Contacts of the helix formed by residues 1068 - 1082 (chain C) in PDB entry 6JOD
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 LEU1068 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010C LEU* 4.9 18.8 - - + -
1033C MET* 5.5 5.8 - - + -
1037C ALA* 4.5 15.7 - - + -
1067C ILE* 1.3 80.7 - - - +
1069C VAL* 1.3 63.2 + - + +
1071C GLN* 3.5 16.2 + - + +
1072C ILE* 3.0 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1069 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034C ARG* 5.3 12.1 - - + +
1037C ALA* 4.1 24.0 - - + +
1038C LEU* 5.2 15.7 - - + -
1067C ILE 3.2 4.8 - - - +
1068C LEU* 1.3 80.3 - - + +
1070C GLY* 1.3 57.1 + - - +
1072C ILE* 3.4 6.5 + - - +
1073C ASP* 2.9 50.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1070 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067C ILE* 3.3 8.6 + - - +
1069C VAL* 1.3 77.4 - - - +
1071C GLN* 1.3 64.6 + - - +
1073C ASP* 3.2 8.2 + - - +
1074C ASP* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1071 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067C ILE* 3.2 35.6 + - + +
1068C LEU* 3.9 20.0 - - + +
1070C GLY* 1.3 74.9 - - - +
1072C ILE* 1.3 59.4 + - + +
1074C ASP* 3.3 8.9 + - - +
1075C ALA* 3.0 27.2 + - - +
1093C GLN* 5.4 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1072 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030C LEU* 3.5 35.3 - - + +
1033C MET* 3.8 40.2 - - + +
1034C ARG* 4.1 15.5 - - + +
1037C ALA* 4.8 3.6 - - + -
1068C LEU* 3.0 49.3 + - + +
1069C VAL* 3.8 5.8 - - - +
1071C GLN* 1.3 74.1 - - + +
1073C ASP* 1.3 61.8 + - - +
1075C ALA* 3.2 6.6 + - - +
1076C LEU* 2.8 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1073 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034C ARG* 3.7 41.3 + - - +
1069C VAL* 2.9 34.5 + - - +
1070C GLY* 3.2 8.7 + - - +
1072C ILE* 1.3 77.8 - - - +
1074C ASP* 1.3 64.3 + - - +
1076C LEU* 3.8 9.3 + - - +
1077C LYS* 3.3 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1074 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070C GLY 3.0 16.4 + - - +
1071C GLN* 3.7 9.6 - - - +
1072C ILE 3.2 0.2 - - - -
1073C ASP* 1.3 79.8 - - - +
1075C ALA* 1.3 63.7 + - - +
1076C LEU 3.2 0.2 - - - -
1077C LYS* 3.1 25.7 + - + +
1078C LEU* 3.1 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1075 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030C LEU* 3.3 27.8 - - + +
1071C GLN 3.0 16.1 + - - +
1072C ILE* 3.2 6.9 + - - +
1074C ASP* 1.3 77.3 - - - +
1076C LEU* 1.3 56.7 + - - +
1078C LEU* 3.2 14.4 + - - +
1079C ALA 3.0 22.2 + - - -
1087C ALA* 4.5 2.8 - - - +
1090C ALA* 4.3 18.6 - - + +
1091C ALA* 4.5 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1076 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027C LYS* 3.6 39.3 - - + +
1030C LEU* 3.7 12.7 - - + +
1031C THR* 4.0 22.0 - - + -
1034C ARG* 4.0 25.8 - - - +
1072C ILE* 2.8 19.8 + - + +
1073C ASP* 3.9 10.5 - - - +
1075C ALA* 1.3 73.9 - - - +
1077C LYS* 1.3 64.8 + - - +
1079C ALA* 3.3 1.3 + - - +
1080C ASN* 3.0 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1077 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073C ASP* 3.3 18.1 + - - +
1074C ASP* 3.1 25.0 + - + +
1076C LEU* 1.3 79.0 - - + +
1078C LEU* 1.3 57.1 + - + +
1080C ASN* 3.1 10.7 + - - +
1081C GLU* 2.9 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1078 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074C ASP* 3.1 19.5 + - + +
1075C ALA* 3.2 8.9 + - - +
1077C LYS* 1.3 75.5 - - + +
1079C ALA* 1.3 61.7 + - - +
1081C GLU* 3.3 33.8 + - - +
1082C GLY 3.7 7.1 + - - -
1083C LYS* 3.7 17.5 + - + +
1086C GLU* 4.4 28.7 - - + +
1087C ALA* 3.8 15.0 - - + +
1090C ALA* 3.5 29.8 - - + -
64L SER* 5.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1079 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023C ALA* 3.5 25.8 - - - +
1026C VAL* 3.9 14.8 - - + -
1027C LYS* 3.9 32.9 - - + +
1030C LEU* 4.4 1.8 - - + -
1075C ALA 3.0 12.7 + - - +
1076C LEU 3.6 8.1 - - - +
1077C LYS 3.2 0.2 - - - -
1078C LEU* 1.3 79.5 - - - +
1080C ASN* 1.3 61.2 + - - +
1082C GLY 3.4 8.8 + - - -
1087C ALA* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1080 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027C LYS* 3.4 36.1 + - - +
1076C LEU* 3.0 34.2 + - - +
1077C LYS* 3.1 11.9 + - - +
1079C ALA* 1.3 74.0 - - - +
1081C GLU* 1.3 65.7 + - - +
1082C GLY* 3.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1081 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077C LYS* 2.9 26.5 + - + +
1078C LEU* 3.3 31.4 - - - +
1079C ALA 3.3 0.4 - - - -
1080C ASN* 1.3 77.5 - - + +
1082C GLY* 1.3 58.8 + - - +
1083C LYS* 3.5 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1082 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023C ALA* 4.3 9.0 - - - -
1078C LEU 3.7 0.6 + - - -
1079C ALA 3.4 10.3 + - - -
1080C ASN 3.2 5.1 - - - -
1081C GLU* 1.3 77.3 - - - +
1083C LYS* 1.3 60.5 + - - +
1084C VAL* 2.9 20.2 + - - +
----------------------------------------------------------
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