Contacts of the helix formed by residues 1044 - 1060 (chain K) in PDB entry 6R90
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 SER1044 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K TYR* 4.2 1.6 - - - -
1023K PRO 4.7 0.2 + - - -
1025K GLN* 3.6 12.4 + - - -
1043K LEU* 1.3 85.6 - - - +
1045K GLU* 1.3 84.8 + - - +
1046K SER* 3.4 11.4 + - - -
1047K TRP* 3.7 10.3 + - - -
1048K TYR* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1045 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K MET* 5.4 1.3 - - + +
3K TYR* 3.4 35.4 - - + +
1044K SER* 1.3 90.2 + - - +
1046K SER* 1.3 59.9 + - - +
1048K TYR* 3.2 3.1 + - - +
1049K ASN* 2.9 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1046 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044K SER* 4.7 6.3 + - - -
1045K GLU* 1.3 81.8 + - - +
1047K TRP* 1.3 73.7 + - - +
1049K ASN* 3.2 11.5 + - - +
1050K LEU* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1047 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022K THR 5.2 1.0 + - - -
1023K PRO* 3.7 45.8 - - + +
1025K GLN* 6.0 0.7 - - - -
1043K LEU* 3.2 28.3 - - + -
1044K SER* 3.7 10.4 + - - +
1045K GLU 3.4 0.4 - - - -
1046K SER* 1.3 88.8 + - - +
1048K TYR* 1.3 57.0 + - - +
1050K LEU* 3.3 31.5 + - + +
1051K LEU* 2.9 53.2 + - + +
1114K TYR* 5.9 1.8 - + - -
1132K VAL* 3.7 39.3 - - + -
1135K GLU* 5.7 3.8 - - - -
1136K LEU* 5.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1048 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K TYR* 3.3 45.1 - + + -
4K ASN 4.8 1.8 - - - -
1043K LEU* 3.3 9.3 - - + +
1044K SER 3.2 14.5 + - - +
1045K GLU 3.4 8.1 - - - +
1046K SER 3.2 0.2 - - - -
1047K TRP* 1.3 79.3 - - - +
1049K ASN* 1.3 70.3 + - - +
1051K LEU* 3.8 1.5 - - - -
1052K LEU* 2.9 62.2 + - + +
1086K THR* 4.0 6.2 + - - -
1087K GLY* 2.9 47.5 + - - -
1088K PHE 3.8 4.6 + - - -
1089K ILE* 4.0 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1049 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K TYR* 5.7 1.6 - - - -
1045K GLU* 2.9 30.0 + - - +
1046K SER* 3.5 10.0 - - - +
1048K TYR* 1.3 90.0 - - - +
1050K LEU* 1.3 60.4 + - - +
1052K LEU* 3.3 6.0 + - - +
1053K ASP* 2.6 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1050 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046K SER 2.9 13.2 + - - +
1047K TRP* 3.5 41.7 - - + +
1049K ASN* 1.3 78.3 - - - +
1051K LEU* 1.3 59.6 + - + +
1053K ASP* 3.3 8.2 + - - +
1054K MET* 2.9 48.1 + - + +
1112K LEU* 5.0 14.8 - - + -
1113K GLN 5.1 8.1 - - - +
1114K TYR* 4.6 28.7 - - + -
1115K ASP 5.8 0.9 - - - +
1129K LEU* 5.1 4.0 - - + -
1132K VAL* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1051 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K TYR* 4.0 23.6 - - + -
1023K PRO* 6.1 0.2 - - + -
1043K LEU* 3.8 21.5 - - + -
1047K TRP* 2.9 43.9 + - + +
1050K LEU* 1.3 74.6 - - + +
1052K LEU* 1.3 60.2 + - - +
1054K MET* 3.3 29.5 + - + +
1055K GLN* 2.9 30.8 + - - +
1089K ILE* 3.9 20.4 - - + -
1094K ILE* 4.0 10.5 - - + +
1132K VAL* 4.8 1.1 - - + -
1136K LEU* 4.5 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1052 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1048K TYR* 2.9 52.2 + - + +
1049K ASN* 3.7 5.8 - - - +
1051K LEU* 1.3 74.8 - - - +
1053K ASP* 1.3 71.2 + - - +
1055K GLN* 3.1 10.3 + - + +
1056K ASN* 3.0 55.5 + - - +
1089K ILE* 3.7 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1053 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049K ASN* 2.6 25.4 + - - +
1050K LEU* 3.6 8.1 - - - +
1052K LEU* 1.3 81.2 - - - +
1054K MET* 1.3 62.2 + - - +
1056K ASN* 3.3 8.9 + - - +
1057K ARG* 3.0 40.1 + - - +
1112K LEU* 4.8 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1054 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050K LEU* 2.9 25.4 + - + +
1051K LEU* 3.4 36.3 - - + +
1053K ASP* 1.3 77.0 - - + +
1055K GLN* 1.3 57.5 + - - +
1057K ARG* 3.9 6.4 - - - +
1058K LEU* 2.8 48.4 + - + +
1094K ILE* 4.2 24.7 - - + -
1097K PHE* 5.3 9.9 - - + -
1108K VAL* 5.6 6.3 - - + -
1112K LEU* 4.9 9.6 - - + +
1129K LEU* 3.4 42.6 - - + +
1132K VAL* 5.2 4.7 - - + -
1133K VAL* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1055 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998K PHE* 6.1 0.2 - - - -
1051K LEU 2.9 16.1 + - - +
1052K LEU* 3.1 13.4 + - + +
1054K MET* 1.3 77.5 - - - +
1056K ASN* 1.3 59.0 + - - +
1058K LEU* 3.8 3.0 - - - +
1059K ASN* 2.8 39.7 + - - +
1070K HIS* 3.5 14.0 + - - -
1088K PHE 3.7 6.5 + - - -
1089K ILE* 3.4 23.6 - - - +
1090K ASP* 3.3 27.7 - - - +
1093K LEU* 3.2 32.9 - - + +
1094K ILE* 4.4 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1056 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052K LEU* 3.0 41.0 + - - +
1053K ASP* 3.3 9.5 + - - +
1055K GLN* 1.3 77.0 - - - +
1057K ARG* 1.3 64.6 + - + +
1059K ASN* 3.2 10.9 + - - +
1060K LYS* 3.0 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1057 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053K ASP* 3.0 29.5 + - - +
1054K MET* 3.9 4.3 - - - +
1056K ASN* 1.3 77.2 - - + +
1058K LEU* 1.3 63.2 + - - +
1060K LYS* 3.2 16.6 + - - +
1061K VAL* 3.3 18.6 - - - +
1107K GLU 4.9 1.4 + - - +
1108K VAL* 3.4 34.9 + - + +
1110K ALA 2.5 28.5 + - - -
1111K ASN* 2.5 31.3 + - - +
1112K LEU* 3.6 32.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1058 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054K MET* 2.8 42.4 + - + +
1055K GLN* 3.8 4.3 - - - +
1057K ARG* 1.3 75.5 - - - +
1059K ASN* 1.3 56.1 + - - +
1061K VAL* 2.7 28.4 + - + +
1062K ILE* 2.8 27.3 + - + +
1093K LEU* 4.1 28.9 - - + +
1094K ILE* 4.4 12.3 - - + -
1096K SER 5.4 0.2 - - - +
1097K PHE* 3.8 34.3 - - + +
1100K ILE* 6.0 4.0 - - + -
1108K VAL* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1059 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58K TYR* 4.5 2.1 + - - -
1055K GLN* 2.8 35.2 + - - +
1056K ASN* 3.6 10.1 - - - +
1058K LEU* 1.3 74.8 - - - +
1060K LYS* 1.3 62.8 + - + +
1061K VAL 3.4 0.3 + - - -
1062K ILE* 4.1 14.4 - - - +
1069K GLU* 4.5 13.3 + - - +
1070K HIS* 3.3 42.2 + - + +
1071K SER* 5.3 1.6 - - - +
1093K LEU* 3.2 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1060 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056K ASN* 3.0 21.8 + - + +
1057K ARG* 3.5 11.0 - - - +
1058K LEU 3.1 0.6 - - - -
1059K ASN* 1.3 77.4 - - + +
1061K VAL* 1.3 62.1 + - + +
1062K ILE 5.0 0.4 - - - -
1069K GLU* 5.4 5.9 + - - -
----------------------------------------------------------
Back to top of page
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