Contacts of the helix formed by residues 85 - 97 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE* 3.8 33.9 - + - -
207C VAL* 4.1 11.0 - - + -
219C ILE* 3.4 31.6 - - + +
221C PRO* 3.4 31.2 - - + -
222C ASP* 3.3 38.4 - - - -
223C PRO* 4.0 1.8 - - + -
226C LYS* 3.8 26.2 - - + -
230C PHE* 3.5 6.0 - - - -
83G PHE 4.7 2.0 - - - -
84G THR* 1.3 96.7 + - + +
86G VAL* 1.3 67.9 + - - +
87G CYS 3.3 0.7 - - - -
88G PRO* 3.2 14.8 - - - +
89G THR* 3.6 1.6 - - - +
163G ARG* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C VAL* 3.6 31.4 - - + -
208C CYS 3.5 21.5 - - - +
209C PRO* 4.6 0.4 - - - -
219C ILE* 4.4 2.9 - - + -
85G PHE* 1.3 73.5 - - - +
87G CYS* 1.3 67.5 + - - +
89G THR* 2.6 29.5 + - - +
90G GLU* 3.1 10.4 + - + +
163G ARG* 3.4 31.1 - - - +
182G LEU 4.3 3.1 - - - +
183G PRO 4.0 5.2 - - - +
185G GLY* 3.5 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G TYR* 3.6 19.0 - - + +
80G PRO* 3.4 22.4 - - - -
81G LEU 3.6 19.1 - - - +
84G THR* 3.5 17.9 - - - -
86G VAL* 1.3 75.0 - - - +
88G PRO* 1.3 71.0 - - + +
90G GLU* 3.0 16.5 + - - +
91G ILE* 3.1 17.5 + - - +
122G TRP* 4.1 3.8 - - + -
163G ARG* 3.2 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 3.6 18.2 - - + -
84G THR 3.4 22.9 - - - +
85G PHE 3.2 20.2 - - - +
87G CYS* 1.3 95.5 - - + +
89G THR* 1.3 54.8 + - - +
91G ILE* 3.9 0.5 - - - +
92G ILE* 2.9 39.1 + - + +
122G TRP* 3.5 21.1 - - + -
130G GLY 4.0 9.0 - - - +
131G GLY 4.5 4.5 - - - +
132G LEU* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C PRO* 3.5 13.2 - - + +
210C ALA* 3.0 23.6 + - - +
219C ILE* 3.8 14.6 - - + -
229C TYR* 3.6 28.7 - - + +
230C PHE* 4.2 4.9 - - + -
233C LEU* 6.1 0.2 - - + -
85G PHE 3.6 17.5 - - - +
86G VAL 2.6 15.3 + - - -
88G PRO* 1.3 76.3 - - - +
90G GLU* 1.3 56.3 + - - +
92G ILE* 4.0 5.9 - - - +
93G ALA* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ALA* 3.8 21.8 - - + -
77G PHE* 4.5 11.4 - - + -
79G TYR* 4.5 1.3 - - + +
86G VAL* 3.1 16.4 + - + +
87G CYS* 3.0 9.1 + - - +
89G THR* 1.3 79.0 + - - +
91G ILE* 1.3 66.0 + - - +
93G ALA* 3.7 0.5 - - - +
94G PHE* 3.0 36.7 + - + -
163G ARG* 2.8 32.0 + - - -
185G GLY* 3.3 2.8 - - - -
186G ARG* 2.7 61.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G PHE* 4.2 17.3 - - + -
79G TYR* 3.6 34.5 - - + +
87G CYS 3.1 15.0 + - - +
88G PRO 3.9 2.9 - - - +
90G GLU* 1.3 76.3 - - - +
92G ILE* 1.3 59.6 + - + +
94G PHE* 3.8 1.7 - - - +
95G GLY* 2.8 27.2 + - - -
110G ALA* 4.5 3.6 - - + -
122G TRP* 3.4 34.5 - - + -
132G LEU* 4.1 16.6 - - + -
135G ILE* 3.1 33.0 - - + +
137G ILE* 4.0 2.8 - - + +
139G LEU* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C PHE* 5.9 5.4 - - + -
234C ASN* 5.7 0.9 - - - +
88G PRO* 2.9 26.6 + - + +
89G THR* 4.0 5.2 - - - +
91G ILE* 1.3 76.1 - - + +
93G ALA* 1.3 59.2 + - - +
95G GLY* 4.3 1.3 - - - +
96G ASP* 2.7 53.7 + - - +
127G ARG* 3.4 43.7 - - + +
131G GLY 3.9 17.7 - - - +
132G LEU* 4.2 15.0 - - + +
135G ILE* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ALA* 3.8 17.0 - - + +
89G THR 2.9 20.1 + - - +
90G GLU 3.3 4.7 + - - +
92G ILE* 1.3 79.7 - - - +
94G PHE* 1.3 64.1 + - - +
96G ASP* 3.7 2.7 + - - +
97G ARG* 3.5 25.8 + - - +
188G VAL* 3.7 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G VAL* 4.3 6.5 - - + -
77G PHE* 3.8 24.7 - + + -
90G GLU* 3.0 33.3 + - + +
91G ILE 4.0 0.9 - - - +
93G ALA* 1.3 74.0 - - - +
95G GLY* 1.3 67.5 + - - +
97G ARG* 3.1 12.3 + - - +
98G LEU* 3.1 14.7 + - - +
101G PHE* 3.7 35.0 - + - -
108G VAL* 4.4 11.0 - - + -
137G ILE* 3.6 18.5 - - + +
165G LEU* 3.7 17.9 - - + -
186G ARG* 5.1 11.4 - - + -
187G SER 4.5 1.8 - - - -
188G VAL* 3.9 24.2 - - + -
191G THR* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G ILE 2.8 20.5 + - - -
92G ILE* 3.7 1.3 - - - -
94G PHE* 1.3 73.8 - - - +
96G ASP* 1.3 63.1 + - - +
97G ARG 3.2 1.0 + - - -
98G LEU* 3.2 18.7 + - - +
135G ILE* 4.7 10.5 - - - -
136G ARG* 5.1 9.0 + - - +
137G ILE* 3.3 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ILE* 2.7 28.2 + - - +
93G ALA* 4.3 3.4 - - - +
95G GLY* 1.3 73.3 - - - -
97G ARG* 1.3 62.6 + - + +
98G LEU 3.5 0.7 - - - -
127G ARG* 2.9 43.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G ALA* 3.5 17.9 + - - +
94G PHE 3.1 6.8 + - - +
96G ASP* 1.3 84.3 - - + +
98G LEU* 1.3 63.8 - - - +
99G GLU* 3.2 3.6 - - - -
100G GLU* 2.8 62.5 + - + +
101G PHE* 3.6 6.5 - - + -
188G VAL* 3.8 32.7 - - + +
189G ASP* 2.9 31.9 + - - +
192G LEU* 3.5 10.1 - - - +
----------------------------------------------------------
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