Contacts of the helix formed by residues 78 - 97 (chain B) in PDB entry 2JJ7
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 78 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 3.1 17.2 + - - +
76B GLN 3.2 2.3 + - - +
77B PHE* 1.3 74.5 - - - +
79B PRO* 1.4 62.1 - - - +
80B ILE* 3.4 11.4 + - - +
81B ASN* 3.2 40.8 + - + +
82B ALA* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 4.4 5.4 - - + -
77B PHE 3.1 9.0 - - - +
78B ASN* 1.4 82.9 - - - +
80B ILE* 1.3 60.7 + - + +
82B ALA* 3.8 6.3 - - + +
83B LEU* 2.9 31.0 + - - +
132B ILE* 3.8 4.8 - - - +
135B GLU* 3.8 10.1 - - + -
136B GLY* 3.5 34.1 - - - +
139B GLN* 3.4 31.6 - - + +
141B VAL* 4.1 7.4 - - + -
142B PHE* 3.5 9.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASN* 3.4 8.5 + - - +
79B PRO* 1.3 76.2 - - + +
81B ASN* 1.3 65.6 + - - +
83B LEU* 3.3 2.4 + - - +
84B ARG* 2.8 34.5 + - - +
141B VAL* 3.4 31.2 - - + -
142B PHE* 3.8 23.8 - - + -
177B ILE* 4.2 21.9 - - + +
181B THR* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 3.7 18.1 + - + +
78B ASN* 3.2 35.5 + - + +
80B ILE* 1.3 80.7 - - - +
82B ALA* 1.3 66.0 + - - +
84B ARG* 3.3 10.8 + - - +
85B GLU* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.5 29.4 - - + +
72B LEU* 4.0 18.6 - - + +
75B ASN* 3.5 13.1 - - + +
78B ASN 2.9 19.5 + - - +
79B PRO 3.8 4.3 - - - +
81B ASN* 1.3 75.9 - - - +
83B LEU* 1.3 58.4 + - - +
85B GLU* 3.2 2.4 + - - +
86B TYR* 2.9 28.8 + - - +
132B ILE* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PRO 2.9 18.9 + - - +
80B ILE* 3.7 3.1 - - - +
82B ALA* 1.3 76.0 - - - +
84B ARG* 1.3 59.8 + - - +
86B TYR* 3.6 7.1 - - + +
87B LEU* 2.8 56.5 + - + +
129B LEU* 3.7 30.1 - - + -
132B ILE* 3.7 16.3 - - + +
133B LEU* 4.6 2.9 - - + -
142B PHE* 3.6 23.1 - - + -
154B ILE* 5.0 1.3 - - + -
176B ILE* 4.9 0.2 - - + -
177B ILE* 3.9 17.3 - - + -
180B LEU* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 2.8 26.6 + - - +
81B ASN* 3.3 11.6 + - - +
83B LEU* 1.3 72.6 - - - +
85B GLU* 1.3 55.9 + - - +
87B LEU 3.8 0.2 - - - -
88B THR* 2.5 42.8 + - - +
170B ALA* 4.5 2.8 + - - +
173B VAL* 3.8 19.3 - - + +
174B SER* 3.1 38.6 + - - +
177B ILE* 3.7 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.5 23.8 - - + -
74B LYS* 2.7 39.8 + - - +
75B ASN* 2.9 27.1 + - - +
81B ASN 3.0 16.3 + - - +
82B ALA 3.7 3.4 - - - +
84B ARG* 1.3 74.3 - - - +
86B TYR* 1.3 66.6 + - - +
88B THR* 3.3 4.9 + - - -
89B VAL* 2.9 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.8 22.4 - + + -
82B ALA 2.9 17.3 + - - +
83B LEU* 3.6 9.6 - - + +
85B GLU* 1.3 77.6 - - - +
87B LEU* 1.3 85.2 + - + +
89B VAL* 3.4 0.9 + - - +
90B PHE* 3.1 60.1 + + + -
125B SER 3.9 4.0 - - - -
126B PHE* 2.6 56.5 + + - -
128B GLN* 4.4 2.9 - - + -
129B LEU* 3.4 34.5 - - + +
132B ILE* 3.7 23.1 - - + -
154B ILE* 4.9 0.7 - - + -
158B VAL* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 2.8 43.3 + - + +
86B TYR* 1.3 94.9 - - + +
88B THR* 1.3 52.3 + - - +
90B PHE* 5.0 1.6 - - - -
91B THR* 2.6 42.2 + - + +
154B ILE* 4.0 22.2 - - + -
158B VAL* 4.0 14.8 - - + -
173B VAL* 3.7 35.4 - - + +
176B ILE* 3.6 28.9 - - + -
177B ILE* 4.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 2.5 29.9 + - - +
85B GLU* 3.3 6.3 + - - -
87B LEU* 1.3 74.1 - - - +
89B VAL* 1.3 66.5 + - + +
91B THR* 3.4 4.8 + - - -
92B THR* 2.9 39.2 + - - +
173B VAL* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.9 8.3 - - + -
68B LEU* 3.9 33.7 - - + -
71B PHE* 4.0 19.1 - - + -
85B GLU* 2.9 28.3 + - + +
86B TYR 3.8 3.8 - - - +
88B THR* 1.3 78.0 - - + +
90B PHE* 1.3 59.5 + - + +
92B THR* 3.8 4.2 - - - +
93B HIS* 2.9 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.0 18.6 - - + -
68B LEU* 3.5 29.6 - - + -
71B PHE* 4.8 0.4 - + - -
86B TYR* 3.1 62.2 + + + +
87B LEU* 4.4 2.2 - - - +
89B VAL* 1.3 76.0 - - + +
91B THR* 1.3 65.7 + - - +
93B HIS* 3.2 3.3 + - + +
94B ILE* 3.0 29.3 + - - +
122B PHE* 3.5 42.2 - + + -
125B SER* 3.7 4.0 - - - -
126B PHE* 3.4 32.8 - + + -
158B VAL* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 2.6 27.0 + - + +
88B THR* 3.4 4.7 + - - -
90B PHE* 1.3 75.5 - - - +
92B THR* 1.3 59.6 + - - +
94B ILE* 3.5 0.4 + - - -
95B LYS* 2.9 29.1 + - - +
158B VAL* 4.1 22.2 - - + -
163B PHE* 3.5 24.0 - - + -
169B SER* 4.2 13.9 - - - +
172B LEU* 4.0 27.8 - - + -
173B VAL* 3.6 19.3 - - + +
176B ILE* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR* 2.9 31.1 + - - +
89B VAL* 3.8 4.7 - - - +
91B THR* 1.3 75.3 + - - +
93B HIS* 1.3 65.1 + - - +
95B LYS* 3.4 20.3 + - - +
96B GLU* 3.1 44.1 + - + +
169B SER* 5.4 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR 2.7 23.8 + - - -
63B GLY* 3.2 29.9 - - - -
64B LEU* 4.1 19.7 - - + +
89B VAL* 2.9 19.5 + - + +
90B PHE* 3.2 7.4 + - - +
92B THR* 1.3 76.4 - - - +
94B ILE* 1.3 56.0 + - + +
96B GLU* 3.2 10.5 + - - -
97B ASN* 2.7 58.0 + - + +
100B ILE* 4.4 1.8 - - + -
122B PHE* 3.9 24.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE 3.0 19.9 + - - +
91B THR 4.0 3.1 - - - +
93B HIS* 1.3 77.4 - - + +
95B LYS* 1.3 65.8 + - - +
97B ASN 4.0 5.4 - - - +
98B PRO* 3.0 26.6 - - + +
100B ILE 4.3 0.7 - - - -
101B GLY* 3.7 26.9 - - - +
122B PHE* 3.7 31.6 - - + -
158B VAL 3.7 25.6 - - - +
159B LEU* 3.9 26.2 - - + +
160B PHE 4.2 6.5 - - - +
161B PRO* 4.4 10.2 - - + +
163B PHE* 3.8 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B THR 2.9 12.2 + - - +
92B THR* 3.4 23.3 + - - +
94B ILE* 1.3 76.7 - - - +
96B GLU* 1.3 64.0 + - + +
98B PRO* 3.7 3.6 - - - +
161B PRO 6.0 0.2 - - - -
163B PHE* 4.6 4.9 - - + -
164B LYS* 3.1 54.6 + - + +
169B SER* 3.0 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS* 3.9 5.4 + - - -
92B THR* 3.1 32.4 + - + +
93B HIS* 3.7 11.4 + - - +
95B LYS* 1.3 79.7 - - + +
97B ASN* 1.3 78.2 + - - +
98B PRO* 3.5 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LYS* 2.8 28.1 + - - +
62B TYR* 3.6 21.5 + - - +
93B HIS* 2.7 44.0 + - - +
94B ILE* 3.2 8.3 + - - +
96B GLU* 1.3 95.3 + - - +
98B PRO* 1.4 66.4 - - - +
99B GLU* 3.2 4.0 - - - -
100B ILE* 3.1 31.3 + - + +
101B GLY 3.6 3.3 + - - -
----------------------------------------------------------
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