Contacts of the strand formed by residues 2225 - 2228 (chain B) in PDB entry 1V9P
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 PHE2225 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2124B VAL* 4.9 5.6 - - + -
2126B LEU* 3.4 42.6 - - + -
2158B ILE* 4.3 11.9 - - + -
2171B VAL* 3.2 27.4 - - + -
2173B GLY* 3.2 27.1 - - - -
2174B GLU 5.3 0.4 - - - -
2223B ALA* 3.9 22.9 - - + -
2224B THR* 1.3 78.3 + - - +
2226B TYR* 1.3 67.2 + - - +
2244B LEU* 5.1 0.7 - - - +
2247B LEU* 3.9 20.5 - - + +
2252B PHE* 3.8 11.2 - + + -
2253B PRO* 3.0 35.4 + - + +
2254B VAL* 4.0 11.2 - - + +
2256B HIS* 3.4 15.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR2226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2082B MET* 5.9 0.9 - - - +
2116B GLU* 3.7 22.9 - - - +
2119B VAL* 5.9 1.3 - - + -
2123B SER* 3.6 12.3 + - - -
2172B ARG* 2.9 25.0 + - + -
2173B GLY 3.2 10.5 + - - -
2174B GLU* 3.2 34.3 + - + +
2224B THR* 4.5 5.6 - - + -
2225B PHE* 1.3 79.3 - - - +
2227B ALA* 1.3 72.9 + - + +
2240B GLN* 3.6 20.8 + - - +
2243B LEU* 4.8 0.2 - - - -
2244B LEU* 4.7 6.3 - - + -
2247B LEU* 3.8 10.1 - - - -
2256B HIS* 4.1 6.1 - + - +
2291B LYS* 4.0 5.7 + - - -
2700B AMP 3.2 59.3 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2171B VAL* 3.7 5.4 - - - +
2172B ARG* 3.1 34.0 + - + +
2226B TYR* 1.3 97.6 - - + +
2228B LEU* 1.3 76.6 + - - +
2240B GLN* 4.8 2.2 - - - +
2243B LEU* 4.3 8.3 - - - -
2247B LEU* 3.7 4.9 - - - +
2291B LYS* 4.6 10.1 - - - +
2298B TRP* 6.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2169B LEU* 3.4 34.3 - - + -
2170B GLU 3.1 7.2 - - - +
2171B VAL* 3.9 13.5 - - + -
2172B ARG* 4.4 2.9 - - - -
2227B ALA* 1.3 88.4 - - - +
2229B GLY* 1.3 63.9 + - - +
2231B GLY 4.7 0.4 - - - -
2232B LEU* 3.6 49.4 - - + +
2235B SER* 4.8 6.3 - - - -
2237B LEU* 4.3 15.0 - - + -
2243B LEU* 4.1 13.5 - - + +
2246B TRP* 4.7 10.3 - - + -
2247B LEU* 4.2 11.0 - - + -
----------------------------------------------------------
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