Contacts of the strand formed by residues 245 - 250 (chain A) in PDB entry 2AVD
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 245 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A TYR* 3.6 22.2 - - - +
199A LEU* 3.6 29.8 - - + -
239A ILE* 4.5 0.7 - - + +
242A ASP* 3.3 21.2 - - + +
243A VAL 3.1 1.4 - - - +
244A ARG* 1.3 86.7 - - - +
246A TYR* 1.3 63.5 + - - +
247A ILE* 3.5 20.9 - - + -
259A ALA* 4.0 17.0 - - + -
260A PHE 3.1 17.9 - - - +
262A ILE* 4.0 8.4 - - - +
64B ARG* 2.8 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLY* 5.1 2.4 - - - -
245A VAL* 1.3 72.1 - - - +
247A ILE* 1.3 63.6 + - - +
260A PHE* 2.8 72.4 + + + +
261A LYS 4.3 7.8 + - - -
262A ILE* 3.6 22.4 - - + -
64B ARG* 4.1 7.9 - - - +
96B ASN* 3.3 50.0 - - - +
99B ARG* 3.6 46.1 + - + +
100B LEU* 3.3 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.8 36.6 - - + +
240A ARG* 4.0 6.7 - - - +
245A VAL* 3.5 26.0 - - + -
246A TYR* 1.3 80.8 - - - +
248A SER* 1.3 59.6 + - - +
249A LEU* 6.3 0.2 - - + -
257A THR* 5.0 3.1 - - + -
258A LEU 3.3 6.7 - - - +
259A ALA* 4.1 7.0 - - + -
61B ARG 3.6 23.8 - - - +
62B SER* 3.6 21.3 - - - +
64B ARG* 4.0 19.3 - - - +
92B GLN* 2.9 22.5 + - - +
96B ASN* 2.8 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 1.3 72.5 + - - +
249A LEU* 1.3 59.2 + - - +
250A LEU* 4.1 13.2 - - - -
256A LEU 3.8 0.9 - - - +
257A THR* 3.4 3.4 - - - +
258A LEU* 2.7 44.0 + - - +
260A PHE* 4.6 1.5 - - - -
62B SER* 4.6 3.4 - - - -
89B GLU 5.0 1.0 + - - -
92B GLN* 4.3 3.3 - - - +
93B LEU* 3.5 37.6 + - - +
96B ASN* 2.9 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A VAL* 3.8 22.9 - - + -
214A LEU* 4.4 14.4 - - + -
236A ASN* 5.1 5.8 - - - +
247A ILE* 6.3 0.7 - - + -
248A SER* 1.3 74.8 - - - +
250A LEU* 1.3 74.9 + - - +
251A PRO* 4.4 0.9 - - - +
255A GLY* 4.5 1.8 - - - -
256A LEU 3.4 3.8 - - - +
257A THR* 3.5 22.7 - - + +
57B TYR* 5.1 3.8 - - + -
58B LEU* 3.4 54.0 - - + +
61B ARG* 4.4 20.2 - - + +
62B SER* 3.6 24.1 + - - +
89B GLU* 5.4 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.8 29.6 - - + -
248A SER* 4.3 13.5 - - - -
249A LEU* 1.3 83.5 - - - +
251A PRO* 1.4 65.3 - - + +
252A LEU* 3.0 17.0 + - + +
255A GLY* 3.5 4.2 - - - -
256A LEU* 2.8 45.8 + - + +
258A LEU* 3.9 21.1 - - + -
58B LEU* 4.0 3.6 - - - -
89B GLU* 5.8 2.2 - - + +
93B LEU* 4.3 13.2 - - + -
250B LEU* 4.4 13.7 - - + -
252B LEU* 4.0 26.9 - - + -
----------------------------------------------------------
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