Contacts of the helix formed by residues 943 - 955 (chain A) in PDB entry 5C53
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 ARG 943 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A SER* 6.2 0.6 - - - -
925A LYS* 5.7 1.1 - - - +
930A ASP* 3.5 30.5 + - - +
932A HIS* 3.4 34.8 - - + +
933A SER* 3.9 27.9 - - - +
936A ALA* 4.6 1.1 - - + -
941A ILE 3.9 0.9 - - - -
942A SER* 1.3 81.8 + - - +
944A GLU* 1.3 75.5 + - + +
945A HIS* 3.1 4.2 + - - -
946A ALA* 3.2 7.0 + - - +
947A LYS* 3.2 27.0 + - - +
4003A 4Y3 2.7 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 944 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A ARG* 1.3 87.1 + - + +
945A HIS* 1.3 65.0 + - + +
947A LYS* 2.7 41.6 + - - +
948A ILE* 2.9 37.5 + - + +
4003A 4Y3 4.8 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 945 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941A ILE* 3.6 23.4 - - + +
942A SER 4.1 19.1 + - - -
943A ARG 3.1 1.2 + - - -
944A GLU* 1.3 85.0 + - + +
946A ALA* 1.3 60.3 + - - +
948A ILE* 3.2 7.6 + - + +
949A PHE* 2.9 26.5 + - - +
969A PHE* 3.5 58.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 946 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A HIS* 3.5 25.4 - - - +
935A THR* 3.6 11.6 + - - +
936A ALA* 3.8 8.7 - - + +
941A ILE* 3.7 19.0 + - + +
943A ARG 3.2 9.0 + - - +
945A HIS* 1.3 78.4 - - - +
947A LYS* 1.3 56.1 + - - +
949A PHE* 3.4 8.5 - - - +
950A ASN* 2.9 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A HIS* 3.5 19.9 + - + +
943A ARG* 3.2 16.6 + - - +
944A GLU* 2.7 44.2 + - - +
945A HIS 3.2 0.2 - - - -
946A ALA* 1.3 74.9 - - - +
948A ILE* 1.3 60.2 + - - +
950A ASN* 3.9 0.3 - - - +
951A TYR* 2.9 54.5 + - + +
4003A 4Y3 3.0 80.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944A GLU* 2.9 23.7 + - + +
945A HIS* 3.2 9.6 + - + +
947A LYS* 1.3 76.5 - - + +
949A PHE* 1.3 57.4 + - - +
951A TYR* 4.9 0.4 - - - -
952A GLY* 2.9 25.6 + - - -
961A PHE* 5.9 0.4 - - + -
965A LEU* 4.1 22.3 - - + +
969A PHE* 4.5 19.5 - - + -
4003A 4Y3 3.9 26.7 - - - +
4T G 3.1 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A THR* 6.1 2.7 - - - -
945A HIS 2.9 14.5 + - - +
946A ALA* 3.4 12.3 - - - +
947A LYS 3.2 0.2 - - - -
948A ILE* 1.3 78.2 - - - +
950A ASN* 1.3 67.6 + - - +
952A GLY* 3.7 0.7 - - - -
953A ARG* 2.9 42.7 + - + +
962A ALA* 4.0 26.5 - - + -
965A LEU* 4.4 19.7 - - + -
966A LEU* 3.8 47.6 - - + -
969A PHE* 5.9 1.8 - + + -
981A LYS* 5.4 4.7 - - + -
984A GLN* 4.8 26.0 - - + -
985A MET* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 950 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A LEU* 5.1 9.2 - - + +
931A LEU* 4.7 7.2 - - - +
932A HIS* 3.5 31.5 + - + +
935A THR* 3.3 37.5 + - - +
946A ALA 2.9 18.0 + - - +
947A LYS 3.9 2.9 - - - +
949A PHE* 1.3 80.9 - - - +
951A TYR* 1.3 61.4 + - - +
952A GLY 3.1 1.6 - - - -
953A ARG* 2.8 41.6 + - - +
954A ILE* 2.9 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 951 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A SER* 3.9 2.4 - - - -
895A GLU* 4.0 10.0 + - + +
896A LEU* 3.4 48.6 + - + +
932A HIS* 3.8 6.9 + + - -
947A LYS* 2.9 38.6 + - + +
948A ILE* 4.9 0.2 - - - -
950A ASN* 1.3 73.6 - - - +
952A GLY* 1.3 59.8 + - - +
954A ILE* 4.0 15.0 - - + +
955A TYR* 3.1 42.8 + - + -
4003A 4Y3 2.9 78.0 + + + +
4T G 3.8 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 952 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A ILE 2.9 20.2 + - - -
949A PHE 3.7 1.6 - - - -
951A TYR* 1.3 76.9 - - - +
953A ARG* 1.3 62.1 + - - +
955A TYR 3.8 2.5 + - - -
956A GLY 3.0 27.5 + - - +
957A ALA* 3.7 1.8 + - - -
961A PHE* 5.2 5.0 - - - -
965A LEU* 6.2 0.4 - - - -
4T G 3.4 29.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916A PHE* 4.1 20.4 - - - -
931A LEU* 5.8 2.0 - - - +
949A PHE* 2.9 32.1 + - + +
950A ASN* 2.8 26.7 + - - +
952A GLY* 1.3 76.1 - - - +
954A ILE* 1.3 71.1 + - - +
956A GLY 3.4 0.9 + - - -
957A ALA* 3.3 39.9 + - + +
984A GLN* 4.5 21.0 + - - -
985A MET* 6.0 2.2 - - - -
987A ALA* 3.4 15.9 - - - +
988A ALA* 6.3 2.2 - - + -
1056A GLU* 3.4 36.3 + - - +
1058A PHE* 4.0 12.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A GLU 5.5 0.9 - - - +
896A LEU* 4.1 20.9 - - + -
899A ALA* 4.8 10.3 - - + -
916A PHE* 4.3 13.5 - - + -
950A ASN* 2.9 15.6 + - + +
951A TYR* 4.0 25.8 - - + +
952A GLY 3.4 0.2 - - - -
953A ARG* 1.3 88.6 - - - +
955A TYR* 1.3 80.4 + - + +
956A GLY 3.3 2.8 + - - -
1056A GLU* 5.5 1.8 - - - +
1057A MET* 4.6 5.8 - - + -
1058A PHE* 3.1 35.6 - - + -
1061A LEU* 4.3 13.7 - - + -
1097A VAL* 4.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 955 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A GLU* 2.4 32.0 + - - +
951A TYR* 3.1 29.2 + + + +
952A GLY 3.8 3.1 + - - +
953A ARG 3.3 0.6 - - - -
954A ILE* 1.3 102.6 - - + +
956A GLY* 1.3 56.0 + - - -
1061A LEU* 5.6 0.4 - - + -
1094A THR* 4.2 21.7 - - - +
1097A VAL* 4.3 17.3 - - + -
1098A ASN* 3.4 21.1 - - + -
1101A VAL* 3.2 34.9 - - + +
4003A 4Y3 4.2 2.0 - - - -
4T G 3.2 52.2 + + - +
5T A 4.7 6.9 - - - +
----------------------------------------------------------
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