Contacts of the helix formed by residues 85 - 97 (chain B) in PDB entry 3TKR
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 PHE 85 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE 4.8 1.8 - - - -
84B THR* 1.3 94.3 + - - +
86B VAL* 1.3 68.7 + - - +
87B CYS 3.2 0.4 - - - -
88B PRO* 3.1 15.6 - - - +
89B THR* 3.6 2.9 - - - +
117G PHE* 3.7 34.3 - + - -
207H VAL* 4.1 10.5 - - + -
219H ILE* 3.4 30.8 - - + +
220H ILE 4.3 0.2 - - - -
221H PRO* 3.4 41.5 - - + -
222H ASP* 3.4 26.7 - - - -
223H PRO* 4.0 1.8 - - + -
226H LYS* 3.9 25.6 - - + -
230H PHE* 3.6 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 1.3 78.0 - - - +
87B CYS* 1.3 64.7 + - - +
89B THR* 2.7 30.2 + - - +
90B GLU* 3.2 10.5 + - + +
163B ARG* 3.4 32.2 - - - +
182B LEU 4.4 3.4 - - - +
183B PRO 4.1 5.2 - - - +
185B GLY* 3.6 29.6 - - - +
207H VAL* 3.5 31.2 - - + -
208H CYS 3.4 21.1 - - - +
209H PRO* 4.5 0.4 - - + -
219H ILE* 4.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B TYR* 3.7 19.4 - - + +
80B PRO* 3.4 22.9 - - - -
81B LEU 3.6 18.2 - - - +
84B THR* 3.4 18.6 - - - +
86B VAL* 1.3 75.3 - - - +
88B PRO* 1.3 70.6 - - + +
90B GLU* 3.1 7.9 + - - +
91B ILE* 3.1 24.3 + - - +
122B TRP* 4.1 4.3 - - + -
163B ARG* 3.2 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR 3.4 21.8 - - - +
85B PHE 3.1 18.4 - - - +
87B CYS* 1.3 95.3 - - + +
89B THR* 1.3 55.9 + - - +
91B ILE* 3.3 0.5 + - - +
92B ILE* 2.9 39.1 + - + +
122B TRP* 3.5 27.3 - - + -
130B GLY 3.9 10.8 - - - +
131B GLY 4.5 4.5 - - - +
132B LEU* 3.9 11.9 - - + -
230H PHE* 3.6 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE 3.6 16.2 - - - +
86B VAL 2.7 14.8 + - - -
88B PRO* 1.3 75.3 - - - +
90B GLU* 1.3 56.8 + - - +
92B ILE* 3.9 6.3 - - - +
93B ALA* 2.9 30.5 + - - +
209H PRO* 3.4 12.8 - - + +
210H ALA* 3.0 24.9 + - - +
219H ILE* 3.8 8.3 - - + -
229H TYR* 3.5 36.6 - - + +
230H PHE* 4.1 6.1 - - + -
233H LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.6 12.3 - - + -
79B TYR* 4.5 1.1 - - + +
86B VAL* 3.7 16.8 - - + +
87B CYS* 3.1 8.3 + - - +
89B THR* 1.3 79.8 + - - +
91B ILE* 1.3 65.1 + - - +
93B ALA* 3.2 1.4 + - - +
94B PHE* 3.1 37.0 + - + -
163B ARG* 2.8 26.8 + - - -
185B GLY* 3.4 2.6 - - - -
186B ARG* 2.7 67.5 + - + +
210H ALA* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.2 17.5 - - + -
79B TYR* 3.6 33.9 - - + +
87B CYS 3.1 14.0 + - - +
88B PRO 3.8 4.5 - - - +
90B GLU* 1.3 75.4 - - - +
92B ILE* 1.3 58.3 + - - +
95B GLY* 2.8 27.0 + - - -
110B ALA* 4.5 3.6 - - + -
122B TRP* 3.4 34.8 - - + -
132B LEU* 4.0 22.9 - - + -
135B ILE* 3.9 22.3 - - + +
137B ILE* 4.0 6.6 - - + +
139B LEU* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PRO* 2.9 26.5 + - + +
89B THR* 4.1 5.6 - - - +
91B ILE* 1.3 76.1 - - + +
93B ALA* 1.3 58.1 + - - +
95B GLY* 4.3 1.1 - - - +
96B ASP* 2.7 41.5 + - - +
127B ARG* 3.5 55.4 - - + +
131B GLY 3.8 17.5 - - - +
132B LEU* 4.1 14.8 - - + +
135B ILE* 5.1 4.7 - - + -
230H PHE* 5.7 5.2 - - + -
233H LEU* 6.5 0.7 - - + -
234H ASN* 6.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR 2.9 21.1 + - - +
90B GLU 3.2 4.2 + - - +
92B ILE* 1.3 79.6 - - - +
94B PHE* 1.3 61.4 + - + +
96B ASP* 4.2 2.3 - - - +
97B ARG* 3.4 27.4 + - - +
188B VAL* 3.7 20.4 - - + +
210H ALA* 3.8 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.3 6.3 - - + -
77B PHE* 3.8 23.6 - + + -
90B GLU* 3.1 32.0 + - + +
91B ILE 4.1 0.4 - - - +
93B ALA* 1.3 72.5 - - - +
95B GLY* 1.3 66.8 + - - +
97B ARG 3.1 4.3 + - - -
98B LEU* 3.0 23.6 + - - +
101B PHE* 3.7 38.5 - + + -
108B VAL* 4.3 12.3 - - + -
137B ILE* 3.6 18.1 - - + +
165B LEU* 3.7 16.8 - - + -
186B ARG* 5.1 11.4 - - + -
187B SER 4.5 1.8 - - - -
188B VAL* 4.0 22.9 - - + -
191B THR* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE 2.8 19.9 + - - -
92B ILE* 3.7 0.7 - - - -
94B PHE* 1.3 76.1 - - - +
96B ASP* 1.3 63.8 + - - +
97B ARG 3.2 0.9 + - - -
98B LEU* 3.3 11.4 + - - +
135B ILE* 3.8 15.9 - - - -
136B ARG* 3.3 18.7 + - - -
137B ILE* 3.3 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 2.7 27.2 + - + +
93B ALA* 4.3 3.4 - - - +
95B GLY* 1.3 73.7 - - - +
97B ARG* 1.3 63.4 + - + +
98B LEU 3.4 1.3 + - - -
127B ARG* 2.9 42.6 + - - -
135B ILE* 5.9 0.2 - - - +
136B ARG* 4.4 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA* 3.4 17.1 + - - +
94B PHE 3.1 6.6 + - - +
96B ASP* 1.3 83.0 - - + +
98B LEU* 1.3 64.9 + - - +
99B GLU* 3.2 3.1 - - - -
100B GLU* 2.7 61.2 + - + +
101B PHE* 3.6 6.3 - - - -
188B VAL* 3.7 32.9 - - + +
189B ASP* 3.0 30.1 + - - -
192B LEU* 3.4 12.7 - - - +
----------------------------------------------------------
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