Contacts of the helix formed by residues 152 - 164 (chain A) in PDB entry 1FLS
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 PRO 152 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASP* 5.4 5.2 - - - +
134A GLY* 3.5 27.4 - - - +
135A ALA* 3.9 7.9 - - + -
149A PHE* 4.2 7.2 - - + -
150A MET 3.0 8.0 - - - +
151A LEU* 1.3 89.1 - - - +
153A ASP* 1.3 66.6 + - - +
154A ASP* 3.2 8.3 - - + +
155A ASP* 3.2 27.2 + - - +
156A VAL* 3.0 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PRO* 1.3 75.2 - - - +
154A ASP* 1.3 64.8 + - - +
156A VAL* 4.2 8.1 - - - +
157A GLN* 2.8 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A SER* 3.5 22.4 + - - +
132A ASP* 4.2 19.5 + - + +
135A ALA* 5.3 0.2 - - + -
152A PRO* 3.2 8.6 - - + +
153A ASP* 1.3 81.3 - - - +
155A ASP* 1.3 70.9 + - - +
157A GLN* 4.0 5.2 - - - +
158A GLY* 3.2 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TRP* 5.0 10.4 - - + -
127A LEU* 4.9 6.9 - - + +
130A SER* 4.5 5.7 - - - -
135A ALA* 3.6 25.1 - - - +
136A LEU* 3.7 9.7 + - - +
137A MET* 4.6 10.1 + - - +
151A LEU* 4.1 24.7 - - + +
152A PRO* 3.2 26.9 + - - +
153A ASP 3.2 0.4 - - - -
154A ASP* 1.3 80.7 - - - +
156A VAL* 1.3 61.7 + - - +
158A GLY* 3.2 1.3 + - - -
159A ILE* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.6 18.8 - - + -
151A LEU* 3.6 22.7 - - + +
152A PRO 3.0 22.7 + - - +
153A ASP* 3.1 8.5 + - - +
155A ASP* 1.3 76.4 - - - +
157A GLN* 1.3 65.5 + - + +
159A ILE* 3.7 7.4 - - + -
160A GLN* 2.9 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASP* 2.8 34.0 + - + +
154A ASP* 4.0 4.7 - - - +
156A VAL* 1.3 74.1 - - + +
158A GLY* 1.3 57.6 + - - +
160A GLN* 4.0 7.1 - - - +
161A SER* 2.9 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.8 14.1 - - - -
154A ASP 3.2 13.4 + - - -
155A ASP* 3.7 2.0 - - - -
156A VAL 3.2 0.2 - - - -
157A GLN* 1.3 77.0 - - - +
159A ILE* 1.3 65.5 + - - +
161A SER* 2.4 27.7 + - - -
162A LEU* 3.1 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TRP* 4.2 8.3 - - + -
45A VAL* 4.2 16.8 - - + +
46A THR* 3.4 28.5 - - + -
125A LEU* 3.9 20.0 - - + -
127A LEU* 3.7 30.8 - - + +
151A LEU* 5.7 0.2 - - + -
155A ASP 2.8 24.2 + - - +
156A VAL* 3.3 12.8 - - - +
158A GLY* 1.3 71.6 - - - -
160A GLN* 1.3 68.3 + - + +
162A LEU* 3.1 3.0 + - - -
163A TYR* 2.9 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.6 19.7 + - + +
156A VAL* 2.9 42.3 + - + +
157A GLN* 4.0 6.2 - - - +
159A ILE* 1.3 89.3 - - + +
161A SER* 1.3 56.3 + - - +
163A TYR* 4.9 0.7 - - - -
164A GLY* 2.4 53.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLN 2.9 17.3 + - - -
158A GLY* 2.4 29.5 + - - -
160A GLN* 1.3 77.5 - - - +
162A LEU* 1.3 67.2 + - - +
164A GLY* 4.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A THR* 3.1 31.6 - - - +
8A LEU 4.8 2.9 - - - +
9A LYS* 3.7 36.9 + - + +
125A LEU 4.0 8.1 - - - +
126A GLY* 3.6 28.9 - - - +
127A LEU* 3.7 23.8 - - + -
158A GLY 3.1 6.4 + - - +
159A ILE* 3.7 6.3 - - - +
160A GLN 3.1 0.4 - - - -
161A SER* 1.3 89.8 + - - +
163A TYR* 1.3 71.4 + - + +
164A GLY 3.3 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 4.3 10.7 - - + -
10A TRP* 3.4 34.1 + + + -
13A MET* 4.7 15.4 - - + +
46A THR* 4.9 4.9 - - + -
47A PRO* 5.0 20.1 - - + +
48A LEU* 3.9 29.6 - - + -
125A LEU* 3.1 50.6 + - + +
159A ILE* 2.9 42.6 + - + +
160A GLN* 5.3 0.4 - - - -
162A LEU* 1.3 84.6 - - + +
164A GLY* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 5.7 5.5 - - - +
160A GLN* 2.4 51.3 + - - +
161A SER 4.2 1.3 + - - -
162A LEU 3.3 2.0 - - - -
163A TYR* 1.3 75.8 - - - +
----------------------------------------------------------
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