Contacts of the helix formed by residues 1054 - 1068 (chain D) in PDB entry 6AH0
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 GLU1054 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029D VAL* 5.5 7.3 - - - -
1052D ILE 3.3 5.0 + - - -
1053D GLU* 1.3 73.4 - - - +
1055D PRO* 1.3 66.8 - - - +
1056D SER 3.3 2.8 + - - -
1057D ALA 3.3 8.8 + - - -
1058D LYS* 3.4 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1055 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019D SER 5.7 0.9 - - - -
1027D ILE 4.3 17.9 - - - +
1028D THR* 5.1 6.9 - - - -
1029D VAL 5.2 3.2 - - - +
1054D GLU* 1.3 72.6 - - - +
1056D SER* 1.3 63.8 + - - +
1058D LYS* 3.1 3.1 + - - +
1059D ILE* 2.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1056 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016D ARG* 6.2 0.4 - - - +
1019D SER* 4.8 20.6 - - - +
1054D GLU 3.3 1.4 - - - -
1055D PRO* 1.3 75.4 - - - +
1057D ALA* 1.3 55.9 - - - +
1059D ILE* 3.4 1.0 + - - -
1060D ASN* 2.9 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1057 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051D SER* 5.7 6.8 - - - +
1052D ILE 4.3 15.0 + - - -
1053D GLU* 5.6 1.3 - - - +
1054D GLU 3.3 6.8 + - - +
1055D PRO 3.2 0.6 - - - -
1056D SER* 1.3 72.6 - - - +
1058D LYS* 1.3 58.9 + - - +
1060D ASN* 3.2 1.2 + - - +
1061D VAL* 2.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1058 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053D GLU* 6.0 0.4 - - - +
1054D GLU 3.4 9.0 + - - -
1055D PRO* 3.1 6.7 + - - -
1057D ALA* 1.3 75.5 - - - +
1059D ILE* 1.3 57.6 + - - +
1061D VAL 3.9 0.2 - - - -
1062D LEU* 2.9 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1059 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019D SER* 5.7 6.7 - - - +
1055D PRO 2.9 12.8 + - - -
1056D SER 3.8 2.5 - - - -
1058D LYS* 1.3 76.0 - - - +
1060D ASN* 1.3 61.8 + - - +
1062D LEU* 3.3 1.7 + - - +
1063D LEU* 2.9 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1060 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015D PHE* 5.4 9.9 - - - +
1019D SER* 5.4 3.2 - - - +
1056D SER 2.9 15.6 + - - -
1057D ALA* 3.7 2.5 - - - +
1059D ILE* 1.3 74.6 - - - +
1061D VAL* 1.3 63.0 + - - +
1063D LEU* 3.0 13.7 + - - -
1064D GLN* 3.0 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1061 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040D LEU 5.6 7.8 - - - +
1041D LEU* 6.0 4.9 - - - +
1057D ALA 2.8 18.8 + - - -
1058D LYS 4.1 0.4 - - - -
1060D ASN* 1.3 71.4 - - - +
1062D LEU* 1.3 56.7 + - - +
1064D GLN* 3.5 2.0 + - - +
1065D ALA* 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1062 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058D LYS 2.9 15.9 + - - -
1059D ILE* 3.6 4.3 - - - +
1060D ASN 3.0 0.2 - - - -
1061D VAL* 1.3 74.5 - - - +
1063D LEU* 1.3 64.3 + - - +
1065D ALA* 3.0 2.8 + - - +
1066D PHE* 2.9 21.1 + - - -
1081D MET* 5.5 13.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1063 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059D ILE 2.9 14.0 + - - -
1060D ASN 3.0 3.1 + - - -
1062D LEU* 1.3 73.0 - - - +
1064D GLN* 1.3 62.6 + - - +
1066D PHE* 3.2 2.9 + - - +
1067D ILE* 2.9 19.9 + - - -
1084D VAL 6.4 0.9 - - - -
1085D THR* 6.1 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1064 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044D VAL* 6.4 2.7 - - - +
1060D ASN 3.0 12.1 + - - -
1061D VAL* 3.9 3.4 - - - +
1063D LEU* 1.3 77.0 - - - +
1065D ALA* 1.3 51.3 + - - +
1067D ILE* 4.4 0.9 - - - +
1068D SER* 2.6 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1065 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061D VAL 2.9 16.1 + - - -
1062D LEU* 3.0 4.7 + - - +
1064D GLN* 1.3 76.2 - - - +
1066D PHE* 1.3 56.4 + - - +
1068D SER* 3.5 1.4 - - - +
1069D GLN 2.8 22.7 + - - -
1070D LEU* 2.8 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1066 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062D LEU 2.9 13.4 + - - -
1063D LEU* 3.2 3.3 + - - +
1065D ALA* 1.3 77.2 - - - +
1067D ILE* 1.3 61.0 + - - +
1069D GLN* 3.1 12.9 + - - +
1070D LEU 5.0 2.0 - - - +
1121D ARG* 4.8 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1067 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063D LEU 2.9 14.0 + - - -
1064D GLN* 3.7 2.5 - - - +
1066D PHE* 1.3 72.8 - - - +
1068D SER* 1.3 58.6 + - - +
1069D GLN 2.9 9.3 + - - -
1117D MET 4.8 6.7 - - - -
1118D ILE* 6.0 1.8 - - - +
1121D ARG* 3.5 31.6 - - - +
1122D MET* 3.8 10.6 - - - +
1123D TRP 4.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1068 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2317A PHE* 5.2 9.9 - - - -
1064D GLN 2.6 20.8 + - - -
1065D ALA* 3.5 2.2 - - - +
1067D ILE* 1.3 70.9 - - - +
1069D GLN* 1.3 65.7 + - - +
1070D LEU* 3.7 0.4 - - - -
----------------------------------------------------------
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