Contacts of the strand formed by residues 150 - 157 (chain A) in PDB entry 3VNG
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 LEU 150 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE* 4.2 2.7 - - - -
146A VAL* 3.3 5.0 - - - +
147A LEU 3.0 31.3 + - - +
148A ASN* 3.6 15.3 - - + +
149A ARG* 1.3 88.6 - - + +
151A LEU* 1.3 61.3 + - - +
152A TYR* 3.4 15.8 - - + +
168A CYS* 3.5 26.5 - - - -
169A TYR 3.6 9.2 - - - +
170A TYR* 3.4 45.5 - - + +
171A PRO* 4.3 1.3 - - + -
172A GLU* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY* 3.7 21.1 - - - -
100A ILE* 3.8 14.5 - - + +
105A TYR* 3.6 34.1 - - + -
107A VAL* 3.8 17.3 - - + -
119A VAL* 4.8 1.1 - - + -
144A VAL* 3.3 29.8 - - + -
145A ALA 3.8 0.7 - - - -
146A VAL* 3.7 11.9 - - + -
150A LEU* 1.3 72.5 - - - +
152A TYR* 1.3 61.8 + - - +
168A CYS* 3.4 3.1 - - - -
169A TYR* 2.7 49.8 + - + +
176A TRP* 3.9 18.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
143A GLY 3.5 0.7 - - - +
144A VAL* 3.1 29.9 - - - +
145A ALA* 2.8 20.3 + - + +
147A LEU* 3.8 25.7 + - + +
148A ASN* 5.7 0.3 + - - -
150A LEU* 3.4 31.4 - - + +
151A LEU* 1.3 76.9 - - - +
153A ALA* 1.3 59.2 + - - +
154A VAL* 4.5 13.8 - - + +
167A GLU 3.4 9.2 - - - -
168A CYS* 3.7 21.6 - - + -
179A ILE* 4.0 30.3 - - + -
198A ILE* 4.1 22.0 - - + -
216A TYR* 4.2 12.9 - + - -
218A VAL* 3.7 23.1 - - + +
223A TRP* 6.1 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 4.3 4.7 - - + -
135A MET* 3.5 31.4 - - - -
139A ARG* 4.1 6.6 - - - -
142A VAL* 3.9 10.1 - - + -
143A GLY 3.4 4.7 - - - -
144A VAL* 4.5 1.6 - - + -
151A LEU 4.2 0.8 + - - -
152A TYR* 1.3 72.7 - - - +
154A VAL* 1.3 59.8 + - - +
166A ALA* 3.3 4.7 - - - +
167A GLU* 3.0 35.7 + - + +
176A TRP* 3.8 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLY 4.7 0.3 - - - +
142A VAL* 3.6 1.6 - - - +
143A GLY* 2.7 42.9 + - - +
152A TYR* 4.5 12.8 - - + -
153A ALA* 1.3 81.3 - - - +
155A GLY* 1.3 68.7 + - - +
156A GLY 3.7 0.5 + - - -
166A ALA* 4.1 12.6 - - + -
182A MET* 3.4 35.0 - - + -
186A ARG 4.5 1.0 - - - +
189A ALA* 5.9 2.1 - - - +
191A VAL* 4.1 28.5 - - + +
198A ILE* 4.7 1.6 - - + -
200A ALA* 4.5 0.2 - - + -
223A TRP* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 2.8 31.2 + - - +
142A VAL* 4.0 1.3 - - - +
154A VAL* 1.3 78.5 - - - +
156A GLY* 1.3 59.8 + - - -
163A LEU* 3.4 16.8 - - - -
165A SER 2.9 20.4 + - - -
182A MET* 3.9 6.7 - - - -
186A ARG 3.3 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE 3.3 15.7 - - - -
141A GLY 3.5 14.1 + - - -
142A VAL* 4.2 0.9 - - - -
154A VAL 3.7 0.6 + - - -
155A GLY* 1.3 75.2 - - - -
157A PHE* 1.3 56.4 + - - -
162A ARG* 3.4 1.0 - - - -
163A LEU* 2.7 29.4 + - - -
186A ARG 2.7 12.8 + - - -
187A SER* 3.4 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A HIS* 3.9 15.3 - + - -
138A ARG 3.9 3.1 - - - -
139A ARG* 3.6 0.7 - - - -
140A ILE* 3.0 50.4 + - + +
156A GLY* 1.3 73.8 - - - +
158A ASP* 1.3 59.7 + - - +
159A GLY* 3.2 43.0 + - - -
160A THR* 3.3 24.9 - - - -
161A ASN 3.3 9.2 - - - -
162A ARG* 3.2 49.1 - - + -
163A LEU* 4.3 0.8 - - - +
187A SER* 4.4 8.3 - - - +
----------------------------------------------------------
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