Contacts of the helix formed by residues 92 - 105 (chain A) in PDB entry 1TAU
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 92 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 4.8 3.4 - - - -
23A ALA* 3.7 17.5 - - + -
24A TYR* 3.3 55.6 - + + -
27A PHE* 3.5 37.3 - + + -
43A ALA* 5.6 1.8 - - + -
85A ARG 5.9 2.2 - - - -
88A THR* 5.3 8.1 - - + -
89A PRO* 3.4 27.6 - - + +
91A ASP* 1.3 76.9 - - - +
93A PRO* 1.3 68.0 - - + +
94A ARG 3.2 0.3 + - - -
95A GLN* 3.2 4.4 + - + +
96A LEU* 2.8 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ARG 5.7 7.4 - - - +
88A THR* 5.7 2.0 - - - +
89A PRO 3.2 16.6 - - - +
90A GLU 3.5 13.7 - - - +
91A ASP 3.4 0.4 - - - -
92A PHE* 1.3 93.8 - - + +
94A ARG* 1.3 58.8 + - + +
96A LEU* 3.1 11.9 + - + +
97A ALA* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 3.2 31.9 + - - +
40A PRO* 2.6 43.0 + - - +
41A VAL* 4.8 2.0 - - - +
91A ASP* 2.9 45.0 + - - +
93A PRO* 1.3 80.8 - - - +
95A GLN* 1.3 71.8 + - - +
97A ALA* 3.3 12.9 + - - +
98A LEU* 3.3 42.2 + - + +
276A LEU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.6 6.8 - - - -
40A PRO* 3.3 20.5 - - - +
41A VAL* 3.3 5.9 - - - -
42A GLN* 2.7 22.1 + - - +
43A ALA* 2.8 42.3 + - + +
44A VAL* 3.2 18.5 + - + +
91A ASP* 2.9 24.0 + - - +
92A PHE* 3.2 8.1 + - - +
94A ARG* 1.3 91.4 - - - +
96A LEU* 1.3 60.5 + - - +
98A LEU* 3.1 6.0 + - - +
99A ILE* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 5.6 1.8 - - - +
23A ALA* 3.8 27.4 - - + -
66A PHE* 4.1 22.4 - - + -
92A PHE* 2.8 41.1 + - + +
93A PRO* 3.4 10.3 - - + +
95A GLN* 1.3 77.3 - - - +
97A ALA* 1.3 61.9 + - - +
99A ILE* 3.0 10.2 + - + +
100A LYS* 3.0 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO 2.9 12.5 + - - +
94A ARG* 3.6 11.0 - - - +
95A GLN 3.2 0.2 - - - -
96A LEU* 1.3 73.6 - - - +
98A LEU* 1.3 62.7 + - + +
100A LYS* 3.4 11.1 + - - +
101A GLU* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 5.8 1.3 - - - +
41A VAL* 5.4 0.2 - - + -
44A VAL* 3.4 28.9 - - + -
94A ARG* 3.5 38.1 - - + +
95A GLN* 3.1 7.2 + - - +
97A ALA* 1.3 75.3 - - + +
99A ILE* 1.3 57.7 + - - +
101A GLU* 3.5 22.8 - - - +
102A LEU* 2.7 38.7 + - - +
272A PHE* 3.9 12.5 - - + -
275A ARG* 5.0 4.5 - - - +
276A LEU* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 4.4 12.3 - - + -
43A ALA* 3.8 5.8 - - + +
44A VAL* 3.7 24.0 - - + +
47A PHE* 3.3 52.7 - - + -
66A PHE* 3.3 31.0 - - + -
95A GLN* 2.8 20.2 + - + +
96A LEU* 3.1 16.2 - - + +
98A LEU* 1.3 76.8 - - - +
100A LYS* 1.3 58.1 + - - +
102A LEU* 3.5 7.5 - - + +
103A VAL* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.7 42.0 - - + +
67A ASP 4.8 4.8 + - - -
85A ARG* 6.1 0.6 - - - +
96A LEU* 3.0 38.7 + - + +
97A ALA* 3.8 8.7 - - - +
98A LEU 3.3 0.2 - - - -
99A ILE* 1.3 71.5 - - - +
101A GLU* 1.3 67.2 + - - +
103A VAL* 3.2 4.3 + - - +
104A ASP* 2.9 19.4 + - - -
110A ARG* 3.5 40.7 - - - +
112A GLU* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA 2.9 17.4 + - - +
98A LEU* 3.5 18.6 - - - +
100A LYS* 1.3 74.3 - - - +
102A LEU* 1.3 57.8 + - - +
104A ASP* 3.0 10.9 + - - +
105A LEU* 2.8 39.6 + - + +
110A ARG* 4.6 1.9 - - - +
272A PHE* 3.0 31.1 - - + -
275A ARG* 3.9 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.9 7.9 - - + +
47A PHE* 4.2 18.6 - - + -
48A ALA* 3.9 30.1 - - + +
51A LEU* 4.5 8.1 - - + -
98A LEU 2.7 20.8 + - - +
99A ILE* 3.5 5.4 - - - +
101A GLU* 1.3 71.6 - - - +
103A VAL* 1.3 65.4 + - - +
105A LEU* 3.0 9.7 + - - +
106A LEU* 3.0 30.1 + - + +
269A LEU* 4.6 9.4 - - + -
272A PHE* 3.8 32.1 - - + -
273A LEU* 4.8 3.4 - - + -
285A PHE* 4.2 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 4.0 15.7 - - + -
51A LEU* 4.3 5.4 - - + -
64A VAL* 3.6 35.4 - - + -
66A PHE* 4.3 2.7 - - + -
99A ILE 2.9 15.8 + - - +
100A LYS* 3.2 9.4 + - - +
102A LEU* 1.3 77.0 - - - +
104A ASP* 1.3 63.7 + - - +
106A LEU 3.4 3.5 + - - -
108A LEU* 3.3 44.0 + - + +
109A ALA 4.0 10.1 - - - +
110A ARG* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS 2.9 12.2 + - - +
101A GLU* 3.3 9.9 - - - +
103A VAL* 1.3 76.6 - - - +
105A LEU* 1.3 67.1 + - + +
107A GLY* 3.0 15.2 + - - -
108A LEU 4.1 8.2 - - - +
110A ARG* 2.6 49.7 + - - +
265A ASP* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLU* 2.8 30.9 + - + +
102A LEU* 3.0 8.7 + - - +
104A ASP* 1.3 74.2 - - + +
106A LEU* 1.3 59.1 + - - +
107A GLY 3.3 0.2 - - - -
264A PRO* 3.3 3.3 - - - +
265A ASP* 2.9 41.4 + - + -
268A ARG* 3.8 34.1 - - + +
269A LEU* 4.1 21.5 - - + +
272A PHE* 3.5 47.1 - - + -
275A ARG* 5.4 1.3 - - - +
----------------------------------------------------------
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