Contacts of the helix formed by residues 77 - 92 (chain J) in PDB entry 5AN5
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 ASN 77 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3C GLY 5.0 2.6 - - - +
76C THR* 3.7 23.8 - - + +
77C ASN* 4.3 6.9 + - - -
80C ILE* 4.0 22.7 - - + +
-1D MET* 5.1 4.7 - - - +
0D ALA* 4.5 9.0 - - - +
-1J MET* 3.2 20.4 + - - +
76J THR* 1.3 88.9 + - - +
78J PHE* 1.3 64.6 + - - +
79J ASP 3.4 2.5 - - - -
80J ILE* 3.2 24.1 + - + +
81J LEU* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E GLU* 5.7 3.6 - - + -
92E PHE* 3.1 37.3 - + - -
83F ARG* 4.8 2.9 - - + -
86F ASN* 3.2 69.8 - - + +
87F LEU* 3.9 13.7 - - + -
90F HIS* 3.7 25.8 - + + -
-1J MET 3.7 8.4 + - - +
0J ALA 4.3 2.9 - - - +
76J THR 3.4 3.4 - - - -
77J ASN* 1.3 75.0 - - - +
79J ASP* 1.3 59.9 + - - +
81J LEU* 3.3 6.9 + - + +
82J LYS* 3.0 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 6.1 2.7 - - + -
76J THR 5.0 2.3 + - - +
77J ASN 3.4 0.2 - - - -
78J PHE* 1.3 76.5 - - - +
80J ILE* 1.3 67.6 + - + +
82J LYS* 3.3 6.3 + - - +
83J ARG* 3.0 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ILE* 4.0 26.7 - - + -
0D ALA* 4.0 17.5 - - + -
80D ILE* 3.9 35.2 - - + -
81D LEU* 4.0 24.0 - - + -
84D LEU* 4.0 10.3 - - + +
76J THR 5.0 3.6 - - - +
77J ASN* 3.2 30.2 + - - +
79J ASP* 1.3 79.0 - - + +
81J LEU* 1.3 57.7 + - - +
83J ARG* 3.3 2.8 + - - +
84J LEU* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C THR* 5.5 0.2 - - + -
80C ILE* 3.8 29.2 - - + -
83C ARG* 4.1 12.3 - - - +
92E PHE* 3.7 29.0 - - + +
94E SER* 3.9 20.4 - - - +
-1J MET* 3.5 39.9 - - + +
77J ASN* 2.9 26.0 + - + +
78J PHE* 3.8 4.5 - - - +
80J ILE* 1.3 74.2 - - - +
82J LYS* 1.3 66.1 + - - +
84J LEU* 3.7 6.0 - - + +
85J SER* 2.9 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E PHE* 3.9 14.6 - - + -
90F HIS* 4.2 22.4 - - + +
78J PHE* 3.0 21.4 + - + +
79J ASP* 3.6 8.3 - - - +
81J LEU* 1.3 75.5 - - - +
83J ARG* 1.3 58.4 + - - +
85J SER* 3.7 3.1 - - - -
86J ASN* 3.0 27.8 + - + +
1098J GOL 3.2 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 4.1 26.4 + - - +
84D LEU* 4.1 23.4 - - + +
85D SER* 3.7 25.5 - - - +
88D GLU* 2.8 40.9 + - - +
79J ASP* 3.0 32.2 + - - +
80J ILE 3.7 2.9 - - - +
82J LYS* 1.3 74.2 - - - +
84J LEU* 1.3 60.2 + - - +
86J ASN* 3.5 2.2 + - - +
87J LEU* 3.0 33.1 + - - +
1098J GOL 3.4 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ILE* 3.9 43.3 - - + +
83C ARG* 4.3 20.0 - - + +
84C LEU* 3.9 32.3 - - + +
87C LEU* 3.9 13.1 - - + +
80D ILE* 6.2 0.2 - - + -
84D LEU* 3.8 20.2 - - + +
80J ILE* 2.9 25.6 + - + +
81J LEU* 3.7 11.7 - - + +
83J ARG* 1.3 74.9 - - - +
85J SER* 1.3 66.4 + - - +
87J LEU* 3.3 4.9 + - - +
88J GLU* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ARG* 3.7 9.8 - - - +
91E VAL 4.2 7.0 + - - -
92E PHE* 3.6 28.6 + - - -
93E GLY* 5.4 0.3 - - - -
81J LEU 2.9 17.9 + - - -
82J LYS* 3.7 5.8 - - - -
84J LEU* 1.3 76.1 - - - +
86J ASN* 1.3 58.4 + - - +
88J GLU* 3.2 5.7 + - - +
89J LYS* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLU* 5.4 1.0 + - - -
92D PHE* 3.7 25.3 - - - -
82J LYS* 3.0 18.2 + - + +
83J ARG 3.8 3.8 + - - +
85J SER* 1.3 74.5 + - - +
87J LEU* 1.3 65.3 + - - +
89J LYS* 3.3 7.1 + - - +
90J HIS* 3.2 43.8 + - - -
1098J GOL 3.4 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 3.8 17.5 - - + -
84D LEU* 3.8 24.5 - - + +
87D LEU* 3.9 29.4 - - + -
88D GLU* 4.0 38.6 - - + +
91D VAL* 4.1 18.8 - - + -
92D PHE* 4.2 10.1 - - + -
83J ARG 3.0 21.4 + - - +
84J LEU 3.6 3.8 - - - +
86J ASN* 1.3 76.9 - - - +
88J GLU* 1.3 59.6 + - - +
90J HIS* 3.2 3.9 + - - -
91J VAL* 2.9 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ARG* 2.7 63.3 + - - +
87C LEU* 4.2 13.5 - - + -
93E GLY* 4.5 3.6 - - - +
84J LEU 3.0 13.3 + - - +
85J SER* 3.6 6.7 - - - +
87J LEU* 1.3 76.1 - - - +
89J LYS* 1.3 57.9 + - - +
92J PHE* 2.8 53.5 + - + +
93J GLY* 3.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85J SER 3.0 12.7 + - - +
86J ASN* 3.5 12.8 - - - +
87J LEU 3.2 0.2 - - - -
88J GLU* 1.3 76.4 - - - +
90J HIS* 1.3 72.4 + - + +
93J GLY* 3.1 32.5 + - - +
94J SER 4.6 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D VAL* 4.5 8.5 - - + -
92D PHE* 3.5 38.3 - + + -
95D LYS* 3.8 29.6 + - + +
86J ASN* 3.2 37.7 + - - +
87J LEU 3.2 4.7 + - - +
89J LYS* 1.3 90.5 - - + +
91J VAL* 1.3 60.7 + - - +
93J GLY 4.9 2.8 + - - +
95J LYS* 5.6 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 4.0 12.3 - - + -
90C HIS* 3.4 35.7 - - + +
91C VAL* 3.9 15.0 - - + -
91D VAL* 3.9 33.0 - - + -
95D LYS* 6.0 0.2 - - - +
87J LEU* 2.9 20.3 + - + +
88J GLU 4.3 0.2 - - - +
90J HIS* 1.3 83.0 - - - +
92J PHE* 1.3 77.3 + - + +
93J GLY 3.8 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASN* 4.3 14.6 - - + -
87C LEU* 3.7 25.6 - - + -
90C HIS* 3.6 48.0 - + + -
88J GLU* 2.8 36.9 + - + +
91J VAL* 1.3 80.9 - - + +
93J GLY* 1.3 63.5 + - - +
----------------------------------------------------------
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