Contacts of the helix formed by residues 3 - 15 (chain D) in PDB entry 4K9P
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 3 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ALA* 1.3 74.1 - - - +
4D VAL* 1.3 59.7 + - - +
5D HIS* 3.3 10.0 + - - +
6D GLY* 3.0 20.7 + - - +
7D THR* 2.9 30.8 + - - -
163D TRP 4.0 5.2 - - - -
164D ASP* 4.3 10.8 - - - -
165D LYS 3.5 12.3 - - - -
166D ASP* 4.4 3.4 - - - +
167D ALA* 3.7 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 4 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D SER* 1.3 71.2 - - - +
5D HIS* 1.3 57.2 + - - +
7D THR* 3.9 1.6 - - - -
8D THR* 2.9 37.3 + - - +
132D ALA 3.5 19.3 - - - +
133D ALA* 4.6 0.7 - - - -
135D VAL* 3.8 34.5 - - + -
136D PRO* 3.9 8.3 - - + -
162D ASP 3.6 21.1 - - - +
163D TRP* 3.8 10.7 + - + +
165D LYS* 3.0 17.7 + - + +
166D ASP 3.9 14.1 - - - +
167D ALA* 3.7 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 5 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D SER* 3.4 7.4 + - - +
4D VAL* 1.3 78.5 - - - +
6D GLY* 1.3 65.9 + - - +
8D THR* 3.7 1.6 - - - -
9D TYR* 3.1 53.1 + + - -
30D PRO 3.6 20.6 - - - -
31D PHE* 3.1 21.7 + + - -
33D LYS* 2.9 29.9 + - + -
34D ASP* 3.9 19.2 + - + +
36D PRO* 5.1 0.2 - - + -
163D TRP* 3.0 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 6 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ALA* 5.8 2.2 - - - -
3D SER* 3.0 13.8 + - - -
5D HIS* 1.3 85.8 + - - +
7D THR* 1.3 62.4 + - - +
9D TYR* 3.5 5.2 + - - +
10D GLU* 3.0 24.5 + - - +
13D ARG* 5.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ALA* 3.8 15.0 - - - +
3D SER 2.9 18.3 + - - +
4D VAL 3.9 2.7 - - - -
6D GLY* 1.3 75.8 - - - +
8D THR* 1.3 57.5 + - - +
10D GLU* 3.4 4.3 + - - -
11D LEU* 2.9 25.3 + - - +
136D PRO* 3.9 15.5 - - + -
167D ALA* 3.3 17.4 - - + +
168D ASP 5.4 0.2 + - - -
171D SER* 3.8 28.7 - - - -
174D LEU* 5.9 0.4 - - + -
175D PHE* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 2.9 29.0 + - - +
5D HIS 3.7 2.9 - - - -
7D THR* 1.3 76.4 - - - +
9D TYR* 1.3 62.7 + - - +
11D LEU* 3.1 10.3 + - - +
12D LEU* 3.0 37.0 + - + +
31D PHE* 4.4 8.1 - - + -
135D VAL* 4.1 5.4 - - - +
136D PRO* 4.1 13.4 - - - +
139D MET* 4.3 21.0 - - + +
163D TRP* 3.7 27.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D HIS* 3.1 58.4 + + - +
6D GLY* 4.0 4.7 - - - +
8D THR* 1.3 79.5 - - - +
10D GLU* 1.3 61.6 + - - +
12D LEU* 3.3 9.5 + - + +
13D ARG* 3.0 33.5 + - - +
20D VAL* 5.2 1.3 - - + -
31D PHE* 2.8 52.4 + + - -
32D LEU 4.7 0.2 - - - -
35D PHE* 3.4 26.9 - + - -
36D PRO* 3.3 37.7 - - + -
39D PHE* 3.8 24.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLY 3.0 18.2 + - - +
7D THR* 3.7 4.7 - - - +
9D TYR* 1.3 75.4 - - - +
11D LEU* 1.3 57.3 + - - +
13D ARG* 2.9 34.7 + - - +
14D ARG* 2.8 69.2 + - + +
175D PHE* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D THR* 2.9 15.1 + - + +
8D THR* 3.1 9.4 + - - +
10D GLU* 1.3 77.6 - - - +
12D LEU* 1.3 63.7 + - - +
14D ARG* 3.3 1.3 + - - +
15D GLN* 3.0 37.7 + - + +
136D PRO* 3.3 30.5 - - + +
139D MET* 3.9 15.7 - - + -
140D SER* 3.5 23.8 - - - +
143D ILE* 4.1 7.9 - - + -
144D HIS* 6.2 0.2 - - - +
174D LEU* 3.7 38.6 - - + +
175D PHE* 3.8 15.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D THR* 3.0 31.3 + - + +
9D TYR* 3.3 18.6 + - + +
11D LEU* 1.3 75.2 - - - +
13D ARG* 1.3 58.4 + - - +
15D GLN* 3.1 12.7 + - - +
16D GLY 3.1 0.2 + - - -
17D ILE* 2.8 44.8 + - + +
20D VAL* 5.7 0.4 - - + -
31D PHE* 4.8 2.5 - - + -
39D PHE* 3.9 21.5 - - + -
66D PHE* 4.0 43.1 - - + -
139D MET* 4.1 10.8 - - + -
143D ILE* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLY 5.1 1.0 + - - -
9D TYR* 3.0 18.6 + - - +
10D GLU* 2.9 52.7 + - - +
12D LEU* 1.3 76.2 - - - +
14D ARG* 1.3 59.3 + - + +
16D GLY* 3.1 19.4 + - - -
17D ILE 3.6 10.5 + - - -
18D ASP* 6.1 0.4 - - - -
36D PRO* 3.4 21.6 - - - +
38D ASP* 2.8 42.8 + - - +
39D PHE* 3.7 11.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLU* 2.8 56.1 + - + +
11D LEU 3.9 2.2 - - - +
13D ARG* 1.3 75.6 - - + +
15D GLN* 1.3 58.8 + - - +
16D GLY 3.2 2.8 + - - -
172D HIS 5.2 0.8 + - - -
175D PHE* 3.4 53.5 - - + +
176D ASP* 2.7 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 3.0 33.5 + - + +
12D LEU 3.1 3.3 + - - +
14D ARG* 1.3 77.7 + - - +
16D GLY* 1.3 60.5 + - - +
17D ILE* 3.4 9.5 + - + +
64D PRO* 5.6 4.2 - - - +
143D ILE* 4.0 29.3 - - + +
144D HIS* 3.6 23.7 - - - +
174D LEU 4.1 3.6 + - - -
175D PHE 3.2 19.7 + - - +
176D ASP* 4.2 1.6 - - - +
177D ARG 2.9 29.4 + - - +
----------------------------------------------------------
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