Contacts of the helix formed by residues 154 - 159 (chain B) in PDB entry 1RVC
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 154 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ASN* 2.8 23.2 + - - +
153B ILE* 1.3 81.6 - - - +
155B GLU* 1.3 60.5 + - + +
156B LEU 3.5 1.0 + - - -
157B ASN* 5.1 0.9 + - - +
158B GLU* 5.3 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LYS* 5.0 8.0 + - - -
150B THR 4.3 1.6 - - - +
151B TYR* 3.2 28.7 - - + -
152B ASN* 2.8 52.9 + - - +
154B ASN* 1.3 81.6 - - + +
156B LEU* 1.3 63.0 + - - -
157B ASN 3.2 2.7 - - - -
158B GLU* 2.9 44.0 + - - +
159B ILE* 3.6 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.9 20.9 - - + -
25A SER 3.8 10.1 - - - +
26A ALA* 3.7 28.3 - - - +
27A GLU 4.9 0.2 - - - -
28A GLY* 4.1 9.9 - - - +
153A ILE* 4.6 8.7 - - + -
21B CYS* 3.9 30.2 - - - -
30B ILE* 3.7 25.8 - - + -
152B ASN 3.9 1.6 + - - -
153B ILE* 3.5 17.2 + - + +
154B ASN 3.5 3.2 + - - -
155B GLU* 1.3 75.9 - - - +
157B ASN* 1.3 63.8 + - - +
158B GLU 3.4 0.9 + - - -
159B ILE* 3.6 21.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 4.2 21.2 + - - +
154B ASN 5.1 0.8 + - - +
155B GLU 3.0 1.6 + - - -
156B LEU* 1.3 81.0 + - - +
158B GLU* 1.3 62.0 + - + +
159B ILE 3.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LYS* 5.7 1.9 + - - -
151B TYR* 4.2 13.1 + - + -
154B ASN 5.3 1.0 - - - +
155B GLU* 2.9 39.3 + - + +
157B ASN* 1.3 81.2 - - + +
159B ILE* 1.3 63.7 - - - +
160B PRO* 3.3 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B CYS* 3.3 33.0 - - + +
30B ILE* 3.6 30.7 - - + -
32B PRO* 4.4 8.5 - - + -
151B TYR* 3.6 38.1 - - + -
155B GLU 3.7 9.4 - - - +
156B LEU* 3.6 31.2 + - + +
157B ASN 3.5 3.5 - - - +
158B GLU* 1.3 76.6 - - - +
160B PRO* 1.3 77.3 - - + +
161B LYS* 3.4 12.5 + - - +
----------------------------------------------------------
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