Contacts of the helix formed by residues 74 - 89 (chain C) in PDB entry 1TLF
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 HIS 74 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ALA 3.7 10.1 + - - -
73C LEU* 1.3 74.3 - - - +
75C ALA* 1.3 65.7 + - - +
77C SER* 2.8 17.5 + - - -
78C GLN* 2.9 23.1 + - + +
248C GLN* 2.9 34.0 + - + +
276C THR* 3.9 25.6 - - + -
278C ASP* 4.6 8.3 + - + -
282C TYR* 5.0 5.2 - - - -
998C IPT 4.9 0.2 + - - -
74D HIS* 3.6 49.3 + + + -
78D GLN* 6.2 0.4 - - - -
277D GLU* 5.9 4.3 - - + -
278D ASP* 2.9 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C HIS* 1.3 76.4 - - - +
76C PRO* 1.4 58.5 - - + +
78C GLN* 2.8 6.1 + - - +
79C ILE* 2.7 39.7 + - - +
248C GLN* 4.9 0.2 + - - -
274C ASP* 3.8 10.3 - - - +
276C THR* 3.9 9.7 - - + +
293C PHE* 3.9 20.1 - - + -
998C IPT 3.3 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C THR* 4.0 4.7 - - - +
69C SER* 3.6 25.4 - - - +
70C SER 3.6 16.2 - - - +
71C LEU* 3.8 9.2 - - + -
73C LEU* 3.4 13.9 - - + +
75C ALA* 1.4 91.2 - - + +
77C SER* 1.3 51.5 + - - +
79C ILE* 2.8 9.7 + - + +
80C VAL* 2.7 35.9 + - - +
125C ASN* 3.8 16.2 - - - +
998C IPT 3.6 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 3.4 19.6 + - - +
73C LEU 2.7 23.0 + - - -
74C HIS* 2.8 15.4 + - - -
76C PRO* 1.3 76.3 - - - +
78C GLN* 1.3 55.9 + - - +
80C VAL* 4.2 1.8 - - - +
81C ALA* 3.1 29.3 + - - +
71D LEU* 3.0 37.0 + - - +
72D ALA* 4.7 2.7 + - - -
74D HIS* 5.6 1.9 + - - -
77D SER* 3.5 11.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C HIS* 2.9 17.5 + - + +
75C ALA 2.8 10.3 + - - +
77C SER* 1.3 75.7 - - - +
79C ILE* 1.3 64.9 + - - +
81C ALA* 3.7 5.9 + - - +
82C ALA* 3.2 21.5 + - - +
275C ASP 5.0 1.6 - - - +
276C THR* 3.2 41.2 - - - +
277C GLU* 3.2 36.2 + - - +
293C PHE* 4.3 22.5 - - + +
72D ALA* 5.0 18.3 + - + +
74D HIS* 6.1 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ALA 2.7 21.8 + - - +
76C PRO* 2.8 6.6 + - + +
78C GLN* 1.3 74.4 - - - +
80C VAL* 1.3 68.2 + - + +
82C ALA* 2.7 17.4 + - - +
83C ILE* 3.0 21.5 + - + +
125C ASN* 3.9 19.1 - - + +
148C LEU* 3.8 26.7 - - + -
293C PHE* 3.5 35.2 - - + +
296C LEU* 3.8 14.4 - - + -
998C IPT 3.5 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL* 4.3 12.6 - - + -
68C THR* 3.5 37.2 - - + +
71C LEU* 4.0 8.7 - - + -
76C PRO 2.7 16.9 + - - +
77C SER* 4.2 3.1 - - - +
79C ILE* 1.3 72.2 - - + +
81C ALA* 1.3 62.7 + - - +
83C ILE* 3.0 14.7 + - + +
84C LYS* 2.9 20.4 + - - +
94C VAL* 5.6 1.5 - - + +
96C VAL* 3.7 16.4 - - + -
125C ASN* 4.9 2.2 - - - +
71D LEU* 4.4 6.3 - - + -
98D MET* 3.4 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C SER 3.1 22.1 + - - +
78C GLN* 3.7 7.9 - - - +
79C ILE 3.1 0.2 - - - -
80C VAL* 1.3 77.0 - - - +
82C ALA* 1.3 57.6 + - - +
84C LYS* 3.4 4.8 + - - +
85C SER* 2.9 27.0 + - - -
70D SER* 4.7 5.6 - - - +
72D ALA* 4.6 17.0 - - + +
98D MET* 4.2 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLN 3.2 10.6 + - - +
79C ILE 2.7 12.1 + - - +
81C ALA* 1.3 69.4 - - - +
83C ILE* 1.3 60.4 + - - +
85C SER* 3.0 9.7 + - - -
86C ARG* 2.9 31.4 + - - +
293C PHE 2.9 31.6 - - - +
294C ARG* 4.0 15.5 - - + +
297C GLY* 3.8 11.3 - - - -
298C GLN 4.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 4.7 1.8 - - + -
66C VAL* 4.0 25.8 - - + -
79C ILE* 3.0 31.4 + - + +
80C VAL* 3.2 11.2 - - - +
82C ALA* 1.3 77.1 - - - +
84C LYS* 1.3 57.3 + - - +
87C ALA* 3.0 30.8 + - - +
94C VAL* 3.9 17.7 - - + -
123C ILE* 3.8 38.6 - - + -
148C LEU* 4.2 2.9 - - + -
297C GLY* 4.3 12.8 - - - +
300C SER* 4.4 4.0 - - - +
301C VAL* 3.4 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C VAL 2.9 12.1 + - - +
81C ALA* 3.6 9.6 - - - +
83C ILE* 1.3 74.0 - - - +
85C SER* 1.3 66.8 + - - +
88C ASP* 2.9 60.0 + - - +
93C SER* 6.3 0.4 - - - +
94C VAL* 4.0 21.4 - - + +
98D MET* 3.0 57.1 + - + +
99D VAL 4.6 0.9 - - - -
100D GLU* 3.2 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ALA 2.9 14.5 + - - -
82C ALA* 3.2 13.9 - - - -
84C LYS* 1.3 81.1 - - - +
86C ARG* 1.3 63.3 + - - +
88C ASP* 3.6 10.8 + - - +
89C GLN* 3.6 15.5 + - - +
294C ARG* 5.5 7.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ALA 2.9 12.6 + - - +
85C SER* 1.3 72.2 + - - +
87C ALA* 1.3 56.4 + - - +
88C ASP 3.1 2.0 - - - -
89C GLN* 2.6 59.7 + - - +
90C LEU* 3.0 31.6 + - - +
298C GLN* 3.5 42.4 + - + +
301C VAL* 3.6 20.6 - - + -
302C ASP* 2.8 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 4.3 6.1 - - + -
83C ILE 3.0 19.8 + - - +
84C LYS 3.7 3.6 - - - +
86C ARG* 1.3 76.6 - - - +
88C ASP* 1.3 63.6 + - - +
90C LEU 3.1 3.9 + - - +
91C GLY 3.1 3.6 + - - -
92C ALA* 2.7 48.1 + - + +
93C SER 4.6 0.2 - - - -
94C VAL* 3.5 24.5 - - + -
301C VAL* 4.1 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LYS* 2.9 55.5 + - - +
85C SER* 3.6 8.0 - - - +
86C ARG 3.1 0.4 - - - -
87C ALA* 1.3 79.6 - - - +
89C GLN* 1.3 63.5 + - + +
91C GLY* 3.3 11.9 + - - +
92C ALA 4.5 8.5 - - - +
93C SER* 5.5 1.6 - - - -
94C VAL* 5.7 0.2 - - - +
100D GLU* 3.6 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C SER* 3.6 14.0 + - - +
86C ARG* 2.6 49.8 + - - +
88C ASP* 1.3 70.6 - - + +
90C LEU* 1.3 66.0 + - + +
91C GLY* 2.8 9.7 + - - -
----------------------------------------------------------
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