Contacts of the strand formed by residues 147 - 152 (chain A) in PDB entry 1VCN
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 ILE 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 3.4 24.7 - - + +
15A VAL* 4.1 17.3 - - + -
38A LEU* 3.8 39.0 - - + -
43A TYR* 3.7 43.1 - - + -
44A ARG 3.1 3.3 + - - +
45A VAL* 3.3 30.5 - - + +
46A THR 3.3 3.8 + - - -
145A ALA* 4.1 2.4 - - - +
146A GLU* 1.3 84.1 - - - +
148A VAL* 1.3 64.4 + - - +
149A VAL* 4.1 0.7 - - + -
275A LEU* 4.4 4.0 - - + -
277A LEU* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 4.0 13.2 - - - -
13A LYS 2.9 9.6 + - - +
14A TYR* 3.2 40.6 - - + -
15A VAL 3.1 22.1 + - - +
46A THR* 3.4 23.3 - - + +
48A ILE* 3.7 31.6 - - + -
136A ILE* 5.0 0.2 - - + -
140A ALA* 4.3 7.6 - - + -
145A ALA* 4.5 1.6 - - + -
147A ILE* 1.3 74.1 - - - +
149A VAL* 1.3 63.3 + - - +
150A VAL* 3.7 12.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.4 15.0 - - + +
17A ILE* 3.7 22.0 - - + -
31A THR* 3.5 31.2 - - + +
34A LEU* 4.4 8.3 - - + -
35A GLY* 4.4 8.7 - - - -
38A LEU* 4.1 24.9 - - + -
45A VAL* 4.2 11.7 - - + -
46A THR 2.9 13.2 + - - +
47A ALA* 3.2 7.1 - - + +
48A ILE 2.8 25.8 + - - +
147A ILE* 4.8 1.1 - - + -
148A VAL* 1.3 73.4 - - - +
150A VAL* 1.3 62.0 + - - +
151A GLU 4.0 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 4.8 1.8 - - + -
15A VAL 2.9 8.7 + - - -
16A PHE* 3.4 35.0 - - + +
17A ILE* 2.9 27.8 + - - +
48A ILE* 3.5 21.8 - - + +
50A ILE* 3.7 32.1 - - + -
136A ILE* 4.2 15.3 - - + -
148A VAL* 3.8 24.5 - - + +
149A VAL* 1.3 75.0 - - - +
151A GLU* 1.3 61.2 + - - +
152A VAL* 3.9 2.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 3.6 8.3 - - + +
27A LYS* 2.6 52.1 + - + +
28A GLY* 3.5 13.7 + - - -
31A THR* 3.2 27.6 + - + +
48A ILE 2.8 9.7 + - - +
49A LYS* 3.7 12.6 - - - +
50A ILE* 2.8 30.6 + - - +
81A ASP* 4.1 2.9 - - - +
85A TYR* 2.7 35.1 + - - +
149A VAL 4.0 1.2 + - - -
150A VAL* 1.3 71.9 - - - +
152A VAL* 1.3 60.9 + - - +
153A GLY 3.7 0.3 + - - -
610A SO4 3.6 7.3 + - - -
620A SO4 5.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 5.6 0.2 - - + -
17A ILE 3.0 11.8 + - - +
18A THR* 4.0 22.5 - - + -
19A GLY 4.5 0.5 + - - -
27A LYS* 2.9 23.8 + - - -
50A ILE* 4.0 29.8 - - + -
52A PRO* 4.8 0.7 - - + -
150A VAL* 4.6 5.6 - - + +
151A GLU* 1.3 74.3 - - - +
153A GLY* 1.3 72.3 + - - +
154A GLY 4.1 1.6 - - - +
156A VAL* 6.5 0.2 - - + -
161A SER* 4.7 7.6 - - - -
164A PHE* 4.6 10.5 - - + -
165A LEU* 4.4 16.8 - - + -
168A ILE* 4.3 20.4 - - + -
----------------------------------------------------------
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