Contacts of the strand formed by residues 2321 - 2326 (chain B) in PDB entry 3ISW
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 PHE2321 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2243B ALA* 4.5 8.3 - - + -
2248B LEU* 3.6 50.5 - - + +
2306B GLU* 3.5 2.8 - - - -
2307B VAL* 2.6 41.0 + - + +
2309B VAL* 4.1 19.3 - - + -
2316B ILE* 4.5 9.4 - - + -
2317B PRO 4.0 5.4 - - - -
2318B ASP* 3.3 38.4 - - + -
2319B SER* 4.0 12.6 - - - -
2320B PRO* 1.3 73.4 - - - +
2322B VAL* 1.3 58.2 + - - +
2323B VAL* 3.2 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2248B LEU 5.0 2.3 - - - +
2249B GLU* 4.6 3.1 - - - +
2304B ASP* 5.4 10.8 - - + +
2305B TYR 3.7 8.7 - - - +
2306B GLU* 4.4 17.5 - - + +
2320B PRO* 3.7 6.1 + - + +
2321B PHE* 1.3 67.6 - - - +
2323B VAL* 1.3 63.7 + - - +
2324B PRO* 3.8 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2247B GLY 3.9 6.5 - - - +
2248B LEU* 3.5 35.9 - - - +
2249B GLU 4.4 0.2 - - - -
2250B ARG* 4.0 21.5 - - - -
2251B ALA* 4.3 3.8 - - + +
2297B TYR* 3.7 19.7 - - - +
2304B ASP* 5.1 0.2 - - - -
2305B TYR* 3.0 38.4 + - + +
2307B VAL* 4.1 11.0 - - + -
2321B PHE* 3.2 18.6 + - + +
2322B VAL* 1.3 74.8 - - - +
2324B PRO* 1.4 67.2 - - - +
2325B VAL* 3.8 3.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2249B GLU 3.3 21.1 - - - +
2250B ARG* 3.7 8.2 - - + +
2251B ALA 3.1 24.1 + - - +
2303B GLY 4.0 5.6 - - - +
2304B ASP* 4.0 18.4 - - - +
2322B VAL* 3.8 11.4 - - + +
2323B VAL* 1.4 82.9 - - - +
2325B VAL* 1.3 60.2 + - - +
2326B ALA 4.2 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2251B ALA* 3.3 16.8 - - + -
2252B GLU 3.8 3.6 - - - -
2253B ALA* 3.3 37.9 - - + +
2297B TYR* 5.8 1.6 - - + +
2299B VAL* 3.8 22.4 - - + -
2301B GLU 3.9 17.7 - - - +
2302B PRO* 3.4 4.2 - - + +
2303B GLY* 2.9 38.2 + - - +
2305B TYR* 3.9 16.2 - - + -
2323B VAL* 4.3 5.8 - - + +
2324B PRO* 1.3 78.7 - - - +
2326B ALA* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA2326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2251B ALA 3.2 9.0 + - - +
2252B GLU* 3.4 7.8 - - + -
2253B ALA 3.0 24.3 + - - -
2302B PRO* 4.6 4.9 - - - -
2324B PRO 4.2 0.8 - - - -
2325B VAL* 1.3 75.4 - - - +
2327B SER* 1.3 66.1 - - - +
----------------------------------------------------------
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