Contacts of the helix formed by residues 910 - 932 (chain I) in PDB entry 4XLN
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 THR 910 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908I GLY 3.8 9.4 - - - +
909I ALA* 1.3 78.8 - - - +
911I GLU* 1.3 65.6 + - - +
912I PRO* 3.4 16.7 - - - +
913I GLU* 2.9 25.1 + - - +
914I ILE* 3.0 26.4 + - - +
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Residues in contact with GLU 911 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552I HIS* 6.3 0.9 - - + -
886I LEU* 5.8 4.7 - - + -
910I THR* 1.3 72.6 - - - +
912I PRO* 1.3 63.2 - - + +
914I ILE* 4.0 7.9 - - + +
915I LYS* 2.9 54.2 + - + +
951J ILE* 3.4 17.1 - - + +
952J ASP* 4.3 0.3 - - - +
1062J ARG* 2.5 55.1 + - - +
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Residues in contact with PRO 912 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910I THR* 3.4 17.0 - - - +
911I GLU* 1.3 94.2 - - + +
913I GLU* 1.3 58.1 - - + +
915I LYS* 3.7 7.4 - - + +
916I GLU* 2.9 28.5 + - - +
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Residues in contact with GLU 913 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I PHE* 4.1 24.3 - - + +
908I GLY 3.8 4.7 - - - +
909I ALA* 3.2 11.1 - - - -
910I THR* 2.9 38.6 + - - +
912I PRO* 1.3 75.1 - - + +
914I ILE* 1.3 59.8 + - - +
916I GLU* 3.1 10.4 + - - +
917I LEU* 2.9 32.9 + - + +
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Residues in contact with ILE 914 (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 29.4 - - + -
886I LEU* 4.8 18.8 - - + +
889I HIS* 4.3 15.0 - - + -
890I LEU* 3.7 25.1 - - + -
909I ALA* 3.8 13.2 - - + -
910I THR 3.0 19.7 + - - +
911I GLU* 4.0 6.5 - - + +
913I GLU* 1.3 74.1 - - - +
915I LYS* 1.3 58.1 + - + +
917I LEU* 3.0 11.3 + - + +
918I LEU* 2.9 49.6 + - + +
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Residues in contact with LYS 915 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911I GLU* 2.9 42.7 + - + +
912I PRO* 3.7 6.7 - - + +
914I ILE* 1.3 77.7 - - + +
916I GLU* 1.3 56.8 + - - +
918I LEU* 3.5 8.0 + - - +
919I ALA* 2.9 27.9 + - - +
968I ASP* 3.3 41.5 + - + +
969I LEU* 4.5 3.4 - - - -
951J ILE* 4.7 4.8 - - - +
952J ASP* 2.9 39.3 + - - -
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Residues in contact with GLU 916 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912I PRO 2.9 14.5 + - - +
913I GLU* 3.1 13.7 + - - +
915I LYS* 1.3 74.5 - - - +
917I LEU* 1.3 71.8 + - + +
919I ALA* 3.0 11.3 + - - +
920I GLU* 2.9 38.5 + - - +
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Residues in contact with LEU 917 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I LYS* 5.8 4.7 - - + -
6I PHE* 3.7 19.1 - - + -
890I LEU* 3.7 23.1 - - + -
893I ALA* 3.9 15.0 - - + -
897I LEU* 3.5 15.7 - - + +
899I GLN* 4.4 5.2 - - - +
901I TYR* 3.5 39.0 - - + +
913I GLU 2.9 17.5 + - - +
914I ILE* 3.0 9.6 + - - +
916I GLU* 1.3 81.2 - - + +
918I LEU* 1.3 57.4 + - + +
920I GLU* 3.3 6.8 + - - +
921I ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 918 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889I HIS* 3.3 22.7 - - + +
892I LEU* 3.7 17.9 - - + -
893I ALA* 3.6 30.5 - - + +
914I ILE* 2.9 39.4 + - + +
915I LYS 3.7 4.5 - - - +
917I LEU* 1.3 74.9 - - - +
919I ALA* 1.3 61.0 + - - +
921I ALA* 4.2 0.9 - - - -
922I PHE* 2.9 26.2 + - - +
967I PHE* 3.3 32.6 - - + +
968I ASP* 3.7 34.3 - - - +
970I GLY* 5.4 1.1 - - - +
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Residues in contact with ALA 919 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915I LYS 2.9 16.3 + - - +
916I GLU* 3.0 19.3 + - - +
918I LEU* 1.3 74.8 - - - +
920I GLU* 1.3 60.2 + - - +
922I PHE* 3.8 4.5 - - - +
923I ASN* 2.9 43.1 + - - +
964I LYS* 4.8 14.4 - - - +
968I ASP* 5.2 4.7 - - + -
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Residues in contact with GLU 920 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897I LEU* 3.4 26.1 - - + +
899I GLN* 5.2 3.1 - - - +
916I GLU* 2.9 26.4 + - - +
917I LEU* 3.7 11.4 - - - +
919I ALA* 1.3 74.0 - - - +
921I ALA* 1.3 64.8 + - - +
923I ASN* 3.0 10.4 + - - +
924I LEU* 3.0 39.8 + - + +
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Residues in contact with ALA 921 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893I ALA* 4.1 13.5 - - - -
896I PHE* 3.8 33.1 - - + +
897I LEU* 3.7 19.2 - - + +
917I LEU 2.9 17.7 + - - +
918I LEU* 3.8 4.9 - - - +
920I GLU* 1.3 76.0 - - - +
922I PHE* 1.3 57.1 + - - +
924I LEU* 3.3 5.1 + - - +
925I TYR* 2.9 27.9 + - - +
967I PHE* 4.3 2.0 - - + -
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Residues in contact with PHE 922 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918I LEU 2.9 18.8 + - - +
919I ALA* 3.8 3.6 - - - +
921I ALA* 1.3 73.6 - - - +
923I ASN* 1.3 72.9 + - - +
925I TYR* 3.1 13.2 + + - -
926I PHE* 2.9 62.0 + + + +
960I GLU* 3.9 13.9 - - + -
963I LEU* 4.0 25.4 - - + -
964I LYS* 3.5 42.8 - - + -
967I PHE* 3.5 39.8 - + + -
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Residues in contact with ASN 923 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919I ALA* 2.9 31.4 + - - +
920I GLU* 3.4 10.3 - - + +
922I PHE* 1.3 81.5 - - - +
924I LEU* 1.3 64.8 + - + +
926I PHE* 4.9 2.8 - - - +
927I GLY* 3.5 15.8 + - - -
964I LYS* 3.3 30.8 + - - +
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Residues in contact with LEU 924 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896I PHE* 6.0 2.7 - - + -
897I LEU* 5.2 5.8 - - + -
920I GLU* 3.0 34.4 + - + +
921I ALA* 3.7 8.5 - - - +
923I ASN* 1.3 82.7 - - + +
925I TYR* 1.3 59.6 + - - +
927I GLY* 3.2 2.8 + - - -
928I LYS* 2.9 27.7 + - - +
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Residues in contact with TYR 925 (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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861I LEU* 4.8 3.4 - - + +
862I PRO* 3.4 35.5 - - + +
863I ASP* 3.9 24.4 + - + -
896I PHE* 3.7 41.7 - + + +
921I ALA 2.9 17.7 + - - +
922I PHE* 3.1 14.6 + + - +
924I LEU* 1.3 75.3 - - - +
926I PHE* 1.3 67.0 + - + +
928I LYS* 3.0 22.9 + - + +
929I ARG* 3.0 31.2 + - + +
963I LEU* 6.5 1.3 - - + -
967I PHE* 4.5 14.1 - + - -
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Residues in contact with PHE 926 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922I PHE* 2.9 49.5 + + + +
923I ASN* 4.9 2.7 - - - +
925I TYR* 1.3 78.2 - - - +
927I GLY* 1.3 58.0 + - - +
929I ARG* 3.1 32.4 + - - +
930I GLN* 2.9 60.4 + - + +
935I GLY* 5.6 2.5 - - - -
936I VAL* 5.2 5.2 - - + -
960I GLU* 3.2 45.8 - - + -
963I LEU* 6.4 1.3 - - + -
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Residues in contact with GLY 927 (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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923I ASN 3.5 13.9 + - - -
924I LEU* 3.2 8.0 + - - -
925I TYR 3.0 1.2 - - - -
926I PHE* 1.3 77.9 - - - +
928I LYS* 1.3 58.5 + - - +
930I GLN* 3.5 14.3 + - - +
931I GLY* 2.9 27.4 + - - -
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Residues in contact with LYS 928 (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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200G TRP* 6.3 1.1 - - - -
924I LEU 2.9 13.2 + - - +
925I TYR* 3.0 14.8 + - + +
927I GLY* 1.3 75.5 - - - +
929I ARG* 1.3 58.2 + - - +
931I GLY* 4.9 1.3 - - - -
932I GLU* 2.9 58.5 + - + +
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Residues in contact with ARG 929 (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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180G GLN* 3.3 22.0 + - - -
198G ARG* 5.7 2.7 - - - +
862I PRO* 3.3 35.9 - - - +
925I TYR* 3.0 35.1 + - + +
926I PHE* 3.3 38.4 - - - +
927I GLY 3.1 0.2 - - - -
928I LYS* 1.3 74.4 - - - +
930I GLN* 1.3 66.2 + - - +
932I GLU* 3.1 16.0 + - - +
933I GLY 3.7 0.2 + - - -
934I PHE* 3.4 29.7 + - + +
935I GLY* 3.8 19.1 + - - +
936I VAL* 5.3 0.4 - - - +
940I GLU* 3.1 25.8 + - - -
963I LEU* 5.4 5.2 - - - +
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Residues in contact with GLN 930 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926I PHE* 2.9 52.9 + - + +
927I GLY* 3.5 11.9 + - - +
929I ARG* 1.3 75.5 - - - +
931I GLY* 1.3 63.6 - - - +
933I GLY* 3.4 11.7 + - - -
934I PHE 3.7 17.8 + - - +
935I GLY* 5.9 0.9 - - - -
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Residues in contact with GLY 931 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927I GLY 2.9 20.4 + - - -
928I LYS* 3.8 1.6 - - - -
930I GLN* 1.3 75.3 - - - +
932I GLU* 1.3 59.4 + - - +
933I GLY 3.2 7.5 + - - -
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Residues in contact with GLU 932 (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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20G TYR* 4.1 8.1 + - + +
22G GLU* 4.9 3.6 - - - +
198G ARG* 3.1 42.5 + - - +
200G TRP* 4.1 15.7 + - - -
233H LEU* 5.3 8.7 - - - +
928I LYS* 2.9 50.6 + - + +
929I ARG* 3.1 6.0 + - - +
931I GLY* 1.3 76.0 - - - +
933I GLY* 1.3 61.0 + - - +
934I PHE* 3.6 4.4 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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