Contacts of the strand formed by residues 942 - 945 (chain B) in PDB entry 1OFD
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 942 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B CYS* 4.5 9.2 - - + -
873B GLY* 5.7 0.2 - - - -
898B LYS* 3.9 26.9 - - + -
899B SER 3.0 16.0 + - - +
900B ASN* 3.5 31.6 - - + +
901B SER 2.9 28.1 + - - -
940B SER* 3.6 4.3 - - - -
941B ALA* 1.3 78.9 - - - +
943B LYS* 1.3 63.8 + - - +
962B GLN* 3.4 25.1 - - + +
963B LEU 4.7 0.7 - - - -
964B GLU* 3.7 24.7 - - + +
1032B SER* 5.0 0.2 - - - +
1103B ARG* 3.7 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 943 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B SER* 3.7 17.9 - - - +
906B GLU* 3.2 28.7 + - - -
911B TYR* 3.8 8.9 - - - -
939B ASN* 2.8 24.7 + - - -
940B SER 2.7 25.2 + - - +
941B ALA 4.0 0.2 + - - -
942B ILE* 1.3 73.2 - - - +
944B GLN* 1.3 62.9 + - - +
945B ILE* 3.7 2.9 - - - +
956B TYR* 3.3 35.9 - - + +
959B SER* 2.9 20.9 + - - +
960B GLY* 3.9 9.6 - - - -
962B GLN 3.0 6.7 + - - -
963B LEU* 3.3 20.9 - - + -
964B GLU 2.9 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 944 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874B GLY* 4.4 1.8 - - - -
900B ASN* 3.8 10.0 + - - +
901B SER 3.1 21.8 + - - +
902B GLY* 3.3 19.7 - - - +
903B GLU* 3.3 10.5 + - - +
943B LYS* 1.3 72.9 - - - +
945B ILE* 1.3 65.0 + - - +
946B ALA* 4.0 1.4 + - - +
952B VAL* 4.0 3.8 - - - +
956B TYR* 2.6 31.2 + - - -
964B GLU* 3.2 37.0 + - + +
966B LYS* 3.7 21.3 - - + +
1034B LYS* 4.4 0.4 - - - +
3508B FMN 2.8 42.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 945 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943B LYS 3.7 11.0 - - - +
944B GLN* 1.3 78.6 - - - +
946B ALA* 1.3 57.0 + - - +
949B ARG* 3.3 41.5 - - - +
952B VAL* 4.2 13.0 - - + -
957B LEU* 3.7 32.1 - - + -
963B LEU* 3.9 15.3 - - + -
964B GLU 2.7 17.5 + - - +
965B ILE* 3.5 5.9 - - + -
966B LYS 3.0 22.5 + - - -
1006B HIS* 3.3 7.6 - - - -
1018B LEU* 4.5 14.6 - - + -
1022B LEU* 4.0 17.3 - - + -
1316B PHE* 6.3 0.9 - - + -
----------------------------------------------------------
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