Contacts of the helix formed by residues 7 - 19 (chain A) in PDB entry 5TDF
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 SER 7 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 1.3 78.6 - - - +
8A GLU* 1.3 64.5 + - - +
9A GLN* 3.5 5.0 + - - +
10A THR* 2.9 32.5 + - - -
11A GLY* 3.0 19.9 + - - -
60A ASP* 3.5 23.7 + - - -
62A LEU* 4.4 7.6 - - - -
104A ASN* 5.7 1.8 - - - -
217A LEU* 5.0 1.1 - - - +
218A ALA* 6.4 0.2 - - - -
237A GLU 4.9 0.6 + - - -
239A PRO* 4.1 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE 3.8 1.0 + - - -
7A SER* 1.3 70.1 - - - +
9A GLN* 1.3 64.1 + - - +
11A GLY 3.3 0.9 + - - -
12A LYS* 2.7 59.6 + - + +
58A LYS* 2.9 21.2 + - - -
60A ASP* 2.9 18.5 + - - +
62A LEU* 5.5 0.8 - - - +
66A ARG* 2.9 35.4 + - - +
106A LEU* 4.2 8.0 - - + +
216A ASP* 3.3 14.2 - - - +
217A LEU* 3.4 28.9 + - + +
218A ALA* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER* 3.8 4.0 - - - +
8A GLU* 1.3 75.9 - - - +
10A THR* 1.3 58.6 + - - +
12A LYS* 3.8 4.4 - - - +
13A GLU* 2.9 34.7 + - + +
31A TYR* 3.7 32.5 + - + -
33A ARG* 3.4 48.8 + - - +
60A ASP* 2.9 18.4 + - - +
104A ASN* 5.2 1.9 + - - -
106A LEU* 3.7 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.9 22.0 - - + -
7A SER* 2.9 27.6 + - - -
9A GLN* 1.3 76.9 - - - +
11A GLY* 1.3 62.8 + - - +
13A GLU* 3.4 11.5 + - - +
14A LEU* 3.1 31.9 + - + +
236A ILE* 3.9 23.1 - - + -
237A GLU* 4.6 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.6 20.4 - - - +
7A SER 3.0 11.7 + - - -
8A GLU 3.8 2.0 - - - -
10A THR* 1.3 76.1 - - - +
12A LYS* 1.3 56.9 + - - +
14A LEU* 3.3 5.9 + - - +
15A LEU* 2.9 29.3 + - - +
191A PHE* 4.4 2.9 - - - -
197A PHE* 5.1 3.6 - - - -
217A LEU* 3.8 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 2.7 52.2 + - + +
9A GLN* 3.9 3.1 - - - +
11A GLY* 1.3 72.8 - - - +
13A GLU* 1.3 61.7 + - - +
15A LEU* 4.3 3.1 - - - -
16A TYR* 2.8 59.6 + - + +
31A TYR* 4.4 8.3 - - + -
106A LEU* 5.1 2.5 - - + -
108A GLU* 2.7 33.4 + - - +
214A VAL* 3.2 30.8 + - + -
215A LEU 3.1 20.0 + - - -
216A ASP 4.2 3.6 - - - +
217A LEU* 4.0 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 2.9 21.0 + - + +
10A THR* 3.6 11.3 - - - +
12A LYS* 1.3 76.8 - - - +
14A LEU* 1.3 62.7 + - + +
16A TYR 3.5 0.3 + - - -
17A LYS* 2.9 60.7 + - + +
29A PHE* 3.9 11.6 - - + -
31A TYR* 3.2 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.5 9.6 - - + -
10A THR* 3.1 34.3 + - + +
11A GLY 3.7 3.1 - - - +
13A GLU* 1.3 80.2 - - + +
15A LEU* 1.3 64.1 + - - +
17A LYS* 3.2 6.2 + - + +
18A PHE* 2.9 39.4 + - + -
191A PHE* 3.4 17.3 - - + -
195A LEU* 4.1 15.0 - - + -
197A PHE* 4.5 6.7 - - + -
221A VAL* 5.7 0.7 - - + -
232A LYS 3.5 25.1 - - - +
233A TRP* 4.2 14.4 - - + +
236A ILE* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY 2.9 16.7 + - - +
12A LYS* 3.3 5.6 + - - +
14A LEU* 1.3 76.3 - - - +
16A TYR* 1.3 82.5 + - + +
19A ILE* 2.9 55.4 + - + +
25A ILE* 4.1 10.8 - - + -
184A PHE* 4.8 1.1 - - + -
188A LEU* 3.8 25.1 - - + -
191A PHE* 3.5 20.5 - - + -
200A LEU* 5.4 0.2 - - + -
202A ILE* 4.1 10.3 - - + -
214A VAL* 4.4 12.3 - - + -
217A LEU* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 2.8 43.5 + - + +
15A LEU* 1.3 87.3 - - + +
17A LYS* 1.3 61.7 + - - +
19A ILE* 4.8 5.7 + - - +
25A ILE* 3.9 22.2 - - + -
26A GLN 4.5 4.2 + - - -
27A ASN* 4.0 14.0 + - - +
28A ARG* 2.8 46.1 + - + +
29A PHE* 3.2 44.2 - + + -
30A LYS 6.1 0.2 - - - -
31A TYR* 3.8 23.1 - + - -
108A GLU* 5.0 2.3 + - - -
214A VAL* 4.0 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 2.9 51.1 + - + +
14A LEU* 3.5 8.4 - - + +
16A TYR* 1.3 79.8 - - - +
18A PHE* 1.3 90.7 + - + +
19A ILE 5.2 0.7 - - - +
28A ARG* 4.7 2.6 + - - +
29A PHE* 3.8 17.6 - - + -
232A LYS 5.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 2.9 35.2 + - + +
17A LYS* 1.3 102.7 - - + +
19A ILE* 1.3 68.5 + - - +
20A CYS* 3.5 4.2 + - - +
191A PHE* 4.0 14.4 - - + +
195A LEU* 4.1 18.6 - - + -
232A LYS* 3.5 65.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 2.9 31.8 + - + +
16A TYR* 5.0 5.4 - - - +
17A LYS 4.0 0.9 - - - +
18A PHE* 1.3 78.6 - - - +
20A CYS* 1.3 64.1 + - - +
21A THR* 4.2 7.3 + - + +
25A ILE* 3.5 24.5 - - + -
28A ARG* 6.3 0.4 - - - +
184A PHE* 3.8 33.0 - - + +
187A GLY* 3.7 17.5 - - - +
188A LEU* 3.6 31.0 - - + +
191A PHE* 4.3 12.6 - - + -
----------------------------------------------------------
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