Contacts of the strand formed by residues 130 - 139 (chain C) in PDB entry 3VA2
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 130 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C SER 4.1 2.2 - - - +
129C ILE* 1.3 81.0 - - - +
131C ASN* 1.3 90.2 + - - +
132C LEU 3.6 1.1 - - - -
157C TRP* 3.4 1.7 - - - -
158C LEU* 2.6 52.7 + - + +
160C GLY* 4.0 25.1 - - - +
161C THR 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C VAL* 1.3 93.5 - - - +
132C LEU* 1.3 64.3 + - - +
133C THR* 3.2 12.9 + - - +
156C THR 3.3 8.1 - - - +
157C TRP* 3.6 2.9 - - - -
158C LEU* 4.3 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ILE* 4.0 8.5 - - + +
130C VAL 3.6 1.6 - - - -
131C ASN* 1.3 72.2 - - - +
133C THR* 1.3 60.8 + - - +
134C CYS* 3.9 14.8 - - - -
155C CYS* 4.3 3.4 - - + -
156C THR 3.4 14.4 - - - +
157C TRP* 4.0 20.4 - - + -
213C VAL* 3.9 25.4 - - + +
215C VAL* 4.3 13.5 - - + -
227C PHE* 3.7 38.7 - - + -
229C GLN* 3.6 29.2 + - + +
231C PHE* 4.1 13.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ASN* 3.5 11.9 + - - +
132C LEU* 1.3 75.9 + - - +
134C CYS* 1.3 68.2 + - - +
135C THR* 5.0 5.6 + - - +
154C HIS 3.8 0.9 - - - +
155C CYS* 3.3 1.2 - - - -
156C THR* 2.8 51.7 + - - +
231C PHE* 5.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 3.9 10.8 - - - -
133C THR* 1.3 79.9 - - - +
135C THR* 1.3 66.3 + - - +
153C LEU* 4.2 7.4 - - + -
154C HIS 3.3 3.6 - - - -
155C CYS* 2.0 44.9 - - - -
211C LEU* 5.2 0.2 - - + -
213C VAL* 4.2 9.0 - - + -
231C PHE* 3.9 39.5 - - + -
236C ILE* 3.6 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C THR* 5.0 6.8 - - - +
134C CYS* 1.3 77.8 + - - +
136C THR* 1.3 72.2 + - - +
137C ASN* 5.6 1.3 - - + -
152C SER* 3.6 0.9 + - - +
153C LEU* 3.6 3.4 - - - +
154C HIS* 2.8 47.8 + - + +
236C ILE* 3.7 13.0 + - - +
238C GLN* 4.0 17.9 - - + +
321C LEU* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C THR* 1.3 75.8 - - - +
137C ASN* 1.3 61.7 + - - +
151C VAL* 4.2 10.5 - - + -
152C SER 3.1 13.5 - - - +
153C LEU* 3.9 13.7 - - + -
203C ILE* 4.0 19.3 - - + -
211C LEU* 4.4 0.2 - - + -
233C LEU* 4.4 8.7 + - + +
236C ILE* 3.1 31.8 + - + +
237C ASP* 3.1 26.9 - - - +
238C GLN* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C THR* 4.3 2.9 + - + -
136C THR* 1.3 75.6 - - - +
138C THR* 1.3 67.4 + - - +
139C THR* 3.9 21.8 + - - +
150C GLN 3.9 0.2 - - - +
151C VAL* 3.4 5.7 - - - -
152C SER* 2.9 42.7 + - - +
237C ASP* 3.8 4.0 - - - -
238C GLN* 2.9 27.6 - - + +
240C ASN* 3.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ASN* 1.3 79.2 + - - +
139C THR* 1.3 67.2 + - - +
149C TYR* 3.7 23.8 - - + -
150C GLN 3.4 12.6 - - - +
151C VAL* 4.1 5.4 - - - +
205C SER* 4.0 18.4 + - - -
237C ASP* 4.1 16.1 + - - -
238C GLN 4.8 0.2 + - - -
240C ASN* 2.6 30.9 + - - +
262C VAL* 3.3 10.2 - - - +
263C SER* 3.9 24.1 - - - -
264C ALA 4.2 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ASN* 3.9 20.1 + - - +
138C THR* 1.3 79.3 - - - +
140C GLU* 1.3 60.6 + - - +
149C TYR* 3.2 10.0 - - - +
150C GLN* 2.3 60.7 + - - +
152C SER* 5.2 5.1 - - - +
240C ASN* 5.2 0.7 - - - +
262C VAL* 3.8 11.2 - - - -
----------------------------------------------------------
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