Contacts of the helix formed by residues 144 - 155 (chain H) in PDB entry 5AYZ
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 PHE 144 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G THR* 3.4 18.4 - - + -
142G PRO* 3.8 39.9 - - + +
22H TRP* 3.8 22.9 - + - -
107H THR* 4.3 14.4 - - - -
110H ARG* 4.0 18.8 - - + -
141H THR* 3.0 23.9 + - + +
142H PRO 3.2 0.9 - - - +
143H GLY* 1.3 76.5 - - - +
145H ARG* 1.3 64.5 + - - +
146H LEU* 3.3 2.9 - - - -
147H VAL* 3.1 50.6 + - + -
148H GLU* 3.2 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G GLU* 3.2 29.3 + - - +
26G ASP* 2.6 49.3 + - - +
102G ARG* 4.9 1.2 - - - +
103G VAL* 5.3 3.2 - - - +
106G ASN* 4.4 6.5 - - - +
138H ARG* 3.5 29.4 + - - +
140H THR* 3.0 32.9 + - + +
141H THR 3.8 1.8 + - - -
144H PHE* 1.3 76.7 - - - +
146H LEU* 1.3 64.1 + - - +
148H GLU 3.0 1.4 + - - +
149H LYS* 2.9 45.1 + - + +
162H TYR* 3.1 45.9 + - + +
163H ASP* 3.8 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G GLU* 4.6 1.4 + - - -
10H LEU* 4.1 14.4 - - + -
11H PRO* 5.1 3.4 - - + -
14H THR* 3.9 20.2 - - + -
15H LEU* 4.4 7.9 - - + -
18H LEU* 3.6 34.3 - - + -
59H PHE* 4.0 13.5 - - + -
143H GLY 5.3 0.8 + - - +
144H PHE 3.2 1.6 + - - -
145H ARG* 1.3 76.7 - - - +
147H VAL* 1.3 59.5 + - - +
149H LYS* 4.6 0.5 - - - +
150H TYR* 3.2 23.9 + - - +
162H TYR* 3.3 26.4 + - + +
28J PRO 5.7 0.2 - - - +
29J GLY* 4.4 12.1 - - - +
30J LEU* 3.6 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H LEU* 5.5 0.2 - - + -
22H TRP* 3.7 20.9 - - + -
59H PHE* 3.5 38.6 - - + -
107H THR* 4.3 5.6 - - + -
111H CYS* 3.5 32.3 - - + -
144H PHE* 3.1 40.1 + - + +
146H LEU* 1.3 78.7 - - + +
148H GLU* 1.3 53.3 + - + +
150H TYR* 3.4 2.6 + - - +
151H GLY* 2.7 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G THR* 4.9 0.2 - - - +
110H ARG* 5.7 2.1 - - - +
114H ILE* 3.5 32.6 - - + +
140H THR* 3.1 25.0 - - + +
141H THR* 2.7 48.4 + - - -
144H PHE* 3.3 30.5 - - + +
145H ARG 3.0 4.6 + - - +
147H VAL* 1.3 73.8 - - - +
149H LYS* 1.3 59.5 + - - +
151H GLY* 3.2 1.7 + - - -
152H LEU* 2.9 32.1 + - - +
273H THR* 3.9 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H THR 2.8 30.3 + - - +
138H ARG* 4.5 1.3 - - - +
140H THR* 4.6 6.5 - - + -
145H ARG* 2.9 37.6 + - + +
146H LEU 4.6 0.7 - - - +
148H GLU* 1.3 71.9 - - - +
150H TYR* 1.3 64.5 + - - +
152H LEU* 3.3 15.0 + - + +
153H LEU* 3.2 28.4 + - - +
159H SER* 2.4 49.1 + - - +
160H HIS* 4.2 1.2 - - - +
161H ARG 3.0 23.8 + - - -
162H TYR* 3.8 30.3 - - + +
30J LEU* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 150 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ALA 4.5 0.3 + - - -
6H LEU* 3.8 35.7 - - + +
7H ALA* 4.1 8.0 + - - +
9H LEU* 5.5 1.1 - - + -
10H LEU* 4.0 27.1 - - + -
56H GLY* 3.8 7.6 - - - -
58H PRO* 3.4 21.5 - - + +
59H PHE* 3.8 18.6 - + + -
77H GLU* 2.6 38.6 + - - +
111H CYS* 3.8 8.7 - - - -
146H LEU 3.2 21.6 + - - +
147H VAL 3.5 2.9 - - - +
149H LYS* 1.3 74.1 - - - +
151H GLY* 1.3 66.9 + - - +
153H LEU* 3.3 13.7 + - + +
154H VAL* 3.1 33.4 + - + +
30J LEU* 5.3 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 151 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H ALA* 4.6 1.3 - - - -
111H CYS* 3.7 27.4 - - - -
114H ILE* 4.0 9.2 - - - -
115H ALA* 3.3 13.6 - - - +
147H VAL 2.7 20.1 + - - -
148H GLU 3.2 4.9 + - - -
150H TYR* 1.3 74.7 - - - +
152H LEU* 1.3 60.6 + - - +
154H VAL 3.2 2.3 + - - -
155H GLY 3.1 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H ILE* 3.6 18.1 - - + +
118H ALA* 3.9 9.1 - - + +
136H GLY* 3.6 26.9 - - - +
137H THR 4.7 1.8 - - - +
148H GLU 2.9 18.6 + - - +
149H LYS* 3.5 20.2 - - + +
150H TYR 3.3 0.4 - - - -
151H GLY* 1.3 74.8 - - - +
153H LEU* 1.3 63.1 + - - +
155H GLY* 3.2 8.7 + - - -
156H GLY 3.3 0.2 + - - -
157H ALA* 3.1 31.3 + - + +
158H ALA 4.5 3.8 - - - +
159H SER* 4.2 13.7 - - - -
272H LEU* 3.8 37.0 - - + -
273H THR* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 3.6 25.9 - - + +
9H LEU* 3.6 30.3 - - + -
149H LYS 3.2 15.0 + - - +
150H TYR* 3.7 11.4 - - + +
151H GLY 3.3 0.2 - - - -
152H LEU* 1.3 76.6 - - - +
154H VAL* 1.3 63.4 + - - +
156H GLY* 3.2 12.3 + - - -
157H ALA 3.5 15.7 - - - +
158H ALA* 4.5 2.0 - - - -
159H SER* 4.0 21.8 - - - +
30J LEU* 4.0 18.4 - - + -
32J TYR* 5.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ALA* 4.4 10.1 - - + +
6H LEU* 4.0 16.2 - - + -
53H VAL* 4.2 6.7 - - + +
54H LEU 3.8 1.8 - - - +
55H ALA* 3.6 24.7 - - + -
77H GLU* 4.1 7.2 - - + +
78H GLY* 3.7 29.1 - - - +
150H TYR* 3.1 48.6 + - + +
151H GLY 3.7 6.5 - - - +
153H LEU* 1.3 75.5 - - - +
155H GLY* 1.3 60.6 + - - +
156H GLY* 3.2 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H VAL* 4.9 2.7 - - - -
115H ALA* 3.4 26.4 - - - +
118H ALA* 3.6 6.5 - - - +
119H ALA* 3.2 30.2 + - - +
122H VAL* 4.2 3.5 - - - +
151H GLY 3.1 10.7 + - - -
152H LEU 3.2 4.2 + - - -
154H VAL* 1.3 76.9 - - - +
156H GLY* 1.3 56.8 + - - +
157H ALA 3.5 3.1 - - - -
----------------------------------------------------------
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