Contacts of the helix formed by residues 114 - 122 (chain B) in PDB entry 1V2E
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 VAL 114 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLN 5.5 0.7 - - - +
250A TRP* 4.0 28.0 - - + +
253A PHE* 6.2 1.6 - - + -
88B THR* 4.6 18.2 - - + +
91B LEU* 4.5 16.6 - - + -
112B PHE* 2.6 37.6 + - + -
113B ASP* 1.3 86.3 - - - +
115B TYR* 1.3 63.0 + - + +
117B PRO* 3.2 2.5 - - - +
118B ASP* 2.6 61.9 + - - +
1520B KMT 5.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.7 27.8 - - + -
95B LEU* 3.8 7.6 - - + +
107B VAL* 4.3 15.9 - - + +
108B LEU 5.5 0.2 - - - -
111B PHE* 3.9 10.5 - - + -
112B PHE* 2.9 45.7 + + + +
114B VAL* 1.3 80.2 - - + +
116B LEU* 1.3 74.2 + - + +
118B ASP* 3.7 5.1 - - - +
119B ALA* 3.1 22.2 + - - +
157B LEU* 3.6 38.8 - - + +
159B ASN* 2.6 38.4 + - + -
162B MET* 6.4 1.3 - - + -
163B ASN 5.9 0.7 - - - -
191B ASP* 2.9 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B VAL* 4.4 9.4 - - + -
111B PHE* 3.2 54.5 - - + -
112B PHE 4.7 0.6 + - - -
113B ASP 5.0 0.2 - - - -
115B TYR* 1.3 78.0 - - + +
117B PRO* 1.3 66.5 - - + +
119B ALA* 3.0 6.0 + - - +
120B PHE* 2.5 40.0 + - + +
126B ALA* 4.7 12.6 - - + +
128B LEU* 4.2 11.9 - - + -
338B LEU* 4.5 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A TRP* 3.8 41.3 - - + +
9B ALA* 4.4 12.8 - - + +
111B PHE* 5.8 0.7 - - + -
113B ASP 3.1 28.3 - - - +
114B VAL 3.2 8.1 - - - +
116B LEU* 1.3 93.8 - - + +
118B ASP* 1.3 51.5 + - - +
120B PHE* 3.4 6.6 - - + +
121B LEU* 2.6 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A TRP* 3.8 10.6 - - - +
91B LEU* 4.1 4.9 - - - +
92B TYR* 3.2 47.2 + - - +
95B LEU* 3.3 25.4 - - + +
96B GLN* 4.3 3.3 - - - +
114B VAL* 2.6 44.0 + - - +
115B TYR* 4.1 1.2 + - - -
116B LEU 3.1 0.4 - - - -
117B PRO* 1.3 75.0 - - - +
119B ALA* 1.3 67.7 + - - +
121B LEU* 3.0 7.6 + - - +
122B ALA* 2.8 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.8 11.5 - - + +
99B VAL* 5.3 2.5 - - - -
105B VAL* 5.0 12.8 - - + -
107B VAL* 5.8 0.7 - - + -
115B TYR 3.1 11.1 + - - +
116B LEU 3.0 6.2 + - - +
118B ASP* 1.3 76.9 - - - +
120B PHE* 1.3 66.2 + - - +
122B ALA* 2.9 22.8 + - - +
123B GLY 3.4 1.9 + - - -
124B ALA* 3.4 17.9 + - + +
125B LYS 5.1 0.7 - - - -
126B ALA* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 3.8 22.2 - - + -
8B GLU* 2.9 46.7 - - + -
9B ALA* 4.5 13.0 - - + -
116B LEU* 2.5 21.7 + - + +
117B PRO* 3.4 8.3 - - + +
119B ALA* 1.3 72.6 - - - +
121B LEU* 1.3 70.2 + - + +
123B GLY* 3.0 21.0 + - - -
124B ALA 4.2 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 4.5 6.8 + - - +
247A MET* 4.2 21.3 - - + -
250A TRP* 3.9 29.4 - - + -
6B ARG* 3.3 50.5 - - + +
9B ALA* 4.7 5.6 - - + -
92B TYR* 4.3 21.1 - - + -
96B GLN* 3.6 20.3 + - - +
117B PRO 2.6 25.7 + - - +
118B ASP* 3.0 6.0 + - - +
120B PHE* 1.3 78.4 - - + +
122B ALA* 1.3 57.2 + - - +
123B GLY 3.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.3 12.8 + - - +
95B LEU 3.7 15.7 - - - +
96B GLN* 3.7 15.7 - - - +
99B VAL* 3.4 25.8 - - + +
100B GLY* 3.2 21.3 - - - -
101B PRO* 4.2 1.2 - - - +
118B ASP 2.8 11.0 + - - +
119B ALA* 2.9 13.4 + - - +
121B LEU* 1.3 76.6 - - - +
123B GLY* 1.3 58.0 + - - +
----------------------------------------------------------
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