Contacts of the helix formed by residues 146 - 158 (chain A) in PDB entry 2VE7
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 LYS 146 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A THR* 1.3 84.2 - - - +
147A PHE* 1.3 64.8 + - - +
148A GLU* 3.1 22.9 + - - +
149A GLU* 3.0 51.0 + - + +
150A GLU* 3.3 11.9 + - + +
153A ARG* 6.3 0.4 - - - +
166A LYS* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 3.5 28.9 - - + -
125A PHE* 5.4 1.8 - + - -
126A LEU* 3.6 38.4 - - + -
142A LEU* 4.8 9.2 - - + -
143A PRO* 5.1 6.3 - - - +
144A ASP 6.4 0.2 - - - -
145A THR 3.3 4.6 + - - +
146A LYS* 1.3 76.2 - - - +
148A GLU* 1.3 79.6 + - + +
149A GLU 3.0 1.7 + - - -
150A GLU* 4.3 8.7 - - - -
151A VAL* 3.3 27.5 + - + +
152A PRO* 4.1 0.2 - - - +
169A MET* 3.4 39.9 - - + -
170A TYR* 4.3 17.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LYS* 3.3 32.0 + - - +
147A PHE* 1.3 91.7 + - + +
149A GLU* 1.3 63.2 + - - +
152A PRO* 3.2 22.9 - - - +
166A LYS* 3.7 50.3 + - + +
169A MET* 3.8 14.6 - - + +
170A TYR* 3.1 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LYS* 3.0 53.0 + - + +
148A GLU* 1.3 86.8 - - - +
150A GLU* 1.3 64.6 + - - +
152A PRO* 3.5 3.7 - - - +
153A ARG* 3.0 42.4 + - - +
166A LYS* 3.1 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 2.5 36.1 + - - +
142A LEU* 5.7 2.0 - - + -
143A PRO* 3.5 34.6 - - + +
145A THR 5.4 0.2 - - - +
146A LYS* 3.3 11.0 + - + +
147A PHE* 4.0 10.8 - - - +
149A GLU* 1.3 77.4 - - - +
151A VAL* 1.3 56.2 + - + +
153A ARG* 2.7 35.1 + - - +
154A ILE* 2.7 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 4.2 13.5 - - + -
126A LEU* 4.1 20.4 - - + -
129A PHE* 3.8 33.9 - - + -
140A TYR* 5.8 0.4 - - - +
142A LEU* 5.3 3.4 - - + -
147A PHE* 3.3 14.4 + - + +
150A GLU* 1.3 80.2 - - + +
152A PRO* 1.4 70.7 - - + +
154A ILE* 3.2 2.4 + - - +
155A PHE* 3.0 48.8 + - + -
164A LEU* 5.2 0.2 - - + -
169A MET* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU 3.2 29.8 - - - +
149A GLU* 3.5 6.1 - - - +
151A VAL* 1.4 92.1 - - + +
153A ARG* 1.3 62.3 + - - +
155A PHE* 3.2 5.1 + - + +
156A LYS* 2.8 23.9 + - - +
164A LEU* 3.5 39.3 - - + +
165A SER 4.6 1.6 - - - +
166A LYS* 5.0 0.7 - - - +
169A MET* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LYS* 6.3 0.2 - - - +
149A GLU* 3.0 42.4 + - - +
150A GLU* 2.7 52.6 + - - +
152A PRO* 1.3 74.7 - - - +
154A ILE* 1.3 65.1 + - - +
156A LYS* 3.1 9.8 + - + +
157A ASP* 2.9 46.6 + - - +
111C CYS* 5.1 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PHE* 3.7 27.6 - - + -
133A TYR* 3.6 50.5 - - + +
140A TYR* 3.3 29.2 - - + +
150A GLU* 2.7 37.6 + - - +
151A VAL 3.2 4.0 + - - +
153A ARG* 1.3 74.2 - - + +
155A PHE* 1.3 64.2 + - + +
157A ASP* 3.3 5.6 + - - +
158A LEU* 3.1 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 5.5 2.7 - + - -
129A PHE* 3.6 25.6 - + - -
151A VAL* 3.0 34.6 + - + +
152A PRO* 3.7 6.1 - - + +
154A ILE* 1.3 75.8 - - + +
156A LYS* 1.3 64.1 + - - +
158A LEU* 3.2 11.4 + - + +
160A TYR* 3.0 53.1 + + + +
162A PHE 5.7 0.2 - - - +
164A LEU* 3.6 23.6 - - + -
184A ALA* 3.3 41.1 - - + -
185A LEU* 4.6 7.4 - - + -
187A TRP* 4.2 8.7 - + - -
188A LEU* 4.1 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PRO 2.8 17.3 + - - +
153A ARG* 3.1 13.2 + - + +
155A PHE* 1.3 73.2 - - - +
157A ASP* 1.3 65.1 + - - +
159A GLY* 2.9 21.5 + - - -
160A TYR 4.0 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ARG* 2.9 40.1 + - - +
154A ILE* 3.9 5.7 + - - +
156A LYS* 1.3 80.7 - - - +
158A LEU* 1.3 60.0 + - - +
159A GLY 3.0 6.2 + - - -
42C PRO* 5.7 2.8 - - - +
46C HIS* 5.7 2.1 + - - -
81C GLY 5.5 0.3 - - - +
110C LEU* 3.4 49.6 - - + +
111C CYS* 3.8 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 3.8 22.2 - - + +
136A LEU* 3.7 20.4 - - + -
154A ILE* 3.1 25.5 + - + +
155A PHE* 3.2 8.2 + - + +
157A ASP* 1.3 75.2 - - - +
159A GLY* 1.3 58.8 + - - +
187A TRP* 3.5 14.8 - - + -
188A LEU* 3.6 30.7 - - + -
191A CYS* 5.4 0.4 - - - -
81C GLY 4.5 1.8 - - - -
82C PHE* 3.3 47.0 - - + +
85C PHE* 4.8 4.3 - - + -
110C LEU* 3.9 28.5 - - + -
----------------------------------------------------------
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