.6 + - - +
856A HIS* 3.6 35.8 + - + -
857A THR 5.1 0.7 + - - -
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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