Contacts of the strand formed by residues 1236 - 1240 (chain F) in PDB entry 6X34
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 THR1236 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839F LEU* 5.6 7.2 - - + +
1075F PHE* 5.7 5.4 - - - -
1076F ARG 4.3 6.5 - - - -
1077F ALA* 5.1 0.2 - - - +
1234F VAL 3.8 9.9 - - - +
1235F THR* 1.3 80.2 - - - +
1237F TRP* 1.3 69.7 + - - +
1238F PHE* 5.7 0.3 - - - +
1607F ARG* 4.3 0.9 - - - +
1608F MET* 3.4 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1237 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075F PHE* 3.3 8.2 - - - +
1076F ARG* 2.9 40.8 + - - +
1077F ALA 3.5 4.7 - - - +
1078F GLU* 3.4 45.2 - - + +
1235F THR* 4.2 9.1 + - - -
1236F THR* 1.3 83.2 + - - +
1238F PHE* 1.3 62.4 + - - +
1605F TRP* 4.7 25.1 - + + -
1606F SER* 3.4 28.9 - - - -
1607F ARG* 3.6 30.7 - - + -
1652F GLU* 4.5 21.1 - - + -
1653F LEU* 5.8 0.4 - - - -
1654F SER* 5.5 2.9 - - - -
1655F GLU* 3.9 33.2 - - + -
1656F ARG* 5.1 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1238 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695F TYR* 3.8 32.8 - + + -
829F TYR* 3.8 40.4 - + + -
1073F ARG* 4.3 7.2 - - - -
1074F ILE 3.9 5.6 - - - -
1075F PHE* 3.6 28.0 - - + -
1236F THR* 5.7 0.4 - - - +
1237F TRP* 1.3 74.0 - - - +
1239F SER* 1.3 72.9 + - - +
1240F LYS* 3.3 7.3 + - - -
1605F TRP* 4.3 5.1 - - - -
1606F SER* 3.1 44.7 + - - +
1607F ARG 3.3 26.2 - - - -
1608F MET* 4.0 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1239 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072F VAL 4.3 2.6 + - - -
1073F ARG* 3.0 35.1 + - - +
1074F ILE* 2.9 39.4 + - - -
1111F PRO* 4.6 11.0 - - - -
1238F PHE* 1.3 72.1 - - - +
1240F LYS* 1.3 61.9 + - - +
1241F SER* 3.5 1.0 + - - -
1603F VAL* 3.7 20.4 - - - +
1604F SER 3.5 7.6 - - - -
1605F TRP* 5.0 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1240 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695F TYR* 4.7 5.4 - - + -
1073F ARG* 4.5 0.4 - - - +
1238F PHE* 3.3 12.8 + - + -
1239F SER* 1.3 69.6 - - - +
1241F SER* 1.3 64.2 + - - +
1242F LEU* 3.2 14.6 + - + +
1244F GLN* 5.5 3.4 - - - +
1603F VAL* 3.3 5.9 - - - +
1604F SER* 2.9 38.1 + - - +
1605F TRP 4.5 1.6 - - - +
1606F SER* 3.7 26.2 - - - -
----------------------------------------------------------
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