Contacts of the helix formed by residues 907 - 922 (chain J) 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 GLU 907 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786J ILE* 4.0 8.5 - - - -
790J TYR* 4.0 9.2 - - + -
905J PRO 3.8 10.4 - - - +
906J GLN* 1.3 76.7 - - - +
908J LYS* 1.3 62.3 + - - +
909J ASN* 2.8 43.5 + - - +
910J SER* 2.7 29.7 + - - -
911J LEU* 2.7 40.9 + - - +
1025J GLN 4.6 6.5 - - - +
1026J SER* 3.4 25.7 - - - +
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Residues in contact with LYS 908 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780J LYS* 3.3 32.6 - - - +
781J PRO 3.1 25.3 + - - -
782J SER* 5.0 1.0 - - - +
786J ILE* 3.5 22.6 - - + +
907J GLU* 1.3 77.7 + - - +
909J ASN* 1.3 75.9 + - - +
911J LEU* 3.9 3.8 - - - +
912J LYS* 3.0 23.8 + - - +
1026J SER 2.9 19.0 + - - +
1027J GLY* 3.9 16.6 + - - +
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Residues in contact with ASN 909 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907J GLU* 2.8 25.8 + - - +
908J LYS* 1.3 83.9 - - - +
910J SER* 1.3 63.8 + - - +
912J LYS* 2.9 18.3 + - - +
913J ASP* 2.9 23.0 + - - +
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Residues in contact with SER 910 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901J GLN* 3.4 26.1 + - - +
904J VAL* 5.7 3.4 - - - -
905J PRO 4.8 2.9 - - - -
906J GLN* 3.5 16.3 + - - +
907J GLU* 2.7 46.5 + - - -
909J ASN* 1.3 77.4 - - - +
911J LEU* 1.3 57.4 + - - +
913J ASP* 3.3 11.0 + - - +
914J LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 911 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780J LYS* 6.2 0.2 - - + -
781J PRO* 3.7 38.1 - - + +
786J ILE* 4.4 10.3 - - + -
789J LEU* 3.7 25.6 - - + -
882J PHE* 3.6 33.0 - - + -
906J GLN* 3.7 16.6 - - + +
907J GLU* 2.7 37.4 + - - +
908J LYS* 3.9 3.4 - - - +
910J SER* 1.3 70.3 + - - +
912J LYS* 1.3 65.6 + - - +
914J LEU* 3.1 8.2 + - + +
915J VAL* 2.9 28.8 + - - +
934J LEU* 5.2 4.3 - - + -
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Residues in contact with LYS 912 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776J GLU* 4.9 11.2 - - + +
777J PRO* 2.4 60.3 + - + +
780J LYS* 3.3 44.9 - - - +
908J LYS* 3.0 20.8 + - - +
909J ASN* 2.9 13.9 + - - +
911J LEU* 1.3 77.0 - - - +
913J ASP* 1.3 68.6 + - - +
915J VAL* 3.0 8.3 + - - +
916J TYR* 3.0 22.8 + - + +
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Residues in contact with ASP 913 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901J GLN* 5.6 6.9 - - - +
909J ASN* 2.9 24.9 + - - +
910J SER* 3.6 10.7 + - - +
912J LYS* 1.3 79.6 - - - +
914J LEU* 1.3 57.3 + - - +
916J TYR* 3.5 6.3 + - - +
917J GLN* 2.9 32.3 + - - +
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Residues in contact with LEU 914 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882J PHE* 5.1 7.9 - - + -
886J VAL* 4.2 23.6 - - + -
899J LEU* 3.3 42.8 - - + +
900J ILE* 3.6 26.7 - - + -
901J GLN* 4.5 6.7 - - - +
906J GLN* 5.3 1.6 - - - +
910J SER 2.9 13.1 + - - +
911J LEU* 3.1 15.7 + - + +
913J ASP* 1.3 77.8 - - - +
915J VAL* 1.3 57.8 + - + +
917J GLN* 3.8 3.9 - - + +
918J ALA* 2.9 31.8 + - + +
930J LEU* 4.6 13.5 - - + -
934J LEU* 5.8 4.7 - - + -
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Residues in contact with VAL 915 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769J LEU* 6.4 1.6 - - + -
770J LEU* 6.0 0.7 - - + -
777J PRO* 4.1 18.6 - - + -
779J ALA 4.6 3.6 - - - +
780J LYS* 4.5 3.6 - - + -
781J PRO* 4.0 16.6 - - + -
911J LEU 2.9 20.9 + - - +
912J LYS* 3.0 6.9 + - - +
914J LEU* 1.3 76.1 - - + +
916J TYR* 1.3 59.9 - - - +
918J ALA* 3.3 5.8 + - - +
919J PHE* 2.9 28.8 + - + +
927J THR* 3.7 11.7 - - + +
930J LEU* 5.1 3.6 - - + -
931J LEU* 4.0 35.2 - - + -
934J LEU* 4.7 10.5 - - + -
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Residues in contact with TYR 916 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770J LEU* 4.0 15.5 - - + -
775J GLY 3.9 11.4 - - - -
776J GLU* 4.5 8.5 - - + +
777J PRO* 3.5 34.4 - - + +
912J LYS* 3.0 11.8 + - + +
913J ASP* 3.9 6.3 - - - +
915J VAL* 1.3 76.5 - - - +
917J GLN* 1.3 72.1 + - - +
919J PHE* 3.1 7.6 + + - +
920J LEU* 2.9 54.3 + - + +
1145J TYR* 2.3 46.4 + + - -
1168J LEU* 3.6 32.9 + - + +
1212J ALA* 5.3 1.3 - - + -
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Residues in contact with GLN 917 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899J LEU* 4.0 29.6 - - + +
913J ASP 2.9 19.9 + - - +
914J LEU* 3.9 5.4 - - - +
916J TYR* 1.3 87.6 - - + +
918J ALA* 1.3 56.6 + - - +
920J LEU* 4.6 9.9 - - - +
921J ARG* 2.9 49.7 + - - +
1168J LEU* 5.6 3.3 - - - +
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Residues in contact with ALA 918 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890J VAL* 6.0 1.1 - - + -
899J LEU* 4.5 4.4 - - + +
914J LEU* 2.9 22.8 + - + +
915J VAL 3.5 4.9 - - - +
916J TYR 3.1 0.2 - - - -
917J GLN* 1.3 75.8 - - - +
919J PHE* 1.3 61.4 + - - +
922J LEU* 2.8 53.1 + - + +
923J GLY 3.8 0.2 + - - -
927J THR* 4.0 6.1 - - + +
930J LEU* 3.6 28.0 - - + -
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Residues in contact with PHE 919 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769J LEU* 3.6 37.2 - - + -
770J LEU* 3.6 40.2 - - + -
915J VAL* 2.9 18.2 + - + +
916J TYR* 3.1 8.7 + + - +
918J ALA* 1.3 75.3 - - - +
920J LEU* 1.3 58.8 + - + +
922J LEU 2.9 14.6 - - - +
923J GLY* 4.0 3.3 - - - -
924J MET* 3.8 37.9 - - + -
927J THR* 3.4 19.0 - - + +
1210J SER 3.8 14.4 - - - -
1211J MET 3.9 16.6 - - - -
1212J ALA* 4.0 6.7 - - + -
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Residues in contact with LEU 920 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916J TYR* 2.9 47.5 + - + +
917J GLN* 4.1 11.7 - - - +
919J PHE* 1.3 80.0 - - + +
921J ARG* 1.3 64.8 + - - +
922J LEU 3.3 4.5 - - - +
1167J SER* 5.2 14.6 - - - +
1168J LEU* 5.5 3.1 - - + -
1169J GLU 6.3 0.2 - - - +
1207J TYR* 5.8 5.6 - - + +
1212J ALA* 4.6 24.9 - - + +
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Residues in contact with ARG 921 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894J LYS* 5.6 7.7 - - - +
895J VAL* 3.6 31.4 - - - +
898J GLU* 3.8 24.0 + - - +
899J LEU* 4.3 6.3 - - + -
917J GLN* 2.9 33.8 + - - +
920J LEU* 1.3 71.7 - - - +
922J LEU* 1.3 76.2 + - + +
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Residues in contact with LEU 922 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890J VAL* 3.7 34.3 - - + -
892J ASP* 4.9 3.4 - - - +
895J VAL* 4.2 26.5 - - + -
896J ALA* 6.3 0.2 - - - -
899J LEU* 4.0 27.6 - - + -
918J ALA* 2.8 28.2 + - + +
919J PHE 2.9 15.1 - - - +
920J LEU 3.3 4.5 - - - +
921J ARG* 1.3 87.0 - - - +
923J GLY* 1.3 59.8 + - - +
926J LYS* 4.3 14.8 - - + -
927J THR* 4.9 1.6 - - - +
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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