Contacts of the strand formed by residues 954 - 961 (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 MET 954 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912K LEU* 4.9 2.8 - - - +
913K TYR* 3.6 25.2 + - + -
924K GLY* 4.5 0.9 - - - -
925K ASP 3.2 18.7 - - - +
926K LEU* 3.4 11.5 + - - +
929K SER* 2.9 48.0 - - - +
930K VAL* 3.6 14.6 - - + -
952K ASN* 3.1 14.0 + - - +
953K TRP* 1.3 75.4 - - - +
955K SER* 1.3 60.2 + - - +
956K ALA 3.3 22.7 - - - +
957K VAL* 3.7 2.0 - - + -
967K GLY* 3.5 11.7 - - - -
968K ALA 3.3 22.4 - - - +
970K ASN* 4.1 4.2 - - - +
975K PHE* 3.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 955 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913K TYR* 3.0 29.7 + - - -
954K MET* 1.3 74.2 - - - +
956K ALA* 1.3 66.0 + - - +
968K ALA* 2.9 23.1 + - - +
969K GLU 4.2 4.3 + - - -
970K ASN* 4.7 4.5 - - - -
1003K PHE* 3.9 26.4 - - - -
1004K VAL 2.6 27.8 + - - +
1005K ASN* 3.6 10.9 - - - +
77L LYS* 5.1 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 956 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913K TYR* 3.8 12.8 - - + -
954K MET* 3.3 2.8 - - - +
955K SER* 1.3 82.5 + - - +
957K VAL* 1.3 71.0 + - - +
968K ALA* 3.1 24.5 + - + -
1004K VAL* 4.1 6.5 - - + +
1005K ASN 3.7 22.4 - - - +
1006K VAL* 4.2 2.5 - - - +
1007K PHE* 3.7 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 957 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913K TYR* 4.1 19.1 - - + +
915K LYS* 3.3 31.5 + - + -
922K LEU* 3.6 30.3 - - + +
924K GLY* 3.8 16.8 - - - +
930K VAL* 3.5 29.4 - - + -
954K MET* 3.7 6.3 - - + -
956K ALA* 1.3 82.2 - - - +
958K GLU* 1.3 67.3 + - - +
966K LEU 3.2 10.5 - - - +
1007K PHE* 3.4 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 958 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915K LYS* 4.4 12.6 - - + +
922K LEU* 3.6 9.8 - - - +
957K VAL* 1.3 79.5 - - - +
959K ILE* 1.3 94.8 + - - +
960K LEU* 3.1 19.8 + - - +
965K PHE 3.7 0.2 - - - -
966K LEU* 2.7 44.8 + - + +
1007K PHE* 3.7 32.3 - - + -
1008K CYS* 5.2 0.7 - - - +
1009K HIS* 3.2 17.7 + - + +
1028K VAL* 2.9 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 959 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915K LYS* 3.6 12.7 - - + +
916K THR* 3.2 48.7 - - - +
917K LYS* 3.7 20.4 - - + +
920K PHE* 4.8 4.9 - - + +
921K ILE 5.4 0.2 - - - -
922K LEU* 4.1 21.8 - - + +
932K LEU* 6.5 1.1 - - + -
958K GLU* 1.3 95.2 - - - +
960K LEU* 1.3 62.9 + - - +
961K ASP 3.1 30.7 - - - +
962K ASP* 5.1 0.4 - - - -
964K ASN 4.0 3.8 - - - +
965K PHE* 4.9 8.1 - - + +
1009K HIS* 3.8 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 960 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K SER* 4.2 1.8 - - - +
4K ASN* 3.3 39.5 - - - +
917K LYS* 5.5 1.4 + - - -
958K GLU* 3.1 19.3 + - - +
959K ILE* 1.3 75.2 - - - +
961K ASP* 1.3 65.1 + - - +
964K ASN* 2.9 33.3 + - + +
965K PHE 4.8 0.2 - - - +
966K LEU* 4.3 21.1 - - + -
976K VAL* 4.3 13.7 - - + -
1009K HIS* 5.1 5.4 - - - -
1028K VAL* 4.7 9.2 - - + -
1040K VAL* 4.4 13.5 - - + +
1041K THR* 5.7 1.8 - - - -
1042K SER* 4.2 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 961 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917K LYS* 3.9 13.2 - - - +
959K ILE* 3.1 22.9 - - - +
960K LEU* 1.3 79.5 - - - +
962K ASP* 1.3 72.8 + - - +
963K ASP* 2.8 22.4 + - - -
964K ASN* 2.8 45.0 + - - +
965K PHE* 3.9 2.4 - - - -
1042K SER* 4.9 8.0 + - - -
----------------------------------------------------------
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