Contacts of the strand formed by residues 381 - 388 (chain C) in PDB entry 1RF1
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 LYS 381 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C LYS* 6.1 5.6 - - - +
197C ARG* 3.3 5.4 - - - +
198C LEU* 3.9 25.4 - - + +
249C GLU 4.5 0.4 - - - -
250C LEU* 3.6 4.6 - - - -
251C GLU* 3.1 68.5 + - + +
379C MET* 4.0 3.2 - - - +
380C LYS* 1.3 97.1 - - + +
382C THR* 1.3 65.7 + - - +
383C THR* 5.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C GLN* 2.7 37.5 - - - +
196C LYS* 3.3 6.2 - - - +
197C ARG* 2.7 48.8 + - + +
249C GLU 3.5 6.1 - - - +
250C LEU* 3.6 15.6 - - - +
344C LEU* 3.6 25.6 - - + +
367C ILE* 3.7 10.4 - - - +
379C MET* 4.1 1.7 - - - +
381C LYS* 1.3 77.3 + - - +
383C THR* 1.3 67.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C GLU* 5.4 1.0 + - - -
193C VAL* 4.3 8.7 - - - +
195C GLN* 3.2 8.3 + - - -
196C LYS* 3.6 31.4 + - - +
247C ARG 3.8 1.4 - - - +
248C VAL* 3.6 4.0 - - - +
249C GLU* 3.0 69.6 + - + +
381C LYS* 5.4 2.2 - - + -
382C THR* 1.3 84.0 - - - +
384C MET* 1.3 67.4 + - - +
385C LYS* 4.4 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C VAL* 3.6 2.3 - - - +
194C PHE* 2.8 67.8 + - + -
195C GLN* 2.9 38.1 + - + +
227C TRP* 4.4 0.2 - - - -
246C LEU* 4.4 13.9 - - + -
247C ARG 3.7 4.9 - - - -
248C VAL* 4.4 14.4 - - + -
290C PHE* 4.5 6.3 - - + -
334C TRP* 3.8 34.5 - - + -
335C TRP* 4.5 7.6 - - + -
344C LEU* 4.0 19.5 - - + -
383C THR* 1.3 77.0 + - - +
385C LYS* 1.3 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C GLU* 2.9 38.3 + - - +
191C TRP* 3.4 38.4 - - + +
192C THR 3.5 7.0 - - - +
193C VAL* 3.8 19.1 - - + -
194C PHE 4.4 0.2 - - - +
246C LEU* 3.1 5.2 - - - +
247C ARG* 2.9 59.6 + - - +
249C GLU* 3.0 31.0 + - - -
383C THR* 4.4 8.1 - - - +
384C MET* 1.3 74.8 - - - +
386C ILE* 1.3 65.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C GLY 4.3 0.2 - - - +
191C TRP* 3.4 3.2 - - - -
192C THR* 2.8 42.9 + - - +
194C PHE* 3.9 18.6 - - + -
233C ILE* 5.1 4.7 - - + +
236C ILE* 3.5 37.0 - - + -
237C SER* 4.8 6.1 - - - +
244C TYR* 3.6 17.5 - - + -
245C ALA 3.1 11.7 - - - +
246C LEU* 3.9 3.8 - - + -
265C PHE* 3.6 36.8 - - + -
385C LYS* 1.3 81.2 - - - +
387C ILE* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C GLN* 3.2 21.8 - - - +
189C ASN* 3.9 10.5 - - + -
190C GLY 3.5 22.9 - - - +
191C TRP* 3.4 39.0 - - + -
244C TYR* 3.4 8.2 - - - -
245C ALA* 2.8 30.6 + - + +
386C ILE* 1.3 76.9 - - - +
388C PRO* 1.3 87.4 - - + +
391C ARG* 3.3 20.6 - - + -
392C LEU* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ASP* 4.3 4.3 - - - +
154C GLN* 3.6 25.1 - - + -
190C GLY 4.8 0.2 - - - +
242C ILE* 4.4 10.1 - - + -
243C PRO 3.6 9.9 - - - +
244C TYR* 3.6 29.8 - - + +
387C ILE* 1.3 97.6 - - + +
389C PHE* 1.3 65.8 + - - +
390C ASN* 3.9 23.8 - - - +
391C ARG* 3.0 21.1 + - + +
392C LEU 3.6 2.1 + - - -
----------------------------------------------------------
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