Contacts of the helix formed by residues 907 - 922 (chain D) in PDB entry 4G7Z
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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786D ILE* 4.1 9.6 - - - -
790D TYR* 4.2 8.5 - - + -
904D VAL* 4.6 9.1 - - + +
905D PRO* 3.8 11.2 - - + +
906D GLN* 1.3 74.6 - - - +
908D LYS* 1.3 72.2 + - - +
909D ASN* 2.8 38.4 + - - +
910D SER* 2.6 41.3 + - - +
911D LEU* 3.1 13.9 + - - +
1025D GLN 4.3 6.5 - - - +
1026D SER* 3.1 28.9 - - - +
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Residues in contact with LYS 908 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780D LYS* 2.9 45.3 - - + +
781D PRO* 5.4 1.9 - - - +
786D ILE* 3.4 24.8 - - + +
907D GLU* 1.3 77.6 - - - +
909D ASN* 1.3 68.7 + - - +
911D LEU* 3.9 1.9 - - - +
912D LYS* 2.9 37.3 + - - +
1026D SER 3.0 11.3 + - - +
1027D GLY* 4.4 14.6 - - - +
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Residues in contact with ASN 909 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907D GLU* 2.8 20.1 + - - +
908D LYS* 1.3 81.9 - - - +
910D SER* 1.3 55.0 + - - +
912D LYS* 2.7 30.4 + - - +
913D ASP* 2.6 47.9 + - - +
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Residues in contact with SER 910 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901D GLN* 4.2 24.8 + - - +
904D VAL* 4.5 7.2 - - - -
906D GLN* 3.1 24.2 - - - +
907D GLU* 2.6 49.9 + - - -
909D ASN* 1.3 76.0 - - - +
911D LEU* 1.3 55.5 + - - +
913D ASP* 3.6 3.5 + - - +
914D LEU* 3.0 28.6 + - - +
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Residues in contact with LEU 911 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781D PRO* 3.6 37.9 - - + -
786D ILE* 4.2 17.0 - - + -
789D LEU* 3.8 24.5 - - + -
882D PHE* 3.8 22.2 - - + -
906D GLN* 3.7 28.7 - - + +
907D GLU 3.1 20.9 + - - +
908D LYS 4.0 1.6 - - - +
909D ASN 3.1 0.4 - - - -
910D SER* 1.3 74.1 - - - +
912D LYS* 1.3 62.4 + - - +
914D LEU* 3.7 7.7 - - + +
915D VAL* 3.1 31.5 + - - +
934D LEU* 4.9 7.4 - - + -
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Residues in contact with LYS 912 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776D GLU* 3.3 31.3 + - + +
777D PRO* 3.7 26.4 - - + +
780D LYS* 4.2 33.7 - - + +
781D PRO* 5.0 0.6 - - - +
908D LYS* 2.9 26.1 + - + +
909D ASN* 2.7 32.5 + - - +
911D LEU* 1.3 70.3 - - - +
913D ASP* 1.3 93.7 + - - +
915D VAL* 3.1 9.1 + - - +
916D TYR* 3.1 18.2 + - - +
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Residues in contact with ASP 913 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901D GLN* 5.1 9.2 + - - +
909D ASN* 2.6 36.9 + - - +
910D SER* 4.2 4.7 + - - +
912D LYS* 1.3 95.1 + - - +
914D LEU* 1.3 61.1 + - - +
916D TYR* 3.5 7.7 + - - +
917D GLN* 3.2 30.6 + - + +
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Residues in contact with LEU 914 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882D PHE* 4.7 21.3 - - + -
886D VAL* 4.4 18.2 - - + -
899D LEU* 4.1 38.3 - - + +
900D ILE* 4.7 6.5 - - + +
906D GLN* 5.9 0.9 - - - +
910D SER 3.0 19.3 + - - +
911D LEU* 3.7 13.2 - - + +
913D ASP* 1.3 73.8 - - - +
915D VAL* 1.3 72.3 + - + +
917D GLN* 3.1 8.6 + - - +
918D ALA* 2.9 21.9 + - + +
930D LEU* 4.2 18.8 - - + -
934D LEU* 4.1 24.9 - - + -
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Residues in contact with VAL 915 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769D LEU* 5.4 7.0 - - + +
770D LEU* 5.5 3.4 - - + -
777D PRO* 4.2 18.8 - - + -
779D ALA 4.3 6.3 - - - +
780D LYS* 5.2 0.4 - - - -
781D PRO* 4.3 13.5 - - + -
911D LEU 3.1 21.1 + - - +
912D LYS* 3.1 8.9 + - - +
914D LEU* 1.3 87.7 - - + +
916D TYR* 1.3 64.3 + - - +
918D ALA* 3.2 8.1 + - - +
919D PHE* 2.9 22.6 + - + +
927D THR* 3.7 14.8 - - + +
930D LEU* 5.0 1.3 - - + -
931D LEU* 3.8 28.3 - - + -
934D LEU* 4.9 2.9 - - + -
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Residues in contact with TYR 916 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770D LEU* 3.9 26.5 - - + -
775D GLY 4.0 11.7 - - - -
776D GLU* 5.2 0.2 - - - -
777D PRO* 3.9 19.7 - - + +
912D LYS 3.1 11.9 + - - +
913D ASP* 3.7 10.8 - - - +
915D VAL* 1.3 76.7 - - - +
917D GLN* 1.3 79.5 + - - +
919D PHE* 3.1 16.9 + - + +
920D LEU* 3.1 44.6 + - + +
1145D TYR* 2.7 44.8 + + - -
1168D MET* 3.8 23.6 + - + +
1207D TYR* 5.2 0.2 - - - -
1212D ALA* 4.4 0.2 - - - +
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Residues in contact with GLN 917 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899D LEU* 3.7 23.7 - - + +
913D ASP* 3.2 15.5 + - + +
914D LEU* 3.1 8.9 + - - +
916D TYR* 1.3 104.4 - - - +
918D ALA* 1.3 52.6 + - - +
920D LEU* 2.9 17.6 + - - +
921D ARG* 2.8 46.5 + - - +
1168D MET* 5.8 2.8 - - - +
1169D ASP* 4.9 10.9 + - - +
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Residues in contact with ALA 918 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899D LEU* 3.9 20.1 - - + +
914D LEU 2.9 12.6 + - - +
915D VAL 3.4 8.1 - - - +
917D GLN* 1.3 77.2 - - - +
919D PHE* 1.3 62.8 + - - +
922D LEU* 3.0 37.4 + - + +
927D THR* 3.6 8.6 + - + -
930D LEU* 3.5 30.3 - - + -
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Residues in contact with PHE 919 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769D LEU* 4.1 30.1 - - + -
770D LEU* 4.0 21.3 - - + -
915D VAL* 2.9 13.2 + - + +
916D TYR* 3.1 13.4 + - - +
918D ALA* 1.3 76.2 - - - +
920D LEU* 1.3 61.9 + - + +
922D LEU 2.8 17.3 - - - +
924D MET* 3.9 39.1 + - + -
927D THR* 3.5 19.2 + - + +
1210D SER 3.7 17.5 - - - -
1211D MET* 3.1 35.9 - - - -
1212D ALA* 3.9 9.4 - - + -
1213D ARG* 4.6 5.7 + - - -
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Residues in contact with LEU 920 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916D TYR* 3.1 45.2 + - + +
917D GLN* 2.9 23.1 + - - +
919D PHE* 1.3 84.6 - - + +
921D ARG* 1.3 68.6 + - + +
922D LEU 4.0 1.0 - - - +
1167D SER* 6.1 4.0 - - - -
1168D MET* 5.2 7.2 - - + +
1169D ASP* 5.8 4.0 - - - +
1207D TYR* 6.0 1.6 - - + +
1212D ALA* 4.0 30.5 - - + +
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Residues in contact with ARG 921 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895D VAL* 4.0 33.1 - - + +
898D GLU* 2.9 34.8 + - - +
899D LEU* 4.0 18.7 - - + +
917D GLN* 2.8 28.9 + - - +
920D LEU* 1.3 77.7 - - + +
922D LEU* 1.3 64.0 + - + +
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Residues in contact with LEU 922 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890D VAL* 3.5 46.9 - - + +
892D ASP* 4.4 12.8 - - + +
895D VAL* 4.4 13.7 - - + -
899D LEU* 3.7 29.6 - - + -
918D ALA* 3.0 19.6 + - + +
919D PHE 2.8 23.6 - - - +
920D LEU 4.0 1.4 - - - +
921D ARG* 1.3 79.3 - - + +
923D GLY* 1.3 61.5 + - - +
926D LYS* 3.8 24.0 - - + -
927D THR* 5.2 1.1 - - - +
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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