Contacts of the helix formed by residues 882 - 898 (chain I) in PDB entry 4XLR
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552I HIS* 3.0 30.0 + - + +
876I VAL* 5.2 6.3 - - + +
877I PRO* 6.3 0.2 - - + -
881I ASN* 1.3 77.8 - - - +
883I GLY* 1.3 64.1 + - - +
884I GLN 3.2 2.9 - - - -
885I ILE* 3.0 17.8 + - + +
886I LEU* 3.0 28.3 + - + +
949J ILE* 6.1 3.1 - - + -
951J ILE* 5.4 2.5 - - + -
1038J LEU* 3.7 28.7 - - + +
1061J PHE* 3.5 11.2 - - + -
1062J ARG* 3.3 43.1 - - + +
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Residues in contact with GLY 883 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549I PHE* 3.7 19.0 - - - -
552I HIS* 3.8 2.5 - - - +
553I ASP* 2.9 28.4 + - - -
843I HIS* 3.1 17.7 - - - -
882I LEU* 1.3 79.4 - - - +
884I GLN* 1.3 56.6 + - - +
886I LEU* 3.4 1.8 + - - +
887I GLU* 2.9 24.4 + - - +
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Residues in contact with GLN 884 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841I ASN* 3.0 34.1 + - - +
843I HIS* 3.1 33.2 + - + +
845I ASN* 3.4 20.7 - - - +
876I VAL* 3.3 15.4 - - - +
881I ASN* 2.5 45.4 + - - +
883I GLY* 1.3 73.9 - - - +
885I ILE* 1.3 62.1 + - + +
887I GLU* 3.7 0.7 - - - +
888I THR* 2.6 38.9 + - - +
992I MET* 4.1 7.5 - - + +
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Residues in contact with ILE 885 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676I ILE* 6.2 6.3 - - + -
876I VAL* 3.5 27.6 - - + -
881I ASN 3.9 3.8 - - - +
882I LEU* 3.0 31.1 + - + +
884I GLN* 1.3 79.3 - - + +
886I LEU* 1.3 63.3 + - + +
888I THR* 3.2 6.9 + - - -
889I HIS* 2.9 56.7 + - + +
988I VAL* 5.8 1.3 - - + -
949J ILE* 4.1 21.3 - - + +
950J GLY* 3.7 10.5 - - - -
951J ILE* 3.7 15.3 - - + +
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Residues in contact with LEU 886 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549I PHE* 4.0 23.9 - - + -
552I HIS* 3.4 48.9 - - + +
882I LEU* 3.0 16.5 + - + +
883I GLY 4.0 0.4 - - - +
885I ILE* 1.3 78.4 - - + +
887I GLU* 1.3 57.8 + - - +
889I HIS* 3.1 8.6 + - + +
890I LEU* 2.9 30.1 + - - +
911I GLU* 6.0 2.0 - - + -
914I ILE* 4.4 8.9 - - + +
951J ILE* 3.6 42.2 - - + -
1062J ARG 4.8 2.5 - - - +
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Residues in contact with GLU 887 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548I PRO* 4.0 8.3 - - + -
549I PHE* 3.8 11.1 - - + -
579I VAL* 3.3 28.5 - - + +
842I ARG* 2.8 28.6 + - - +
843I HIS* 3.0 27.5 + - + +
883I GLY 2.9 20.4 + - - +
884I GLN 3.7 2.9 - - - +
886I LEU* 1.3 77.0 - - - +
888I THR* 1.3 55.6 + - - +
890I LEU* 3.5 3.3 + - - +
891I GLY* 2.9 22.7 + - - -
991I GLN 3.3 5.9 - - - +
992I MET* 3.1 30.6 - - - +
993I PHE* 3.2 16.7 + - - +
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Residues in contact with THR 888 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674I VAL* 3.7 25.8 - - + +
676I ILE* 5.2 11.1 - - + +
884I GLN* 2.6 24.4 + - - +
885I ILE* 3.2 7.4 + - - -
887I GLU* 1.3 72.9 - - - +
889I HIS* 1.3 64.2 + - - +
891I GLY 3.4 0.5 + - - -
892I LEU* 2.8 25.6 + - - +
988I VAL* 5.2 3.4 - - + -
989I VAL* 3.5 22.8 - - - +
990I GLY* 3.6 1.9 - - - -
991I GLN 3.6 7.9 - - - -
992I MET* 3.2 19.5 - - - +
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Residues in contact with HIS 889 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885I ILE* 2.9 34.1 + - + +
886I LEU* 3.1 11.6 + - + +
888I THR* 1.3 76.1 - - - +
890I LEU* 1.3 60.6 + - - +
891I GLY 3.0 1.6 - - - -
892I LEU* 2.9 22.5 + - - +
893I ALA* 3.0 15.4 + - - +
914I ILE* 4.3 13.7 - - + -
918I LEU* 4.0 8.8 - - + +
968I ASP 5.9 0.7 - - - +
969I LEU 3.7 6.1 - - - -
970I GLY* 3.3 32.5 + - - -
988I VAL* 4.2 12.1 - - + +
989I VAL 4.9 1.2 + - - -
950J GLY* 3.8 11.7 - - - -
951J ILE* 3.0 43.8 + - + +
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Residues in contact with LEU 890 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I PHE* 5.2 0.4 - - + -
549I PHE* 3.5 28.0 - - + -
579I VAL* 4.3 6.7 - - + -
886I LEU 2.9 15.7 + - - +
887I GLU* 3.8 5.2 - - - +
889I HIS* 1.3 75.8 - - - +
891I GLY* 1.3 56.4 + - - +
893I ALA* 3.9 0.8 - - - +
894I GLY* 2.9 24.3 + - - -
901I TYR* 3.4 60.3 - - + -
903I SER* 5.3 1.8 - - - -
909I ALA* 4.1 12.1 - - + -
914I ILE* 3.7 22.3 - - + +
917I LEU* 3.5 17.5 - - + -
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Residues in contact with GLY 891 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579I VAL* 5.4 4.7 - - - +
887I GLU 2.9 11.4 + - - -
889I HIS 3.0 0.2 - - - -
890I LEU* 1.3 76.7 - - - +
892I LEU* 1.3 59.5 + - - +
894I GLY* 4.6 1.8 - - - -
895I TYR* 2.9 25.5 + - - +
901I TYR* 5.8 0.7 - - - -
991I GLN* 3.1 44.5 + - - +
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Residues in contact with LEU 892 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888I THR 2.8 7.9 + - - +
889I HIS* 2.9 10.7 + - - +
891I GLY* 1.3 79.4 - - - +
893I ALA* 1.3 63.0 + - - +
894I GLY 3.2 0.2 + - - -
895I TYR* 3.6 10.1 + - - +
896I PHE* 4.2 6.4 + - - -
918I LEU* 3.7 9.2 - - + -
967I PHE* 3.4 51.8 - - + +
970I GLY* 3.3 29.6 - - - +
972I VAL* 4.2 3.4 - - + -
989I VAL* 3.4 43.1 - - + +
990I GLY* 3.5 7.2 - - - -
991I GLN 3.5 0.2 - - - +
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Residues in contact with ALA 893 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889I HIS 3.0 8.2 + - - +
890I LEU* 4.4 3.1 - - - +
892I LEU* 1.3 76.9 - - - +
894I GLY* 1.3 58.7 + - - +
895I TYR 3.8 0.2 + - - -
896I PHE 3.9 1.0 + - - -
897I LEU* 3.2 25.3 + - - +
901I TYR* 4.8 0.2 - - - -
917I LEU* 3.6 39.9 - - + +
918I LEU* 3.6 26.5 - - + +
921I ALA* 3.4 16.6 - - - +
967I PHE* 4.7 0.7 - - - -
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Residues in contact with GLY 894 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578I VAL* 6.0 1.3 - - - -
890I LEU 2.9 21.6 + - - -
891I GLY* 3.8 1.6 - - - -
892I LEU 3.1 0.2 - - - -
893I ALA* 1.3 75.2 - - - +
895I TYR* 1.3 55.2 + - - +
896I PHE 3.2 2.0 - - - -
897I LEU* 3.0 1.4 + - - -
898I GLY* 2.4 38.3 + - - -
899I GLN 4.2 0.9 + - - +
901I TYR* 3.6 25.1 - - - -
991I GLN* 4.2 3.8 - - - +
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Residues in contact with TYR 895 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673I LEU* 4.5 26.6 - - + +
865I THR* 4.7 14.8 + - + +
891I GLY 2.9 19.9 + - - +
892I LEU* 4.1 5.2 - - - +
893I ALA 3.6 0.4 - - - -
894I GLY* 1.3 77.2 - - - +
896I PHE* 1.3 88.5 + + - +
897I LEU 3.4 0.3 + - - -
898I GLY* 3.7 8.0 + - - +
990I GLY 5.6 0.9 - - - -
991I GLN* 3.3 38.9 + - + +
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Residues in contact with PHE 896 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863I ASP* 4.9 9.4 - - - -
892I LEU 4.2 4.6 + - - -
893I ALA 3.9 1.7 + - - +
894I GLY 3.2 0.4 - - - -
895I TYR* 1.3 99.4 - + - +
897I LEU* 1.3 64.3 + - + +
921I ALA* 3.9 37.5 - - + +
924I LEU* 6.6 0.2 - - + -
925I TYR* 3.5 46.0 - + + -
928I LYS* 6.2 4.0 - - + -
967I PHE* 4.2 20.9 - + - -
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Residues in contact with LEU 897 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I GLU 5.9 0.7 + - - -
893I ALA 3.2 20.0 - - - +
894I GLY 3.0 3.3 + - - +
895I TYR 4.2 0.2 - - - -
896I PHE* 1.3 84.3 - - + +
898I GLY* 1.3 57.5 + - - +
899I GLN* 3.2 31.5 + - + +
901I TYR* 3.3 20.6 - - - +
917I LEU* 3.9 15.9 - - + +
920I GLU* 3.2 38.6 - - + +
921I ALA* 4.3 11.2 - - + -
924I LEU* 6.0 4.3 - - + -
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Residues in contact with GLY 898 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I GLU 3.9 9.0 + - - +
578I VAL* 4.2 7.1 - - - +
894I GLY 2.4 25.0 + - - -
895I TYR* 3.7 7.9 + - - -
897I LEU 1.3 66.2 - - - +
899I GLN* 1.3 62.3 + - - +
900I ARG* 4.0 16.6 + - - -
991I GLN* 5.7 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
------------------------------------------------------------
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