Contacts of the helix formed by residues 891 - 907 (chain D) in PDB entry 3IKM
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 VAL 891 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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889D ALA 4.2 1.6 - - - +
890D ASP* 1.3 82.2 - - - +
892D ASP* 1.3 64.6 + - - +
894D GLN* 2.6 39.6 + - + +
895D GLU* 3.1 11.2 + - + +
1108D TYR* 5.4 4.7 - - + -
1109D LEU* 5.0 16.6 - - + -
1112D MET* 6.3 1.3 - - + -
1135D ASP* 1.9 70.3 - - + +
1136D GLU* 3.6 3.1 - - - +
1137D VAL* 5.2 2.9 - - + -
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Residues in contact with ASP 892 (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 ASP* 4.9 3.4 + - - +
891D VAL* 1.3 76.1 - - - +
893D SER* 1.3 76.0 + - - +
895D GLU* 3.0 9.8 + - - +
896D LEU* 2.9 26.0 + - - +
927D ARG* 4.7 8.5 + - - -
951D TYR* 3.6 25.5 + - + +
1135D ASP* 2.7 23.3 + - + +
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Residues in contact with SER 893 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890D ASP* 6.1 1.8 - - - +
891D VAL 5.6 0.2 - - - -
892D ASP* 1.3 88.3 + - - +
894D GLN* 1.3 90.8 + - - +
896D LEU* 3.2 4.9 + - - +
897D TRP* 2.9 23.7 + - - +
927D ARG* 3.3 27.4 - - - +
1161D ARG* 5.6 0.5 + - - -
1180D PHE* 6.1 0.2 - - - -
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Residues in contact with GLN 894 (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 ASP* 2.6 26.4 + - - +
891D VAL* 2.6 41.2 + - + +
893D SER* 1.3 108.9 + - - +
895D GLU* 1.3 64.1 + - - +
897D TRP* 2.8 18.7 + - - +
898D ILE* 2.7 18.7 + - - +
1108D TYR* 3.4 35.4 + - + +
1112D MET* 4.9 4.2 - - - +
1157D ASN* 4.5 1.4 + - - -
1161D ARG* 3.9 11.1 + - + +
1180D PHE* 3.2 23.4 - - - -
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Residues in contact with GLU 895 (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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853D ARG* 4.7 16.6 - - - +
891D VAL* 3.1 18.3 + - + +
892D ASP* 3.0 9.3 + - - +
894D GLN* 1.3 77.8 - - - +
896D LEU* 1.3 96.5 + - - +
898D ILE* 2.8 43.6 - - + +
899D ALA* 3.7 4.0 + - - +
951D TYR* 4.4 5.6 - - - -
954D ILE* 5.3 1.0 - - - +
955D TYR* 4.5 15.8 + - + -
1101D VAL* 5.6 4.6 - - + +
1105D ALA* 5.1 5.6 - - + -
1108D TYR* 4.8 4.9 - - + -
1135D ASP* 4.5 9.7 - - - +
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Residues in contact with LEU 896 (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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892D ASP* 2.9 19.1 + - - +
893D SER* 3.6 5.8 - - - +
895D GLU* 1.3 104.3 - - - +
897D TRP* 1.3 67.6 + - - +
898D ILE 3.0 3.6 + - - -
899D ALA* 3.4 6.2 + - + +
900D ALA* 3.2 20.0 + - - +
919D MET* 4.7 19.7 - - + +
951D TYR* 3.5 41.3 - - + +
954D ILE* 3.6 29.6 - - + -
955D TYR* 5.7 0.7 - - - +
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Residues in contact with TRP 897 (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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893D SER 2.9 12.2 + - - +
894D GLN* 2.8 17.0 + - - +
896D LEU* 1.3 72.4 - - - +
898D ILE* 1.3 61.5 + - + +
900D ALA* 3.2 6.9 - - + +
901D VAL* 2.9 41.1 + - + +
916D PHE* 2.8 40.7 - + + -
919D MET* 4.7 16.5 - - + +
1161D ARG* 4.6 16.6 - - + -
1164D PHE* 6.2 1.1 - - + -
1173D LEU* 2.9 58.1 - - + -
1174D PRO* 3.7 4.3 - - + -
1177D VAL* 3.0 45.5 - - + +
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Residues in contact with ILE 898 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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894D GLN 2.7 22.7 - - - +
895D GLU* 2.8 26.2 - - + +
896D LEU 3.0 1.4 - - - -
897D TRP* 1.3 77.4 - - + +
899D ALA* 1.3 83.2 + - + +
900D ALA 3.0 1.1 - - - -
901D VAL* 3.0 11.2 - - - +
902D LEU* 2.8 29.7 + - + +
1101D VAL* 4.6 9.0 - - + +
1104D SER* 4.0 17.3 - - - +
1105D ALA* 3.9 34.3 - - + +
1108D TYR* 4.9 13.2 - - + -
1164D PHE* 4.7 17.5 - - + -
1168D LEU* 5.6 2.8 - - + +
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Residues in contact with ALA 899 (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 GLU* 4.5 6.1 - - - +
896D LEU 3.4 8.6 + - - +
898D ILE* 1.3 85.5 - - + +
900D ALA* 1.3 56.1 + - - +
902D LEU* 3.1 23.4 - - - +
954D ILE* 4.4 19.1 - - + -
1002D GLU* 2.4 26.4 - - - +
1003D TRP* 4.1 24.3 - - + -
1101D VAL* 5.4 5.8 - - + -
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Residues in contact with ALA 900 (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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896D LEU 3.2 10.6 + - - +
897D TRP* 3.2 13.9 - - + +
899D ALA* 1.3 76.6 - - - +
901D VAL* 1.3 61.5 + - + +
903D GLY 3.2 0.5 + - - -
904D ASP* 2.5 25.8 - - - +
915D ALA* 2.6 35.2 - - + +
916D PHE 4.3 0.9 - - - +
919D MET* 3.9 13.7 - - + -
1002D GLU* 3.0 10.8 - - - +
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Residues in contact with VAL 901 (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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897D TRP* 2.9 65.4 + - + +
898D ILE* 3.0 16.8 - - - +
900D ALA* 1.3 69.3 - - - +
902D LEU* 1.3 90.5 + - + +
904D ASP* 2.9 11.9 + - - +
905D ALA* 2.6 28.2 + - + +
910D MET* 4.8 4.7 - - + +
916D PHE* 5.4 2.9 - - + -
1164D PHE* 6.2 3.1 - - + -
1165D ALA* 5.8 4.3 - - - -
1168D LEU* 5.7 7.0 - - + +
1173D LEU* 3.9 16.8 - - + -
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Residues in contact with LEU 902 (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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898D ILE* 3.2 7.0 - - + +
899D ALA* 3.1 22.0 - - - +
901D VAL* 1.3 88.3 - - - +
903D GLY* 1.3 66.2 + - - +
905D ALA* 2.8 14.2 - - - +
906D HIS* 3.5 4.7 + - - +
1002D GLU* 5.9 0.2 - - + -
1003D TRP* 5.4 7.4 - - + -
1005D VAL* 6.0 2.5 - - + -
1006D ARG* 3.9 32.1 - - + +
1100D VAL* 5.9 2.0 - - + -
1101D VAL* 6.4 1.6 - - - -
1104D SER* 5.0 12.6 - - - +
1168D LEU* 3.4 55.4 - - + +
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Residues in contact with GLY 903 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900D ALA 3.2 4.0 + - - -
901D VAL 3.1 0.6 + - - -
902D LEU* 1.3 79.0 - - - +
904D ASP* 1.3 52.5 + - - +
906D HIS* 2.4 34.2 + - - +
907D PHE* 3.0 15.8 - - - -
1002D GLU* 2.9 36.6 + - - +
1005D VAL* 5.1 4.3 - - - -
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Residues in contact with ASP 904 (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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900D ALA 2.5 17.5 - - - +
901D VAL* 2.9 14.8 - - - +
903D GLY* 1.3 65.4 - - - -
905D ALA* 1.3 62.5 + - - +
906D HIS 3.1 0.3 + - - -
907D PHE* 3.1 32.9 - - - +
908D ALA 3.6 0.9 - - - +
909D GLY 3.2 9.0 - - - +
910D MET* 3.0 22.2 - - - +
911D HIS 4.0 2.2 - - - -
912D GLY* 3.2 20.6 - - - -
913D CYS* 4.4 2.3 - - - -
915D ALA* 2.6 37.9 + - - +
916D PHE* 3.6 4.0 + - - +
1002D GLU* 3.4 5.9 - - - +
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Residues in contact with ALA 905 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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901D VAL* 2.6 25.3 + - + +
902D LEU 2.8 10.5 - - - +
903D GLY 2.6 3.6 + - - -
904D ASP* 1.3 73.9 - - - +
906D HIS* 1.3 59.4 + - - +
908D ALA 3.7 9.5 - - - +
910D MET* 4.3 16.4 - - + +
1168D LEU 3.6 21.5 - - - +
1169D GLY* 4.6 8.3 - - - -
1170D LEU* 5.5 5.0 - - + +
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Residues in contact with HIS 906 (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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902D LEU 3.5 3.6 + - - +
903D GLY 2.4 24.3 + - - +
905D ALA* 1.3 73.4 - - - +
907D PHE* 1.3 63.5 + - + +
908D ALA 3.8 2.4 + - - -
1005D VAL* 4.5 27.4 - - + -
1009D ASN* 5.2 10.0 + - - -
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Residues in contact with PHE 907 (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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102D ARG* 6.3 1.3 - - - -
903D GLY* 3.0 26.0 - - - -
904D ASP* 3.1 14.9 + - - +
906D HIS* 1.3 81.4 - - + +
908D ALA* 1.3 73.3 + - + +
909D GLY 3.5 4.0 + - - +
912D GLY 4.5 6.4 - - - +
913D CYS* 3.2 33.4 - - + -
999D ASP 4.4 2.5 - - - -
1001D GLY* 4.4 3.6 - - - -
1002D GLU* 3.1 45.5 - - + -
1005D VAL* 5.0 6.7 - - + -
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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
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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