Contacts of the strand formed by residues 230 - 238 (chain D) in PDB entry 6BAA
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 VAL 230 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PRO* 3.7 26.8 - - + +
222D LYS* 3.7 31.6 - - - +
223D THR 3.7 4.7 - - - +
224D THR* 4.3 15.9 - - + -
228D GLY 3.6 11.8 + - - +
229D GLU* 1.3 85.4 - - - +
231D VAL* 1.3 69.9 + - - +
232D PRO* 4.0 2.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG* 4.7 14.4 - - - +
256A ILE* 5.9 6.5 - - + -
222D LYS* 3.2 9.5 - - - +
223D THR 2.9 38.4 + - - +
229D GLU* 5.6 7.2 - - + -
230D VAL* 1.3 79.0 - - - +
232D PRO* 1.3 65.9 - - + +
233D LEU 3.5 4.7 - - - +
234D HIS* 3.1 54.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PRO* 4.4 16.2 - - + -
318A ILE 5.1 0.9 - - - +
319A VAL* 3.7 49.4 - - + +
326A TYR* 5.2 2.5 - - + -
222D LYS* 3.5 32.5 + - + +
230D VAL* 4.0 7.0 - - + +
231D VAL* 1.3 89.3 - - + +
233D LEU* 1.3 71.1 + - + +
234D HIS 3.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ALA* 4.3 8.5 - - + -
255A LEU* 5.1 5.4 - - - +
319A VAL* 3.7 37.7 - - + -
326A TYR* 3.6 34.5 - - + +
35D PHE* 3.8 29.6 - - + -
44D VAL* 6.3 0.2 - - + -
220D VAL* 3.6 29.4 - - + -
221D ARG 4.5 0.4 - - - -
231D VAL* 3.5 4.8 - - - +
232D PRO* 1.3 91.6 - - + +
234D HIS* 1.3 64.5 + - - +
235D GLN* 3.5 14.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG* 3.7 26.3 + - - -
193A HIS* 6.0 2.0 + - - -
258A TYR* 5.1 7.9 + + - -
219D VAL 2.9 14.9 - - - +
220D VAL* 3.4 1.7 - - - -
221D ARG* 3.0 32.7 + - - +
223D THR* 4.2 17.0 - - + +
231D VAL* 3.1 33.4 - - + +
233D LEU* 1.3 74.0 - - - +
235D GLN* 1.3 78.3 + - - +
236D VAL* 3.6 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 3.8 12.1 - - + +
250A PHE* 3.1 22.2 + - - +
252A VAL 5.1 1.4 - - - +
253A ALA* 5.4 1.8 - - - +
255A LEU* 3.7 27.3 - - + +
35D PHE* 3.9 28.5 - - - -
218D GLN* 2.8 37.9 + - + +
219D VAL 3.4 4.3 - - - -
220D VAL* 4.8 10.0 - - + +
233D LEU* 3.5 13.2 + - - +
234D HIS* 1.3 91.4 + - - +
236D VAL* 1.3 60.5 + - - +
237D ASP* 4.2 3.9 + - - +
284D ILE* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLY* 5.9 2.7 - - - -
218D GLN* 3.1 9.3 - - - -
219D VAL* 2.9 45.7 + - + +
221D ARG* 5.7 7.2 - - + +
223D THR* 5.9 2.0 - - - +
234D HIS* 3.6 24.7 - - + +
235D GLN* 1.3 73.8 - - - +
237D ASP* 1.3 75.9 + - - +
238D ILE* 3.6 2.0 + - + +
264D ASN 5.7 1.6 - - - +
266D PRO* 4.0 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLU 4.7 0.2 - - - +
242A ASN* 3.0 39.0 + - - +
243A GLY* 2.7 35.5 + - - +
244A VAL* 3.8 12.2 - - + +
248A SER 4.6 2.9 - - - +
249A ILE* 5.3 5.2 - - - +
217D MET 3.9 3.8 - - - -
218D GLN* 4.5 15.1 - - - +
235D GLN 5.2 3.4 - - - +
236D VAL* 1.3 82.8 - - - +
238D ILE* 1.3 67.0 + - - +
239D PRO* 3.9 5.0 - - - +
266D PRO* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 3.6 5.6 - - - +
216D HIS* 5.6 0.2 - - - -
217D MET* 2.8 48.8 + - + +
219D VAL* 3.5 34.3 - - + -
236D VAL* 3.8 3.1 - - + +
237D ASP* 1.3 83.3 - - - +
239D PRO* 1.3 65.8 - - + +
240D MET* 3.6 10.7 + - - +
247D ASN* 5.6 1.2 - - - +
259D HIS* 3.3 47.3 - - + +
266D PRO* 3.6 26.0 - - + -
267D LEU* 5.4 2.0 - - + -
----------------------------------------------------------
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