Contacts of the helix formed by residues 151 - 163 (chain A) in PDB entry 2VMX
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 ASP 151 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLY 3.0 20.1 + - - +
143A VAL 4.5 0.7 - - - -
144A ASP* 4.2 23.3 - - + +
145A PRO* 6.0 0.2 - - - +
149A VAL 3.1 2.9 + - - -
150A ILE* 1.3 69.8 - - - +
152A TYR* 1.3 57.6 + - - +
153A ASP* 3.0 18.0 + - - +
154A ASP* 2.9 30.7 + - + +
155A VAL* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A VAL* 4.7 8.7 - - + -
150A ILE* 3.2 38.6 + - + +
151A ASP* 1.3 69.8 + - - +
153A ASP* 1.3 59.9 + - - +
155A VAL* 3.4 7.1 + - + -
156A ARG* 3.0 22.9 + - - +
174A TYR* 4.9 1.0 + - - -
177A ILE 4.4 3.1 + - - -
178A ILE* 3.8 7.4 - - - +
179A ASP* 2.9 42.0 + - + +
182A LYS* 3.8 33.0 - - + +
183A PHE* 3.5 31.0 - + - -
186A ILE* 3.5 8.0 - - + +
701A MPD 3.4 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASP* 3.0 10.8 + - - +
152A TYR* 1.3 78.9 - - - +
154A ASP* 1.3 56.6 + - - +
156A ARG* 3.5 9.1 + - - +
157A GLU* 2.9 29.1 + - - +
701A MPD 3.9 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.3 7.3 - - - -
142A GLY* 2.8 30.0 + - - +
151A ASP* 2.9 33.0 + - + +
153A ASP* 1.3 75.0 - - - +
155A VAL* 1.3 66.0 + - - +
157A GLU* 4.4 8.1 - - - +
158A LYS* 2.8 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.5 9.5 - - + +
141A TYR* 3.6 41.2 - - + +
150A ILE* 3.8 14.6 - - + -
151A ASP 3.0 14.8 + - - +
152A TYR* 3.6 12.1 - - + +
154A ASP* 1.3 74.7 - - - +
156A ARG* 1.3 58.3 + - - +
159A ALA* 2.9 31.0 + - - +
167A ILE* 4.7 2.2 - - + -
183A PHE* 3.6 29.2 - - + -
186A ILE* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR 3.0 18.8 + - - +
153A ASP* 3.7 9.6 + - - +
155A VAL* 1.3 77.3 - - - +
157A GLU* 1.3 58.0 + - - +
159A ALA* 3.3 1.9 + - - +
160A ARG* 2.9 60.7 + - + +
186A ILE* 3.8 20.4 - - + +
189A GLU* 2.8 42.0 + - - +
701A MPD 3.8 40.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASP 2.9 18.4 + - - +
154A ASP* 4.0 9.0 - - - +
156A ARG* 1.3 76.3 - - - +
158A LYS* 1.3 71.5 + - + +
160A ARG* 3.2 9.7 + - - +
161A LEU* 2.8 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.6 22.4 - - + -
139A VAL* 5.5 0.2 - - + -
140A ALA 3.2 27.4 - - - +
141A TYR* 4.4 0.7 - - - -
154A ASP* 2.8 51.2 + - - +
155A VAL* 3.9 1.3 - - - +
157A GLU* 1.3 86.3 + - + +
159A ALA* 1.3 57.3 + - - +
161A LEU* 4.5 4.7 - - + -
162A HIS* 2.9 58.1 + - + +
164A PRO* 4.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.5 15.8 - - + +
155A VAL 2.9 19.4 + - - +
156A ARG 3.6 4.5 - - - +
157A GLU 3.3 0.2 - - - -
158A LYS* 1.3 76.2 - - - +
160A ARG* 1.3 56.8 + - - +
163A ARG* 2.9 26.0 + - - -
164A PRO* 3.2 11.2 - - + +
167A ILE* 4.0 9.0 - - + -
186A ILE* 3.6 21.5 - - + -
190A VAL* 3.6 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 2.9 57.5 + - + +
157A GLU* 3.2 7.0 + - - +
159A ALA* 1.3 76.0 - - - +
161A LEU* 1.3 63.7 + - - +
163A ARG* 3.5 17.7 - - - +
186A ILE* 6.2 0.2 - - + -
189A GLU* 3.4 25.8 + - + +
190A VAL* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU* 2.8 25.6 + - + +
158A LYS* 3.9 7.6 - - + +
160A ARG* 1.3 80.1 - - - +
162A HIS* 1.3 88.0 + - + +
163A ARG* 3.8 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A THR* 3.8 17.8 + - + +
137A ASN* 6.0 0.4 + - - -
139A VAL* 3.8 48.6 - - + +
158A LYS* 2.9 44.1 + - + +
161A LEU* 1.3 99.1 - - + +
163A ARG* 1.3 71.3 + - - +
164A PRO* 3.4 2.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A THR* 4.5 3.6 - - - -
159A ALA 2.9 13.9 + - - -
160A ARG* 3.5 24.0 - - - +
161A LEU 4.4 3.6 - - - +
162A HIS* 1.3 80.5 - - - +
164A PRO* 1.3 70.9 - - - +
165A LYS* 3.7 0.7 + - - -
189A GLU 5.4 0.8 + - - -
190A VAL* 2.9 40.1 + - - +
191A GLY* 5.1 0.4 - - - -
----------------------------------------------------------
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