Contacts of the helix formed by residues 87 - 98 (chain D) in PDB entry 1TF6
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 LYS 87 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D PHE* 3.2 42.3 - - + -
76D ASP* 4.9 10.5 + - - +
86D THR* 1.3 71.5 - - - +
88D ALA* 1.3 59.5 + - - +
89D ASN 2.7 15.1 + - - -
90D MET* 2.8 18.8 + - + +
91D LYS* 2.7 23.3 + - + +
40F C 2.9 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D THR* 4.8 1.7 - - + +
87D LYS* 1.3 81.8 - - - +
89D ASN* 1.3 63.1 + - - +
91D LYS* 3.3 24.5 - - + +
92D LYS* 3.9 5.9 + - - +
40F C 3.8 30.5 - - + -
41F C 3.7 34.3 - - + +
42F A 5.8 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D PHE* 4.7 5.7 - - - -
85D THR* 3.8 19.6 - - - +
86D THR* 3.1 35.6 + - - +
87D LYS 2.7 0.6 + - - -
88D ALA* 1.3 76.0 - - - +
90D MET* 1.3 56.1 + - - +
91D LYS 3.0 1.1 - - - -
92D LYS* 2.6 52.1 + - - +
20E G 4.4 4.4 - - - +
21E G 3.4 24.7 + - - +
22E A 3.0 32.2 + - - +
23E T 5.6 2.0 - - - +
42F A 5.8 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D PHE* 5.4 1.3 - - + -
74D THR 3.0 20.2 - - - +
75D CYS* 3.3 21.5 - - - -
76D ASP* 3.6 27.8 - - + +
84D PHE* 3.1 49.1 - - + -
86D THR 2.8 19.1 + - - +
87D LYS* 2.8 20.9 + - + +
89D ASN* 1.3 73.1 - - - +
91D LYS* 1.3 74.1 + - + +
92D LYS 2.8 2.2 + - - -
93D HIS* 3.0 16.6 + - - +
94D PHE* 3.5 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LYS* 2.7 15.3 + - + +
88D ALA* 3.3 23.8 - - - +
89D ASN 2.9 0.4 + - - -
90D MET* 1.3 81.2 - - + +
92D LYS* 1.3 64.7 + - + +
94D PHE* 3.9 4.8 + - - +
95D ASN* 3.3 40.9 + - - +
41F C 4.3 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ALA 4.6 4.0 - - - +
89D ASN* 2.6 46.1 + - - +
91D LYS* 1.3 70.7 - - + +
93D HIS* 1.3 69.3 + - - +
95D ASN* 2.9 11.7 + - - +
96D ARG* 2.8 57.7 + - - +
20E G 3.9 9.8 + - - -
21E G 2.6 35.8 + - - -
22E A 4.1 0.4 - - - +
42F A 5.6 0.9 - - - +
43F T 3.1 31.4 + - + +
44F C 4.4 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D CYS* 3.3 16.4 - - + -
80D CYS* 3.6 5.4 - - + -
84D PHE* 3.4 37.2 - + + -
90D MET* 3.0 8.5 + - - +
92D LYS* 1.3 77.1 - - - +
94D PHE* 1.3 62.2 + - + +
96D ARG* 2.6 28.3 + - - +
97D PHE* 2.7 39.9 + + + +
98D HIS* 2.8 12.8 + + - -
203D ZN 2.1 37.1 - - - -
20E G 3.6 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D CYS* 4.7 0.7 - - - -
76D ASP 3.1 30.1 - - - -
77D SER* 3.3 13.7 - - - -
78D ASP 5.2 0.2 - - - -
90D MET* 3.5 12.1 + - - +
91D LYS* 4.0 9.2 - - - +
92D LYS 3.0 0.8 + - - -
93D HIS* 1.3 80.6 - - + +
95D ASN* 1.3 61.5 + - - +
97D PHE 2.6 9.2 + - - -
98D HIS* 2.6 67.1 + + + -
99D ASN* 3.0 43.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LYS* 3.3 39.8 + - - +
92D LYS* 2.9 12.0 + - - +
94D PHE* 1.3 82.1 - - - +
96D ARG* 1.3 59.4 + - + +
97D PHE 3.3 3.1 + - - -
99D ASN* 3.5 31.6 - - + +
102D ILE* 3.2 29.3 - - + +
103D CYS* 4.0 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LYS* 2.8 54.4 + - - +
93D HIS* 2.6 18.8 + - - +
95D ASN* 1.3 73.2 - - + +
97D PHE* 1.3 62.3 + - + +
103D CYS* 4.9 2.6 - - - +
19E T 3.7 52.8 + - - +
20E G 3.0 54.2 + - - +
43F T 6.0 0.8 - - - +
44F C 5.7 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D HIS* 2.7 37.2 + + + +
94D PHE 2.6 9.1 + - - -
95D ASN 3.1 1.4 - - - -
96D ARG* 1.3 78.3 - - - +
98D HIS* 1.3 71.1 + + - +
103D CYS* 2.7 30.8 - - - +
114D LYS* 3.2 47.3 - - + -
115D ALA* 3.9 31.9 - - + +
19E T 5.6 4.3 - - - -
20E G 5.1 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D SER* 3.1 11.7 + - - -
78D ASP 4.5 8.6 + - - -
80D CYS* 3.9 11.4 - - + -
93D HIS* 2.8 16.6 + + - -
94D PHE* 2.6 51.2 + + + -
97D PHE* 1.3 85.9 - + - +
99D ASN* 1.3 71.3 + - - +
100D ILE* 2.9 14.2 + - - +
103D CYS* 3.1 5.7 - - - +
106D VAL* 5.7 1.0 - - - +
113D GLY 5.9 3.1 - - - -
114D LYS* 6.1 2.2 - - - -
115D ALA* 5.4 2.7 - - - +
203D ZN 2.1 36.8 - - - -
----------------------------------------------------------
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