Contacts of the helix formed by residues 150 - 159 (chain H) in PDB entry 1RFU
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 ASN 150 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H GLY 2.6 27.9 - - - +
118H ASP* 3.8 6.8 - - - -
119H GLN* 3.4 31.1 + - - +
127H TYR* 5.1 0.3 + - - -
149H PRO* 1.3 72.5 - - - +
151H GLN* 1.3 58.8 + - - +
152H PHE* 4.3 0.7 - - - -
153H GLU* 2.8 36.8 + - + +
154H ALA* 2.4 35.7 + - - +
185H ILE* 4.4 0.2 - - - -
186H THR* 4.3 3.8 - - - -
7402H ADP 3.4 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 151 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H GLN* 3.1 27.3 - - - +
150H ASN* 1.3 71.6 - - - +
152H PHE* 1.3 53.6 + - - +
154H ALA* 3.2 3.7 - - - +
155H GLU* 2.6 60.7 + - - +
162H ILE* 3.8 30.9 + - + +
185H ILE* 3.8 11.8 - - + +
187H SER 3.2 14.4 + - - +
188H SER* 2.9 30.2 - - - -
189H ASN* 2.9 37.9 + - - +
190H LEU* 4.8 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H GLY* 3.5 30.3 - - - -
118H ASP 3.7 4.5 - - - -
119H GLN* 3.5 25.4 - - + +
124H GLY 3.6 27.4 - - - -
125H ALA* 3.5 37.7 - - - -
126H MET* 3.7 11.7 - - + -
150H ASN* 4.3 4.3 - - - +
151H GLN* 1.3 79.5 - - - +
153H GLU* 1.3 54.0 + - - +
155H GLU* 2.9 23.7 + - - +
156H LEU* 2.7 56.6 + - + +
161H LYS* 5.6 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 153 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H ASP* 4.7 2.3 - - - +
114H PRO* 2.7 29.0 - - + +
115H VAL* 3.0 8.7 - - - +
116H MET* 2.6 33.5 + - + +
117H GLY 3.4 24.8 + - - +
127H TYR* 4.6 2.4 + - - -
148H THR 4.5 1.9 - - - +
149H PRO* 3.8 3.6 - - - +
150H ASN* 2.8 40.7 + - + +
152H PHE* 1.3 80.4 - - + +
154H ALA* 1.3 53.4 + - - +
156H LEU* 2.8 12.6 + - - +
157H LEU* 2.8 38.5 + - - +
7401H PLP 5.4 0.7 + - - -
7402H ADP 5.1 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H PRO* 3.9 12.4 - - + +
150H ASN 2.4 32.2 + - - +
151H GLN* 3.2 6.1 - - + +
153H GLU* 1.3 70.0 - - - +
155H GLU* 1.3 66.1 + - + +
157H LEU* 3.2 6.2 + - - +
158H THR* 3.0 22.7 + - - +
162H ILE* 5.9 2.2 - - + -
171H VAL* 3.9 13.4 - - + +
175H LEU* 4.7 1.8 - - + -
185H ILE* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H GLN* 2.6 59.5 + - - +
152H PHE* 3.3 18.5 - - - +
154H ALA* 1.3 73.3 - - - +
156H LEU* 1.3 58.5 + - - +
157H LEU 2.9 0.5 + - - -
158H THR* 3.5 5.3 + - - -
159H GLY* 2.8 28.4 + - - -
160H ARG 3.1 24.6 + - - +
161H LYS* 3.3 30.6 + - - +
162H ILE* 3.1 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H MET* 3.5 35.7 - - + -
126H MET* 3.8 24.5 - - + -
133H LEU* 3.4 39.7 - - + +
137H ARG* 4.6 3.1 + - - -
152H PHE* 2.7 38.8 + - + +
153H GLU* 2.8 14.6 + - - +
155H GLU* 1.3 73.9 - - - +
157H LEU* 1.3 58.9 + - - +
159H GLY* 3.7 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H PRO* 4.0 27.8 - - + -
116H MET* 3.7 19.7 - - + -
133H LEU* 4.4 2.5 - - + -
136H TYR* 4.2 5.2 - - + -
137H ARG* 3.2 48.6 - - + +
141H VAL* 3.9 28.0 - - + -
147H ILE* 5.3 2.9 - - + -
149H PRO* 4.4 8.3 - - + -
153H GLU 2.8 20.0 + - - +
154H ALA* 3.7 3.8 - - - +
156H LEU* 1.3 70.2 - - - +
158H THR* 1.3 60.9 + - - +
159H GLY 2.9 9.5 + - - -
175H LEU* 4.1 22.9 - - + -
178H MET* 4.4 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H ALA 3.0 11.9 + - - -
155H GLU* 3.5 4.2 + - - -
157H LEU* 1.3 77.6 - - - +
159H GLY* 1.3 56.8 + - - +
160H ARG* 3.1 19.0 + - - +
171H VAL* 3.0 43.7 - - + +
174H MET* 3.5 38.8 - - + +
175H LEU* 3.5 24.7 - - + +
178H MET* 4.5 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 159 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H ARG* 5.9 2.0 - - - -
155H GLU 2.8 9.5 + - - -
156H LEU* 4.1 7.2 - - - -
157H LEU 2.9 7.5 + - - -
158H THR* 1.3 76.4 - - - +
160H ARG* 1.3 61.6 + - - +
----------------------------------------------------------
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