Contacts of the helix formed by residues 85 - 97 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE 4.8 1.8 - - - -
84A THR* 1.3 97.1 + - + +
86A VAL* 1.3 67.8 + - - +
87A CYS 3.2 0.7 - - - -
88A PRO* 3.1 16.0 - - - +
89A THR* 3.6 2.8 - - - +
117H PHE* 3.7 35.4 - + - -
207I VAL* 4.1 10.3 - - + -
219I ILE* 3.4 30.2 - - + +
221I PRO* 3.4 40.4 - - + -
222I ASP* 3.5 26.5 - - - -
223I PRO* 4.0 1.8 - - + -
226I LYS* 3.9 26.2 - - + -
230I PHE* 3.7 3.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 1.3 79.1 - - - +
87A CYS* 1.3 63.2 + - - +
89A THR* 2.7 30.6 + - - +
90A GLU* 3.2 10.3 + - + +
163A ARG* 3.3 31.6 - - - +
182A LEU 4.3 2.9 - - - +
183A PRO 4.1 6.1 - - - +
185A GLY* 3.5 30.1 - - - -
207I VAL* 3.6 30.3 - - + -
208I CYS 3.4 20.9 - - - +
209I PRO 4.5 0.2 - - - -
219I ILE* 4.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TYR* 3.8 18.5 - - + +
80A PRO* 3.5 21.1 - - - -
81A LEU 3.6 19.5 - - - +
84A THR* 3.5 18.2 - - - +
85A PHE 3.2 0.2 - - - -
86A VAL* 1.3 76.8 - - - +
88A PRO* 1.3 69.9 - - + +
90A GLU* 3.2 7.5 + - - +
91A ILE* 3.1 25.0 + - - +
122A TRP* 4.0 4.0 - - + -
163A ARG* 3.2 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR 3.4 20.9 - - - +
85A PHE 3.1 18.2 - - - +
87A CYS* 1.3 96.5 - - + +
89A THR* 1.3 54.4 + - - +
91A ILE* 3.8 0.3 - - - +
92A ILE* 2.9 39.1 + - + +
122A TRP* 3.5 21.1 - - + -
130A GLY 4.0 10.5 - - - +
131A GLY 4.5 4.7 - - - +
132A LEU* 3.8 18.6 - - + -
230I PHE* 3.6 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE 3.6 17.5 - - - +
86A VAL 2.7 14.5 + - - -
88A PRO* 1.3 76.1 - - - +
90A GLU* 1.3 57.7 + - - +
92A ILE* 4.1 6.1 - - - +
93A ALA* 2.9 31.2 + - - +
209I PRO* 3.3 12.5 - - + +
210I ALA* 2.9 25.1 + - - +
219I ILE* 3.8 8.7 - - + -
229I TYR* 3.5 36.3 - - + +
230I PHE* 4.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 4.5 11.7 - - + -
79A TYR* 4.5 1.6 - - - +
86A VAL* 3.7 21.5 - - + +
87A CYS* 3.2 7.6 + - - +
88A PRO 3.2 0.4 - - - -
89A THR* 1.3 79.7 + - - +
91A ILE* 1.3 65.9 + - - +
93A ALA* 3.3 0.9 + - - +
94A PHE* 3.1 37.2 + - + -
163A ARG* 2.8 23.0 + - - -
185A GLY* 3.4 2.6 - - - -
186A ARG* 2.7 65.8 + - + +
210I ALA* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 4.2 17.5 - - + -
79A TYR* 3.5 34.5 - - + +
87A CYS 3.1 16.1 + - - +
88A PRO 3.9 2.9 - - - +
90A GLU* 1.3 78.0 - - - +
92A ILE* 1.3 56.8 + - - +
94A PHE 3.9 0.2 - - - -
95A GLY* 2.9 26.0 + - - -
110A ALA* 4.5 4.0 - - + -
122A TRP* 3.4 34.1 - - + -
132A LEU* 4.0 16.2 - - + -
135A ILE* 3.5 23.0 - - + +
137A ILE* 4.0 6.7 - - + +
139A LEU* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO* 2.9 27.5 + - + +
89A THR* 4.1 4.7 - - - +
91A ILE* 1.3 74.9 - - + +
93A ALA* 1.3 57.1 + - - +
95A GLY* 4.3 1.6 - - - +
96A ASP* 2.7 52.9 + - - +
127A ARG* 3.5 39.0 - - + +
131A GLY 3.8 21.5 - - - +
132A LEU* 4.1 14.4 - - + +
135A ILE* 4.8 4.9 - - + -
230I PHE* 5.7 5.6 - - + -
234I ASN* 6.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR 2.9 23.1 + - - +
90A GLU 3.3 3.3 + - - +
92A ILE* 1.3 76.3 - - - +
94A PHE* 1.3 60.8 + - - +
96A ASP* 4.2 2.2 - - - +
97A ARG* 3.5 27.5 + - - +
188A VAL* 3.7 21.8 - - + +
210I ALA* 3.8 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 4.3 6.3 - - + -
77A PHE* 3.9 23.3 - + + -
90A GLU* 3.1 30.4 + - + +
91A ILE 4.0 0.4 - - - +
93A ALA* 1.3 74.6 - - - +
95A GLY* 1.3 66.5 + - - +
97A ARG 3.0 4.3 + - - -
98A LEU* 3.0 24.3 + - - +
101A PHE* 3.7 35.8 - + - -
108A VAL* 4.3 12.8 - - + -
137A ILE* 3.6 18.3 - - + +
165A LEU* 3.7 18.6 - - + -
186A ARG* 5.2 10.3 - - + -
187A SER 4.5 2.7 - - - -
188A VAL* 3.9 22.4 - - + -
191A THR* 3.5 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE 2.9 17.4 + - - -
92A ILE 3.6 0.9 - - - -
94A PHE* 1.3 76.7 - - - +
96A ASP* 1.3 63.3 + - - +
97A ARG 3.3 0.9 + - - -
98A LEU* 3.3 18.0 + - - +
135A ILE* 4.1 13.2 - - - -
136A ARG* 5.0 9.3 + - - +
137A ILE* 3.3 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 2.7 27.7 + - + +
93A ALA* 4.4 3.8 - - - +
95A GLY* 1.3 74.1 - - - +
97A ARG* 1.3 63.5 + - + +
98A LEU 3.5 1.1 + - - -
127A ARG* 2.9 42.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 3.5 16.0 + - - +
94A PHE 3.0 6.6 + - - +
96A ASP* 1.3 83.7 - - + +
98A LEU* 1.3 65.9 + - - +
99A GLU 3.2 2.9 - - - -
100A GLU* 2.7 64.3 + - + +
101A PHE* 3.7 6.0 - - + -
188A VAL* 3.7 35.1 - - + +
189A ASP* 2.9 32.3 + - - +
192A LEU* 4.3 11.9 - - - +
----------------------------------------------------------
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