Contacts of the helix formed by residues 882 - 897 (chain M) in PDB entry 5X22
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 LEU 882 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552M HIS* 3.1 25.7 + - + +
876M VAL* 4.2 14.8 - - + -
880M MET 3.8 0.2 + - - -
881M ASN* 1.3 70.8 - - - +
883M GLY* 1.3 65.0 + - - +
884M GLN 3.2 2.5 - - - -
885M ILE* 2.9 37.5 + - + +
886M LEU* 3.1 13.3 + - - +
949N ILE* 4.8 7.2 - - + -
950N GLY 5.2 2.2 - - - +
951N ILE* 3.9 23.5 - - + +
954N ALA* 4.8 9.0 - - + -
1038N LEU* 3.8 32.3 - - + +
1061N PHE* 3.9 2.2 - - + +
1062N ARG* 3.8 28.0 - - + +
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Residues in contact with GLY 883 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549M PHE* 3.7 22.4 - - - -
552M HIS* 3.9 4.8 + - - +
553M ASP* 2.8 16.2 + - - -
843M HIS* 3.2 17.6 - - - -
882M LEU* 1.3 77.4 - - - +
884M GLN* 1.3 51.9 - - - +
886M LEU* 2.9 5.0 + - - +
887M GLU* 2.7 34.8 + - - +
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Residues in contact with GLN 884 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841M ASN* 3.1 23.8 + - - +
843M HIS* 3.2 25.2 + - + -
845M ASN* 2.8 33.9 + - - +
871M LEU* 4.5 0.9 - - - +
875M GLY 5.2 1.4 + - - -
876M VAL* 3.8 22.0 - - - +
881M ASN* 3.2 44.2 + - - +
883M GLY* 1.3 75.0 - - - +
885M ILE* 1.3 67.8 + - + +
887M GLU* 3.8 2.7 - - - +
888M THR* 2.8 27.9 + - - -
992M MET* 3.4 14.8 - - + +
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Residues in contact with ILE 885 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676M ILE* 3.7 27.4 - - + -
876M VAL* 4.2 17.3 - - + -
882M LEU* 2.9 35.0 + - + +
884M GLN* 1.3 81.0 - - + +
886M LEU* 1.3 65.9 + - - +
888M THR* 2.9 16.6 + - - -
889M HIS* 3.0 37.0 + - + +
988M VAL* 5.5 0.9 - - + -
992M MET* 6.2 0.2 - - + -
949N ILE* 3.8 21.5 - - + +
950N GLY 3.7 4.9 - - - -
951N ILE* 3.4 21.8 - - + +
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Residues in contact with LEU 886 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549M PHE* 3.6 23.5 - - + -
552M HIS* 3.4 49.6 - - + +
882M LEU 3.1 4.9 + - - +
883M GLY 2.9 7.2 + - - +
885M ILE* 1.3 78.8 - - - +
887M GLU* 1.3 63.5 + - - +
889M HIS* 2.9 18.7 + - + +
890M LEU* 2.9 17.0 + - - +
911M GLU* 4.5 11.9 - - + +
914M ILE* 4.1 20.6 - - + +
951N ILE* 3.8 38.6 - - + -
1062N ARG 5.2 0.2 - - - +
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Residues in contact with GLU 887 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548M PRO* 5.0 0.4 - - + -
549M PHE* 3.8 16.2 - - + -
579M VAL* 4.0 17.1 - - + +
841M ASN* 5.0 0.7 - - - +
842M ARG* 3.4 27.1 + - - +
843M HIS* 2.6 38.8 + - - +
883M GLY 2.7 19.0 + - - +
884M GLN* 3.8 4.7 - - - +
886M LEU* 1.3 71.9 - - - +
888M THR* 1.3 56.9 + - - +
890M LEU 3.9 0.3 - - - -
891M GLY* 3.0 21.5 + - - -
991M GLN 3.4 8.5 - - - +
992M MET* 3.4 12.4 - - - +
993M PHE* 2.7 35.2 + - - +
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Residues in contact with THR 888 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674M VAL* 4.3 6.0 - - + +
676M ILE* 4.8 5.1 - - + +
884M GLN 2.8 16.8 + - - -
885M ILE* 2.9 12.4 + - - -
887M GLU* 1.3 75.7 - - - +
889M HIS* 1.3 54.9 + - - +
891M GLY* 2.9 2.3 + - - -
892M LEU* 2.7 32.7 + - - +
988M VAL* 4.1 17.9 - - + -
989M VAL* 4.0 6.1 - - - +
990M GLY* 3.5 33.4 - - - +
991M GLN 3.6 8.1 - - - -
992M MET* 3.2 21.8 - - - +
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Residues in contact with HIS 889 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885M ILE* 3.0 22.4 + - + +
886M LEU* 2.9 12.2 + - + +
888M THR* 1.3 75.8 - - - +
890M LEU* 1.3 58.5 + - - +
892M LEU* 2.9 27.9 + - - +
893M ALA 3.4 4.7 + - - -
914M ILE* 4.1 16.2 - - + -
918M LEU* 3.5 14.8 - - + +
969M GLN 3.4 23.2 + - - -
970M GLY* 3.7 12.7 + - - -
988M VAL* 3.8 26.7 - - + +
989M VAL 5.7 0.2 + - - -
950N GLY* 4.1 2.0 - - - -
951N ILE* 3.1 52.5 + - + +
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Residues in contact with LEU 890 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M PHE* 4.6 3.8 - - + -
549M PHE* 3.9 12.8 - - + -
579M VAL* 3.7 34.3 - - + -
886M LEU 2.9 14.4 + - - +
889M HIS* 1.3 76.0 - - - +
891M GLY* 1.3 60.5 + - - +
893M ALA* 3.8 3.2 + - + +
894M GLY 3.2 15.1 + - - -
901M TYR* 3.3 36.7 - - + -
903M SER* 4.8 1.8 - - - -
909M ALA* 4.5 11.4 - - + -
914M ILE* 3.9 28.8 - - + +
917M LEU* 3.7 32.1 - - + -
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Residues in contact with GLY 891 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578M VAL* 4.2 11.9 - - - -
579M VAL* 4.5 0.6 - - - +
887M GLU 3.0 14.4 + - - -
888M THR 2.9 8.5 + - - -
890M LEU* 1.3 77.2 - - - +
892M LEU* 1.3 53.2 + - - +
894M GLY* 2.9 3.6 + - - -
895M TYR* 2.8 31.7 + - - +
991M GLN* 3.5 27.8 - - - +
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Residues in contact with LEU 892 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673M LEU* 5.4 2.7 - - + -
861M LEU* 6.4 1.6 - - + -
888M THR 2.7 11.4 + - - +
889M HIS* 2.9 11.0 + - - +
891M GLY* 1.3 72.2 - - - +
893M ALA* 1.3 65.0 + - - +
895M TYR* 2.9 22.6 + - + +
896M PHE* 3.4 32.6 + - + -
918M LEU* 4.0 7.0 - - + -
967M PHE* 3.8 30.3 - - + +
970M GLY* 3.9 29.4 - - - +
972M VAL* 4.5 7.6 - - + -
989M VAL* 3.5 32.1 - - + +
990M GLY* 4.1 9.0 - - - -
991M GLN 3.8 0.8 - - - +
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Residues in contact with ALA 893 (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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889M HIS 3.4 3.9 + - - +
890M LEU* 3.9 8.3 - - - +
891M GLY 3.3 0.2 - - - -
892M LEU* 1.3 75.7 - - - +
894M GLY* 1.3 60.2 + - - +
896M PHE* 2.9 4.7 + - - -
897M LEU* 2.9 31.4 + - + +
901M TYR* 3.9 13.9 - - + +
917M LEU* 3.7 29.4 - - + +
918M LEU* 3.5 18.2 - - + +
921M ALA* 3.8 12.7 - - + +
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Residues in contact with GLY 894 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578M VAL* 4.7 2.6 - - - +
890M LEU 3.2 5.0 + - - -
891M GLY 2.9 9.2 + - - -
893M ALA* 1.3 78.7 - - - +
895M TYR* 1.3 60.4 + - - +
898M GLY* 3.4 14.7 + - - -
899M GLN* 3.3 30.9 + - - +
901M TYR* 3.6 13.2 + - - -
991M GLN* 3.7 8.3 - - - +
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Residues in contact with TYR 895 (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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673M LEU* 4.0 31.4 - - + +
861M LEU* 5.1 3.1 - - + -
865M THR* 3.4 28.5 + - + +
891M GLY 2.8 9.7 + - - +
892M LEU* 2.9 15.9 + - + +
894M GLY* 1.3 81.8 - - - +
896M PHE* 1.3 94.2 + + + +
898M GLY* 3.9 5.4 + - - -
991M GLN* 3.6 35.0 - - + +
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Residues in contact with PHE 896 (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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861M LEU* 4.5 11.9 - - + -
863M ASP* 4.7 4.7 - - - -
892M LEU* 3.5 32.3 - - + -
893M ALA 2.9 5.1 + - - +
895M TYR* 1.3 104.1 - + - +
897M LEU* 1.3 61.8 + - - +
898M GLY* 3.1 6.8 + - - -
921M ALA* 4.0 18.4 - - + +
924M VAL* 4.0 21.8 - - + +
925M TYR* 3.4 48.5 - + + -
928M LYS* 6.0 2.7 - - - -
967M PHE* 4.0 20.2 - + - -
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Residues in contact with LEU 897 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893M ALA* 2.9 18.1 + - + +
896M PHE* 1.3 72.3 - - - +
898M GLY* 1.3 63.9 + - - +
899M GLN* 3.4 37.5 + - + +
901M TYR* 4.0 4.9 - - - +
917M LEU* 3.4 33.7 - - + +
920M GLN* 3.7 36.3 - - + +
921M ALA* 3.7 9.6 - - + -
924M VAL* 4.1 11.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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