Contacts of the helix formed by residues 146 - 155 (chain B) in PDB entry 1VI9
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 146 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B HIS* 3.3 29.9 + - - -
145B PRO* 1.3 78.1 - - - +
147B LEU* 1.3 67.8 + - - +
148B VAL* 3.5 4.5 + - - +
149B GLU* 2.9 54.3 + - - +
150B LEU* 2.9 17.4 + - - +
181B VAL* 4.5 1.8 - - - -
182B LYS* 3.6 24.1 - - + +
183B HIS* 3.9 19.7 + - + +
298B SO4 5.0 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ASN* 1.3 72.1 - - - +
148B VAL* 1.3 68.8 + - + +
150B LEU* 3.0 13.7 + - + +
151B GLU* 2.9 28.0 + - + +
158B VAL* 3.9 31.4 - - + +
181B VAL* 4.6 4.5 - - + +
183B HIS 3.1 21.3 + - - +
184B LEU* 3.4 20.4 - - + +
185B ALA* 4.4 6.3 - - + -
186B ARG* 3.8 31.9 - - + +
187B ALA* 3.8 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLY 5.4 1.3 - - - +
117B HIS* 3.6 31.0 - - + +
119B GLU* 6.0 1.6 - - - +
146B ASN* 3.4 3.6 + - - +
147B LEU* 1.3 83.0 - - + +
149B GLU* 1.3 65.4 + - - +
151B GLU* 2.9 27.8 + - - +
152B ILE* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 3.3 25.7 - - + +
114B VAL* 3.7 5.0 - - - +
115B MSE 3.1 32.2 + - + +
117B HIS* 2.6 30.0 + - + +
145B PRO* 3.5 14.6 - - + +
146B ASN* 2.9 30.4 + - - +
148B VAL* 1.3 71.6 - - - +
150B LEU* 1.3 56.4 + - - +
152B ILE* 3.3 1.4 + - - +
153B LEU* 2.9 34.5 + - - +
182B LYS* 2.8 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO* 3.5 15.9 - - + +
146B ASN 2.9 14.1 + - - +
147B LEU* 3.2 11.2 - - + +
149B GLU* 1.3 72.5 - - - +
151B GLU* 1.3 61.9 + - - +
153B LEU* 3.3 2.5 + - - +
154B CYS* 2.9 29.2 + - + -
158B VAL* 4.1 26.0 - - + -
164B ALA* 4.2 8.1 - - + +
167B ALA* 3.8 30.5 - - + -
168B ALA* 4.2 4.0 - - - +
171B LEU* 3.9 25.1 - - + -
179B VAL* 5.3 0.2 - - + -
181B VAL* 4.0 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 2.9 20.3 + - + +
148B VAL* 3.4 20.7 - - + +
150B LEU* 1.3 74.9 - - - +
152B ILE* 1.3 60.7 + - + +
154B CYS* 3.3 2.4 + - - -
155B GLU* 2.8 27.2 + - - -
156B HIS 3.2 20.5 + - - +
157B ALA* 3.5 7.7 - - - +
158B VAL* 2.8 43.2 + - + +
186B ARG* 2.8 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B MSE 3.6 36.1 - - + -
116B GLY 6.2 0.4 - - - +
129B ALA* 5.0 6.5 - - + +
133B VAL* 3.8 17.0 - - + +
148B VAL* 2.9 34.4 + - + +
149B GLU 3.8 5.8 - - - +
151B GLU* 1.3 80.7 - - + +
153B LEU* 1.3 61.3 + - - +
155B GLU* 3.3 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 3.9 15.0 - - + -
115B MSE 3.8 16.2 - - + -
132B HIS* 3.9 11.7 - - + +
133B VAL* 3.7 33.4 - - - +
137B LEU* 4.0 20.1 - - + +
143B ILE* 3.9 15.3 - - + -
145B PRO* 3.8 22.7 - - + -
149B GLU 2.9 24.3 + - - +
150B LEU 3.3 4.5 + - - +
152B ILE* 1.3 75.9 - - - +
154B CYS* 1.3 59.6 + - - +
155B GLU* 4.3 8.8 - - - +
171B LEU* 3.9 26.0 - - + +
174B GLN* 5.0 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 2.9 21.3 + - + +
151B GLU* 4.0 1.8 - - - -
153B LEU* 1.3 76.2 - - - +
155B GLU* 1.3 70.0 + - - +
156B HIS* 3.4 58.3 - - - -
158B VAL* 4.1 1.6 - - - -
167B ALA* 4.0 17.0 - - + +
170B GLU* 4.0 16.5 - - + +
171B LEU* 4.1 14.4 - - + -
174B GLN* 6.1 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
133B VAL* 4.3 15.0 - - + +
151B GLU 2.8 10.8 + - - -
152B ILE* 3.3 15.1 + - - +
153B LEU 4.3 8.6 - - - +
154B CYS* 1.3 77.5 - - - +
156B HIS* 1.3 62.2 + - - +
174B GLN* 5.6 2.3 - - - +
----------------------------------------------------------
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