Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 5A91
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LYS* 3.7 37.5 - - + +
228A SER 3.5 7.2 + - - +
229A TRP* 1.3 72.5 - - - +
231A VAL* 1.3 66.3 + - - +
250A ILE* 4.3 0.3 - - - +
251A TRP* 2.8 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LYS* 3.5 17.1 - - - +
221A ILE* 5.1 1.3 - - + -
222A ARG* 3.0 53.0 + - + +
225A LEU* 3.6 29.2 - - + -
226A PRO 5.9 0.2 - - - +
229A TRP* 3.6 13.2 + - + +
230A VAL* 1.3 83.6 - - - +
232A GLY* 1.3 74.2 + - - +
233A ASP* 4.4 2.0 - - + -
248A ALA* 4.2 13.5 - - + -
249A VAL 3.4 8.7 - - - +
250A ILE* 4.4 7.0 - - + -
251A TRP* 4.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.2 30.9 - - - +
212A LYS* 3.6 5.4 - - - -
222A ARG* 3.9 0.2 - - - -
231A VAL* 1.3 73.3 - - - +
233A ASP* 1.3 62.0 + - - +
248A ALA* 3.1 4.3 - - - +
249A VAL* 2.8 36.3 + - - +
251A TRP* 3.7 6.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU 4.8 0.7 - - - +
211A LEU* 3.1 21.6 + - - +
214A ASN* 3.0 43.4 + - - +
217A GLY* 3.7 3.9 - - - -
221A ILE* 5.7 0.4 - - + -
222A ARG* 2.8 34.7 + - + -
231A VAL* 4.4 3.6 - - + -
232A GLY* 1.3 76.8 - - - +
234A LYS* 1.3 62.0 + - - +
235A THR* 3.5 7.3 - - - +
246A ASP* 2.5 31.9 - - - +
247A ILE 3.1 14.4 - - - +
248A ALA* 3.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER* 3.4 21.3 - - - +
71A THR* 3.4 10.2 - - - +
73A LYS* 3.9 5.6 - - - -
74A VAL* 3.5 29.8 - - + -
126A ALA 3.5 22.2 - - - -
127A LEU* 3.5 31.0 + - + +
130A SER* 2.9 27.9 + - - -
211A LEU* 4.2 2.6 - - + +
214A ASN* 4.4 1.8 - - - +
216A THR* 4.6 1.6 + - - -
233A ASP* 1.3 74.3 - - - +
235A THR* 1.3 90.1 + - - +
246A ASP* 3.2 4.3 - - - -
247A ILE* 2.9 33.8 + - + +
1291A SO4 3.2 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER 3.4 10.2 - - - -
71A THR* 3.7 3.4 - - - -
216A THR* 2.7 40.8 + - - +
217A GLY* 3.7 8.1 - - - -
220A SER* 4.0 10.8 - - - +
233A ASP* 3.5 9.6 + - - +
234A LYS* 1.3 97.8 + - - +
236A GLY* 1.3 59.3 + - - +
245A ASN 3.4 8.7 - - - +
246A ASP* 3.5 17.3 - - - +
276A ASN* 5.1 2.0 - - - +
1291A SO4 2.5 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A CYS* 3.8 6.5 - - - -
70A SER* 3.6 19.3 - - - -
71A THR* 3.7 7.0 - - - +
235A THR* 1.3 77.0 - - - +
237A SER* 1.3 61.6 + - - -
244A THR* 3.7 0.7 - - - +
245A ASN* 2.8 38.8 + - - +
1291A SO4 3.6 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A CYS* 3.7 6.0 - - - +
170A ASN* 3.4 21.0 + - - +
236A GLY* 1.3 75.8 - - - -
238A GLY* 1.3 59.0 + - - +
243A THR 3.1 11.9 - - - -
244A THR* 4.7 4.9 - - - -
274A ASN* 3.7 20.0 + - - -
276A ASN* 5.8 2.0 - - - -
1291A SO4 2.8 26.4 + - - -
----------------------------------------------------------
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