Contacts of the helix formed by residues 5 - 15 (chain D) in PDB entry 5TXV
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 THR 5 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C SER* 3.3 30.3 - - - +
412C ASP* 5.3 3.4 + - - +
3D GLU 4.4 2.9 - - - +
4D MET* 1.3 75.7 - - - +
6D PRO* 1.3 65.8 - - - +
7D ARG* 4.0 5.8 + - - +
8D GLU* 2.8 54.9 + - - +
9D ILE* 3.1 10.5 + - - +
32D ARG* 4.2 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 6 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C SER 4.0 9.6 - - - +
408C TYR* 3.4 43.3 - - + +
411C SER* 2.9 27.4 - - - +
5D THR* 1.3 77.8 - - - +
7D ARG* 1.3 61.5 + - + +
9D ILE* 3.3 4.5 + - + -
10D VAL* 3.2 27.5 + - - +
28D ALA* 3.6 18.8 - - + +
29D ILE* 5.2 0.2 - - - -
32D ARG* 3.7 30.5 - - + -
36D ARG* 4.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C TYR* 3.5 36.0 + - + +
409C ASP* 2.7 39.3 + - - +
411C SER* 6.3 0.9 - - - -
412C ASP* 2.0 40.5 + - - +
413C LEU* 6.3 0.2 - - - +
5D THR* 3.2 5.9 + - - +
6D PRO* 1.3 76.7 - - - +
8D GLU* 1.3 58.9 + - + +
10D VAL* 3.5 1.9 + - - +
11D SER* 3.0 29.3 + - - -
25D ARG* 3.7 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D GLU 4.8 0.2 - - - +
4D MET* 3.3 28.8 - - + +
5D THR* 2.8 45.7 + - - +
7D ARG* 1.3 77.7 - - + +
9D ILE* 1.3 61.4 + - - +
11D SER* 4.0 6.3 - - - -
12D GLU* 3.2 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D MET* 4.1 23.8 - - + +
5D THR 3.1 13.6 + - - +
6D PRO* 3.6 8.3 - - + +
7D ARG 3.2 0.4 - - - -
8D GLU* 1.3 75.1 - - - +
10D VAL* 1.3 60.8 + - - +
12D GLU* 3.2 3.8 + - - +
13D LEU* 2.9 45.8 + - + +
28D ALA* 3.8 37.7 - - + +
31D LEU* 3.7 26.7 - - + -
32D ARG* 4.6 3.1 - - + +
70D LEU* 4.1 12.6 - - + -
73D LEU* 3.7 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C TYR* 3.2 34.1 - - + +
6D PRO 3.2 8.8 + - - +
7D ARG 4.0 2.0 - - - +
8D GLU 3.5 0.2 - - - -
9D ILE* 1.3 75.2 - - - +
11D SER* 1.3 58.5 + - - +
13D LEU* 3.0 8.2 + - - -
14D ASP* 2.8 46.2 + - - +
21D ASP* 3.4 26.2 - - - +
24D LYS* 3.5 39.9 - - + +
25D ARG* 3.9 1.8 - - + +
28D ALA* 4.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ARG 3.0 17.7 + - - -
8D GLU* 4.0 6.7 - - - -
10D VAL* 1.3 77.3 - - - +
12D GLU* 1.3 60.6 + - - +
14D ASP* 3.5 23.1 + - - +
15D LYS* 3.6 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D MET* 5.4 2.2 - - - -
8D GLU 3.2 17.9 + - - +
9D ILE 3.6 4.3 - - - +
10D VAL 3.2 0.6 - - - -
11D SER* 1.3 74.1 - - - +
13D LEU* 1.3 66.8 + - + +
15D LYS* 3.0 57.9 + - - +
16D HIS* 4.1 14.6 + - + -
73D LEU* 3.7 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 2.9 32.2 + - + +
10D VAL* 3.0 6.9 + - - +
12D GLU* 1.3 77.0 - - + +
14D ASP* 1.3 60.5 + - - +
16D HIS* 3.0 4.2 + - - +
17D ILE* 2.9 39.9 + - + +
24D LYS* 4.0 30.5 - - + +
27D VAL* 3.8 28.5 - - + -
66D ILE* 4.5 6.7 - - + +
69D ARG* 3.9 30.5 - - + +
70D LEU* 4.2 14.4 - - + +
73D LEU* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 2.8 34.9 + - - +
11D SER* 3.6 16.8 - - - +
12D GLU 3.2 0.6 - - - -
13D LEU* 1.3 73.1 - - - +
15D LYS* 1.3 61.7 + - - +
16D HIS 3.1 0.7 - - - -
17D ILE 3.2 16.3 - - - +
18D ILE* 4.4 9.4 - - - +
21D ASP* 4.4 4.0 - - - +
24D LYS* 2.8 26.6 + - - +
342D ARG* 5.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER* 3.6 15.0 - - - +
12D GLU* 3.0 46.6 + - - +
13D LEU 3.1 0.8 - - - -
14D ASP* 1.3 76.9 - - - +
16D HIS* 1.3 71.4 + - + +
18D ILE* 6.0 0.7 - - - -
346D GLU 4.4 16.6 - - - +
----------------------------------------------------------
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