Contacts of the strand formed by residues 334 - 341 (chain I) in PDB entry 6RAR
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 ARG 334 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B A 4.9 8.3 + - - -
300D AMP 4.0 10.1 + - - -
147I LEU* 3.7 44.1 - - + +
148I ALA 2.4 42.3 + - - +
149I HIS* 3.2 37.7 + - + +
187I ARG* 5.1 6.5 - - - +
333I LYS* 1.3 85.2 - - - +
335I THR* 1.3 59.6 + - - +
340I LYS* 4.8 2.4 - - - +
501I SO4 5.0 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 335 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146I PRO* 5.0 3.4 - - + -
147I LEU 3.2 17.4 + - - +
149I HIS* 3.5 11.1 - - - -
329I MET 5.9 0.9 - - - +
331I GLU* 3.5 28.1 + - + +
333I LYS* 3.6 14.8 - - - +
334I ARG* 1.3 76.8 - - - +
336I HIS* 1.3 63.5 + - - +
337I SER* 3.1 31.0 + - - -
338I TRP* 3.2 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 336 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B G 4.1 15.9 - - + -
6B A 3.7 23.8 + - - -
149I HIS* 3.5 24.5 + + + -
154I HIS* 3.3 33.3 + + - -
157I LYS* 3.6 44.4 + - + +
162I LYS* 4.7 7.6 + - - -
323I ILE 5.0 0.2 - - - +
325I ASP* 5.2 0.2 - - - +
335I THR* 1.3 72.1 + - - +
337I SER* 1.3 65.1 + - - +
338I TRP 3.1 3.0 + - - -
339I LEU* 3.6 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 337 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162I LYS* 5.5 0.2 + - - -
266I GLN* 5.5 1.6 - - - -
323I ILE 3.5 1.6 - - - +
324I LYS* 3.1 8.3 - - - -
325I ASP* 3.0 38.0 + - - +
328I GLY* 3.7 26.5 - - - -
329I MET 4.4 7.3 + - - -
331I GLU* 4.4 6.2 + - - -
335I THR* 3.1 22.3 + - - -
336I HIS* 1.3 78.5 - - - +
338I TRP* 1.3 67.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 338 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D AMP 3.9 19.5 - + - -
146I PRO* 3.8 32.5 - - + -
147I LEU* 4.2 10.3 - - - +
148I ALA* 3.2 14.4 - - + -
149I HIS 2.9 23.2 + - - -
172I ARG* 3.4 35.4 - - - -
218I ASP* 4.0 5.4 - - - -
249I PHE* 3.9 13.9 - + - -
250I ASP* 3.5 23.3 - - + -
266I GLN* 2.9 24.8 + - - -
269I ARG* 4.5 4.2 - - - +
322I MET* 4.3 7.0 - - + -
323I ILE 3.9 1.8 - - - -
324I LYS* 3.7 27.2 - - + +
330I TYR* 5.2 0.2 - + - -
335I THR* 3.2 11.5 + - + +
336I HIS 3.1 0.2 - - - -
337I SER* 1.3 93.1 - - - +
339I LEU* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I ALA* 4.8 0.2 - - - -
149I HIS* 3.1 33.9 - - + +
151I SER* 4.1 14.1 - - - +
154I HIS* 4.4 10.8 - - + +
157I LYS* 4.4 21.8 - - + +
158I MET* 3.5 28.5 - - + -
162I LYS* 4.5 8.1 - - - +
322I MET* 3.4 8.8 - - - +
323I ILE* 2.7 47.0 + - + +
336I HIS* 3.6 32.5 - - + +
338I TRP* 1.3 74.2 - - - +
340I LYS* 1.3 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 340 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D A 3.6 25.8 + - - -
300D AMP 2.9 42.2 + - - +
148I ALA* 3.9 7.2 + - + -
149I HIS* 2.9 29.4 + - - +
150I ASP* 3.3 25.6 - - - +
151I SER* 2.7 31.6 + - - -
167I LYS* 4.1 10.3 - - + -
321I VAL 3.6 5.2 - - - +
322I MET* 4.0 18.8 - - + -
323I ILE* 4.3 1.1 - - - -
334I ARG* 4.8 2.2 - - - +
339I LEU* 1.3 75.8 - - - +
341I ALA* 1.3 56.5 + - - +
342I LYS* 4.1 18.4 - - + +
501I SO4 4.9 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150I ASP* 5.0 1.6 - - - -
151I SER* 3.6 13.7 - - - +
167I LYS* 5.1 0.2 - - - +
306I PHE* 4.6 7.0 - - + -
310I ASN* 4.3 9.0 - - - +
320I GLY* 3.3 5.2 - - - -
321I VAL* 3.0 49.0 + - + +
323I ILE* 4.0 7.4 - - + -
340I LYS* 1.3 73.6 - - - +
342I LYS* 1.3 64.8 + - - +
----------------------------------------------------------
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