Contacts of the helix formed by residues 86 - 98 (chain i) in PDB entry 3J7Y
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 86 (chain i).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973 PHE* 3.5 20.4 - - - -
1870A A 2.8 33.3 + - - +
1871A A 3.5 8.6 + - - +
85i GLY* 1.3 74.4 - - - +
87i GLU* 1.3 77.3 + - - +
88i LEU* 4.1 4.5 - - - +
89i GLN* 3.1 26.8 + - + +
90i ARG* 2.7 40.6 + - - +
121i PHE* 3.5 17.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1869A A 3.3 30.6 - - - +
156F ARG* 3.5 20.0 - - + +
86i ASN* 1.3 84.7 + - - +
88i LEU* 1.3 64.1 + - - +
90i ARG* 3.3 28.6 + - - +
91i CYS* 3.1 26.6 + - - -
113i ARG* 2.6 31.0 + - - +
117i LEU* 3.5 18.2 - - + +
121i PHE* 4.6 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973 PHE* 3.9 29.6 - - + +
983 SER 4.2 4.7 - - - +
993 ALA* 6.4 0.2 - - - -
1023 GLY* 4.8 0.7 - - - -
86i ASN* 3.5 2.7 + - - +
87i GLU* 1.3 79.2 - - - +
89i GLN* 1.3 69.4 + - + +
91i CYS* 3.2 3.6 + - - +
92i ILE* 3.0 52.9 + - + +
114i ILE* 3.9 23.6 - - + +
117i LEU* 3.7 32.3 - - + -
118i TYR* 4.3 11.4 - - + +
121i PHE* 3.5 26.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973 PHE* 3.6 18.4 - - + -
1013 LYS 5.0 4.0 + - - +
1023 GLY* 3.7 32.0 + - - +
1871A A 4.7 5.4 + - - +
83i TRP* 3.8 27.8 - - + -
85i GLY* 4.6 4.3 - - - -
86i ASN* 3.1 33.5 + - + +
87i GLU 3.2 0.4 - - - -
88i LEU* 1.3 82.3 - - + +
90i ARG* 1.3 55.9 + - - +
92i ILE* 3.2 12.5 + - - +
93i ARG* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F ARG* 3.4 20.4 + - - +
157F GLY* 4.4 4.4 - - - -
158F PRO 3.5 8.7 + - - -
159F THR* 3.2 34.8 - - - +
160F SER 4.7 0.8 + - - +
79i TRP* 4.4 5.1 - - + +
80i LEU* 3.4 29.2 - - + -
83i TRP* 3.7 24.9 - - + -
84i LYS 4.4 8.9 + - - +
85i GLY 5.1 0.2 - - - -
86i ASN* 2.7 28.3 + - - +
87i GLU* 3.5 35.5 + - - +
89i GLN* 1.3 73.5 - - - +
91i CYS* 1.3 60.0 + - - +
93i ARG* 3.2 4.5 + - - +
94i LYS* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F ARG* 5.7 4.0 - - - -
87i GLU* 3.1 17.0 + - - -
88i LEU* 3.3 9.6 - - - +
90i ARG* 1.3 84.2 - - - +
92i ILE* 1.3 58.3 + - - +
94i LYS* 3.2 8.8 + - - +
95i ARG* 2.9 25.8 + - - +
110i LEU* 3.5 30.3 - - + +
113i ARG* 4.6 13.9 - - - -
114i ILE* 3.6 12.6 - - + -
117i LEU* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983 SER 3.9 8.3 - - - +
993 ALA* 3.2 25.1 - - - +
1003 ARG* 3.2 25.6 - - - +
1013 LYS 5.5 0.4 - - - -
1023 GLY* 4.4 7.9 - - - +
88i LEU* 3.0 51.5 + - + +
89i GLN* 3.2 10.3 + - - +
91i CYS* 1.3 75.8 - - - +
93i ARG* 1.3 58.2 + - - +
95i ARG* 3.2 11.3 + - - +
96i LYS* 2.9 34.5 + - + +
114i ILE* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1737A A 2.8 41.2 + - - -
1738A U 3.5 12.0 + - - +
78i ILE 4.4 4.6 + - - -
79i TRP* 2.4 37.6 + - + +
81i ARG* 4.4 7.1 + - - +
83i TRP* 3.2 66.7 - - + +
89i GLN 2.9 12.9 + - - +
90i ARG* 3.5 9.2 - - - +
92i ILE* 1.3 78.2 - - - +
94i LYS* 1.3 52.6 + - - +
96i LYS* 3.2 18.1 + - - +
97i MET* 2.7 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1685A C 3.7 18.3 + - - -
158F PRO* 5.6 2.7 - - - -
3X LEU* 4.5 8.5 - - - +
79i TRP* 3.5 62.8 - - + +
90i ARG 2.9 13.6 + - - +
91i CYS* 3.4 11.7 - - - +
93i ARG* 1.3 74.9 - - - +
95i ARG* 1.3 58.0 + - - +
98i VAL* 2.9 29.5 + - - +
99i GLY 2.9 7.3 + - - -
102i MET* 3.5 28.7 - - + +
110i LEU* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993 ALA 4.5 12.1 + - - -
1003 ARG* 5.9 0.4 - - - +
1731A A 5.8 2.0 - - - -
1732A C 3.9 36.4 + - - -
91i CYS 2.9 13.4 + - - +
92i ILE* 3.4 17.4 + - - +
94i LYS* 1.3 76.3 - - - +
96i LYS* 1.3 63.2 + - - +
99i GLY* 3.1 22.0 + - - +
100i SER 4.3 1.0 + - - -
107i LEU* 4.4 10.8 - - + -
110i LEU* 3.8 18.1 - - + +
111i ASN* 3.0 29.6 + - - +
114i ILE* 3.4 46.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003 ARG 4.8 11.0 + - - +
1013 LYS* 4.3 15.2 - - - +
1737A A 3.8 14.1 - - - +
1738A U 2.9 42.7 + - - +
92i ILE* 2.9 18.6 + - + +
93i ARG* 3.5 19.1 - - - +
95i ARG* 1.3 78.9 - - - +
97i MET* 1.3 74.4 + - + +
98i VAL 4.8 0.2 - - - -
99i GLY 4.5 0.5 + - - -
100i SER* 5.3 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 97 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1737A A 3.6 47.8 - - - +
78i ILE* 3.7 42.0 - - + +
79i TRP* 3.7 24.2 - - + +
93i ARG* 2.7 43.6 + - + +
96i LYS* 1.3 79.2 - - + +
98i VAL* 1.3 63.6 + - + +
100i SER* 4.8 4.7 + - - -
101i ARG* 4.7 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain i).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3X LEU* 3.3 39.5 - - + -
78i ILE* 3.7 15.3 - - + -
79i TRP* 3.4 31.2 - - + -
94i LYS 2.9 10.8 + - - +
97i MET* 1.3 84.9 - - + +
99i GLY* 1.3 51.2 + - - +
100i SER* 2.8 4.1 + - - -
101i ARG* 2.8 59.0 + - + +
102i MET* 3.8 9.6 - - + -
----------------------------------------------------------
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