Contacts of the helix formed by residues 114 - 126 (chain B) in PDB entry 3J9X
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 114 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 2.9 21.4 + - + +
112B ASN 3.7 2.8 + - - +
113B ALA* 1.3 70.7 - - - +
115B PRO* 1.4 62.8 - - - +
116B GLN* 2.8 27.3 + - - +
117B VAL* 2.7 39.3 + - + +
118B LEU* 3.0 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS* 4.5 8.7 - - - +
108B ILE* 3.9 28.7 - - + -
113B ALA 3.3 10.1 - - - +
114B ASN* 1.4 89.0 - - - +
116B GLN* 1.3 56.4 + - - +
118B LEU* 3.5 14.4 - - + +
119B ASP* 2.9 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 3.2 36.3 + - + -
114B ASN* 2.8 23.9 + - - +
115B PRO* 1.3 75.7 - - - +
117B VAL* 1.3 62.7 + - + +
119B ASP* 3.4 10.3 + - - +
120B ALA* 3.1 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 5.5 0.4 - - + -
63B LEU* 3.6 30.1 - - + -
66B TYR* 3.9 28.9 - - + -
68B ILE* 4.3 15.3 - - + -
76B TYR* 3.7 29.4 - - + +
114B ASN* 2.7 21.8 + - + +
116B GLN* 1.3 72.5 - - + +
118B LEU* 1.3 66.8 + - - +
120B ALA* 3.0 10.0 + - + +
121B VAL* 2.9 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 3.7 22.0 - - + -
79B PHE* 3.3 53.4 - - + -
104B LYS* 4.0 17.9 - - + +
107B TYR* 4.4 2.2 - - + -
108B ILE* 3.3 35.9 - - + +
113B ALA* 3.8 18.2 - - + -
114B ASN 3.0 11.9 + - - +
115B PRO* 3.5 13.9 - - + +
117B VAL* 1.3 77.1 - - - +
119B ASP* 1.3 62.7 + - - +
121B VAL* 3.2 3.1 + - - -
122B VAL* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS* 2.7 37.0 + - - +
115B PRO* 2.9 22.0 + - - +
116B GLN* 3.6 11.8 - - - +
118B LEU* 1.3 73.7 - - - +
120B ALA* 1.3 61.3 + - - +
122B VAL* 3.1 9.6 + - - +
123B ASN* 2.8 42.6 + - - +
129B PRO* 5.4 14.3 - - + +
130B THR* 5.2 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.8 12.1 - - + +
66B TYR* 3.5 39.9 - - + +
116B GLN* 3.1 5.5 + - - +
117B VAL* 3.0 10.6 + - - +
119B ASP* 1.3 78.7 - - - +
121B VAL* 1.3 62.2 + - - +
123B ASN* 3.1 20.4 + - - +
124B ILE* 3.3 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 4.1 26.9 - - + -
62B VAL* 5.4 4.5 - - + -
63B LEU* 5.0 2.2 - - + -
76B TYR* 4.2 21.5 - - + +
79B PHE* 3.8 13.7 - - + -
80B GLY* 3.5 31.6 - - - -
117B VAL* 2.9 22.9 + - + +
118B LEU* 3.5 7.9 - - - +
119B ASP 3.2 0.2 - - - -
120B ALA* 1.3 76.4 - - + +
122B VAL* 1.3 62.0 + - + +
124B ILE* 3.0 18.4 + - - +
125B ILE* 3.2 18.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.7 23.6 - - + -
83B VAL* 4.6 7.4 - - + -
100B ILE* 4.3 21.5 - - + -
104B LYS* 6.0 1.3 - - + -
118B LEU 3.1 15.1 + - - +
119B ASP* 3.5 12.1 - - - +
121B VAL* 1.3 75.8 - - - +
123B ASN* 1.3 55.0 + - - +
124B ILE 3.0 0.2 + - - -
125B ILE* 4.6 4.9 - - - +
126B THR* 2.5 52.7 + - + +
128B SER 3.2 22.7 - - - +
129B PRO* 4.3 6.7 - - + -
130B THR* 4.4 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASP* 2.8 29.7 + - - +
120B ALA* 3.1 12.2 + - - +
122B VAL* 1.3 73.6 - - - +
124B ILE* 1.3 64.6 + - + +
127B GLY* 3.2 26.7 - - - +
128B SER* 3.1 1.5 - - - -
129B PRO* 3.0 45.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 5.6 1.3 - - - +
58B ASN* 3.6 39.7 - - + +
59B VAL* 4.7 6.7 - - + +
62B VAL* 3.7 29.2 - - + -
120B ALA 3.3 14.6 - - - +
121B VAL* 3.0 8.9 + - - +
122B VAL 3.0 0.6 - - - -
123B ASN* 1.3 86.2 - - + +
125B ILE* 1.3 72.7 + - + +
126B THR 4.4 0.5 - - - -
127B GLY* 3.9 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 4.0 26.7 - - + -
59B VAL* 4.6 4.5 - - + -
80B GLY* 3.1 42.4 - - - +
83B VAL* 3.9 26.9 - - + -
84B ALA* 4.4 14.8 - - + +
87B LEU* 4.5 19.3 - - + +
121B VAL* 3.2 18.9 + - + +
122B VAL 4.2 1.3 - - - +
124B ILE* 1.3 82.2 - - + +
126B THR* 1.3 63.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 4.5 4.3 - - + -
87B LEU* 6.0 2.5 - - + -
96B LEU* 4.8 10.5 - - + -
100B ILE* 4.1 20.6 - - + -
122B VAL* 2.5 36.1 + - + +
124B ILE 4.4 0.4 - - - -
125B ILE* 1.3 86.1 - - + +
127B GLY* 1.3 58.3 + - - +
128B SER* 2.5 31.0 + - - +
----------------------------------------------------------
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