Contacts of the helix formed by residues 6 - 18 (chain D) in PDB entry 2UZ1
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 GLY 6 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D THR* 1.3 71.6 - - - +
7D GLY* 1.3 56.1 + - - +
9D LEU* 3.1 7.5 + - - +
10D VAL* 2.9 30.0 + - - +
135D THR* 3.8 8.9 - - - +
138D ILE* 3.6 24.3 - - - +
165D ILE 3.7 7.6 - - - -
166D LEU* 2.9 15.2 + - - -
168D ASN 3.0 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D THR* 3.2 1.4 + - - -
6D GLY* 1.3 74.6 - - - +
8D GLU* 1.3 61.8 + - - +
10D VAL* 3.2 5.1 + - - +
11D VAL* 3.1 26.2 + - - +
32D THR* 3.3 31.4 - - - -
33D ILE* 3.9 14.3 - - - +
36D ALA* 4.3 0.2 - - - -
166D LEU* 3.1 15.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
4D ILE* 3.7 20.4 - - + -
5D THR* 3.0 28.8 + - - +
7D GLY* 1.3 77.0 - - - +
9D LEU* 1.3 56.6 + - - +
11D VAL* 3.1 2.1 + - - +
12D ARG* 2.8 64.2 + - - +
32D THR 4.3 0.2 + - - -
36D ALA* 3.2 29.7 - - + +
39D ASP* 4.7 6.6 - - - +
40D HIS* 2.7 32.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.5 24.9 - - + -
5D THR 3.1 11.7 + - - +
6D GLY* 3.1 11.0 + - - +
8D GLU* 1.3 72.4 - - - +
10D VAL* 1.3 61.7 + - - +
12D ARG* 3.5 4.0 + - - +
13D THR* 2.7 33.4 + - - -
135D THR* 3.6 33.9 - - + +
138D ILE* 3.8 11.4 - - + -
139D PRO* 4.0 7.4 - - + +
170D ILE* 3.6 25.1 - - + -
172D GLU 5.8 0.2 - - - +
175D VAL* 3.6 24.0 - - + -
177D ILE* 3.9 17.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
6D GLY 2.9 18.2 + - - +
7D GLY* 3.2 8.3 + - - +
9D LEU* 1.3 76.9 - - - +
11D VAL* 1.3 60.5 + - + +
13D THR* 3.1 3.1 + - - -
14D LEU* 3.0 36.3 + - + +
33D ILE* 4.3 13.2 - - + -
98D LEU* 4.0 26.9 - - + -
138D ILE* 3.6 19.0 - - + +
142D VAL* 4.6 11.7 - - + +
161D LEU* 4.0 15.7 - - + -
166D LEU* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLY 3.1 14.0 + - - +
8D GLU 3.9 1.1 - - - +
10D VAL* 1.3 74.3 - - + +
12D ARG* 1.3 59.7 + - - +
14D LEU* 3.2 11.4 + - + +
15D ILE* 2.8 49.6 + - + +
33D ILE* 3.7 27.1 - - + +
36D ALA* 3.6 26.7 - - + +
37D CYS* 3.7 33.0 - - - +
40D HIS* 4.2 3.8 - - + +
42D VAL* 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.6 38.0 - - - +
8D GLU* 2.8 47.3 + - - +
9D LEU* 4.0 4.0 - - - +
11D VAL* 1.3 75.2 - - - +
13D THR* 1.3 58.7 + - - +
15D ILE* 3.5 8.2 + - - +
16D LYS* 3.1 28.2 + - - +
40D HIS* 4.5 14.0 + - + +
172D GLU* 2.9 31.9 + - - +
177D ILE* 3.8 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU 2.7 22.6 + - - -
10D VAL* 3.1 4.5 + - - -
12D ARG* 1.3 74.5 - - - +
14D LEU* 1.3 64.4 + - - +
16D LYS 3.4 0.9 + - - -
17D ALA* 3.0 22.9 + - - +
139D PRO* 3.3 46.1 - - + +
142D VAL* 3.6 20.9 - - + -
143D MET* 3.7 21.0 - - + +
177D ILE* 3.6 14.1 - - + +
178D PRO* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 3.0 25.6 + - + +
11D VAL* 3.2 15.0 + - + +
13D THR* 1.3 76.2 - - - +
15D ILE* 1.3 63.2 + - + +
17D ALA* 3.2 5.7 + - - +
18D GLY 3.2 5.4 + - - -
19D VAL* 3.0 47.4 + - + +
22D LEU* 4.0 34.8 - - + -
33D ILE* 5.6 0.2 - - + -
69D VAL* 4.5 6.7 - - + -
96D LEU* 3.9 26.9 - - + -
98D LEU* 4.0 15.0 - - + -
142D VAL* 4.0 12.1 - - + -
146D ILE* 4.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 2.8 29.7 + - + +
12D ARG* 3.8 7.4 - - - +
13D THR 3.3 0.2 - - - -
14D LEU* 1.3 75.1 - - + +
16D LYS* 1.3 59.8 + - - +
18D GLY* 3.0 19.8 + - - -
19D VAL 4.2 10.5 - - - +
40D HIS* 3.6 45.1 - - + +
42D VAL* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ARG 3.1 17.5 + - - +
13D THR 3.8 3.6 - - - +
14D LEU 3.3 0.2 - - - -
15D ILE* 1.3 78.2 - - - +
17D ALA* 1.3 60.3 + - - +
18D GLY* 3.4 0.7 + - - -
143D MET* 4.6 1.6 - - - -
177D ILE* 2.8 38.7 + - + +
178D PRO 3.5 17.5 - - - +
179D ASP* 3.4 37.3 + - - +
180D LEU* 4.8 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D THR 3.0 17.3 + - - +
14D LEU 3.2 6.5 + - - +
16D LYS* 1.3 75.7 - - - +
18D GLY* 1.3 57.6 + - - +
19D VAL* 3.6 5.2 - - + -
143D MET* 3.8 16.1 - - - +
146D ILE* 3.6 28.7 - - + -
180D LEU* 3.9 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE 3.0 14.0 + - - -
16D LYS 3.2 1.2 - - - -
17D ALA* 1.3 79.1 - - - +
19D VAL* 1.3 64.6 + - - +
20D GLU* 3.5 16.4 + - - +
66D LYS* 5.8 3.5 - - - -
----------------------------------------------------------
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