Contacts of the helix formed by residues 155 - 162 (chain L) in PDB entry 1RBO
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 ILE 155 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154L GLY* 1.3 70.1 - - - +
156L GLN* 1.3 65.4 + - - +
158L GLU* 3.3 5.1 + - - +
159L ARG* 3.0 32.1 + - + +
324L ASP 5.4 0.6 + - - -
350L ARG* 3.9 31.2 - - + +
373L GLY* 3.2 24.9 + - - +
374L VAL 3.8 15.7 - - - +
375L LEU* 3.6 31.6 - - + +
397L ASP* 3.9 20.2 - - + +
108S ARG* 3.7 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 156 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B SER* 3.7 26.0 - - - +
182B ALA 5.1 2.2 - - - +
211B PHE 4.4 9.8 + - - +
154L GLY 3.5 0.6 - - - -
155L ILE* 1.3 79.0 - - - +
157L VAL* 1.3 84.0 + - + +
159L ARG* 3.3 4.2 + - - +
160L ASP* 3.1 35.9 + - - +
108S ARG 3.3 12.5 - - - +
109S GLU* 3.1 30.9 - - - +
110S VAL* 3.6 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA* 5.8 4.3 - - + -
216B ASP* 3.5 41.3 - - + +
220B PHE* 5.2 4.0 - - + -
153L HIS* 3.7 34.8 - - + +
154L GLY 3.3 2.0 + - - +
156L GLN* 1.3 94.4 - - + +
158L GLU* 1.3 57.5 + - - +
160L ASP* 3.2 8.3 + - - +
161L LYS* 2.9 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153L HIS* 4.7 0.8 - - - +
154L GLY 3.0 19.0 + - - +
155L ILE* 3.7 4.0 - - - +
157L VAL* 1.3 76.5 - - - +
159L ARG* 1.3 62.9 + - - +
161L LYS* 3.3 2.4 + - - +
162L LEU* 3.1 40.4 + - + +
169L LEU* 4.1 4.3 - - + +
199L PHE* 4.0 5.5 - - - -
290L LEU* 3.8 35.8 - - + +
324L ASP* 3.8 13.3 - - - +
325L HIS* 2.7 41.8 + - - -
375L LEU* 3.5 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 159 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155L ILE* 3.0 26.7 + - + +
156L GLN* 3.8 4.9 - - - +
158L GLU* 1.3 78.5 - - + +
160L ASP* 1.3 52.2 + - - +
162L LEU* 5.0 1.6 - - - -
163L ASN* 2.7 31.7 + - - -
164L LYS* 2.9 45.3 + - + +
165L TYR* 3.6 26.5 - - + +
166L GLY 4.7 3.8 - - - -
167L ARG 3.0 19.8 + - - -
168L PRO* 4.6 0.2 - - - +
169L LEU* 4.2 21.7 - - + +
375L LEU* 5.4 6.3 - - + +
396L ASP* 2.7 34.9 + - - +
397L ASP* 3.0 26.3 + - - +
398L SER 4.7 0.6 - - - +
108S ARG* 5.7 0.4 - - - +
110S VAL* 5.5 10.5 - - + -
111S GLN 5.1 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B SER* 4.5 4.2 + - - -
183B LYS* 3.4 33.6 + - + +
220B PHE* 3.6 27.3 - - + -
156L GLN* 3.1 35.2 + - - +
157L VAL* 3.5 9.8 - - - +
159L ARG* 1.3 73.7 - - - +
161L LYS* 1.3 64.2 - - - +
163L ASN* 3.5 8.5 + - - -
165L TYR* 2.8 28.4 + - - -
65S ARG* 4.2 5.2 - - - +
109S GLU 4.8 1.7 - - - +
110S VAL* 5.4 3.1 - - - +
111S GLN* 5.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ARG* 5.6 0.8 - - - +
216B ASP* 2.8 33.3 + - - +
219B LEU* 4.0 19.6 - - + +
220B PHE* 3.8 18.6 - - + -
153L HIS* 3.6 22.0 + - - -
157L VAL* 2.9 31.7 + - + +
158L GLU* 3.9 6.3 - - - +
160L ASP* 1.3 73.1 - - - +
162L LEU* 1.3 67.1 + - + +
288L GLY* 4.6 11.7 + - - -
290L LEU* 5.5 8.9 - - + +
60S GLY* 3.8 25.3 - - - +
62S TYR* 3.9 9.4 - - - -
65S ARG* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158L GLU* 3.1 33.4 + - + +
159L ARG* 4.3 1.8 - - - +
161L LYS* 1.3 81.3 - - + +
163L ASN* 1.3 71.5 + - - +
164L LYS* 3.4 28.5 + - + +
169L LEU* 4.8 3.1 - - + -
199L PHE* 3.7 35.9 - - + -
235L ILE* 3.4 38.5 - - + +
236L LYS 6.1 0.2 - - - -
263L PRO* 4.3 18.2 - - + -
290L LEU* 4.1 18.4 - - + -
13S GLU* 4.9 1.2 - - - +
60S GLY* 6.2 0.7 - - - -
62S TYR* 5.0 2.9 - - + -
----------------------------------------------------------
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