Contacts of the strand formed by residues 240 - 249 (chain A) in PDB entry 5UV6
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 GLY 240 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 6.2 0.4 - - - -
234A VAL* 4.0 24.9 - - - -
238A GLN 3.1 4.2 + - - -
239A LYS* 1.3 73.7 - - - +
241A ILE* 1.3 62.0 + - - +
242A LEU 4.1 0.4 - - - -
282A THR* 3.5 3.3 - - - -
283A PHE* 2.9 43.5 + - - +
311A LEU* 4.8 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 2.9 35.1 + - - +
239A LYS* 4.2 10.1 + - + +
240A GLY* 1.3 76.5 - - - +
242A LEU* 1.3 70.6 + - - +
243A SER* 4.8 3.3 - - - -
271A ARG* 5.0 5.2 - - - +
280A THR* 4.1 20.4 - - + -
281A LEU 3.8 1.1 - - - -
282A THR* 3.3 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LYS 4.7 1.6 - - - +
232A THR* 3.2 24.2 - - - +
240A GLY 4.1 0.4 - - - -
241A ILE* 1.3 74.6 - - - +
243A SER* 1.3 66.2 + - - +
256A TRP* 3.9 10.8 - - + -
280A THR* 3.2 4.9 - - - -
281A LEU* 2.9 35.5 + - + +
283A PHE* 4.0 12.3 - - + -
294A TYR* 3.3 46.9 - - + -
309A ILE* 3.7 23.1 - - + -
310A THR 4.0 20.0 - - - +
311A LEU* 4.2 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LYS 4.8 0.5 - - - -
229A ALA* 4.0 10.4 + - - -
230A LYS 4.3 6.8 + - - +
232A THR* 5.5 1.2 - - - +
241A ILE* 4.2 5.3 + - - -
242A LEU* 1.3 79.6 - - - +
244A CYS* 1.3 65.3 + - - +
256A TRP* 3.8 5.0 - - - -
278A MET* 4.7 9.1 - - - +
279A SER 3.1 12.8 - - - -
280A THR* 3.6 16.8 - - - -
309A ILE* 3.9 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 4.6 5.6 - - + -
228A LYS* 3.3 5.8 - - - +
229A ALA* 3.7 25.4 - - - -
243A SER* 1.3 76.7 - - - +
245A GLU* 1.3 62.9 + - - +
254A PHE* 3.6 15.9 - - + -
256A TRP* 3.9 3.0 - - + -
278A MET* 3.4 6.3 - - - +
279A SER 2.9 29.9 + - - +
296A CYS* 2.0 52.3 - - + -
307A ALA* 5.0 1.6 - - - -
309A ILE* 4.3 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 3.6 3.0 - - - -
227A SER* 2.6 50.6 + - - +
228A LYS* 2.9 36.4 + - + +
244A CYS* 1.3 77.4 - - - +
246A ALA* 1.3 51.8 + - - +
254A PHE* 3.9 2.5 - - - -
277A ARG* 3.5 47.1 + - + +
278A MET* 4.3 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PRO* 4.4 3.8 - - + -
225A TYR 3.3 10.5 - - - +
226A ILE* 4.1 3.6 - - + +
227A SER* 3.6 4.9 + - - +
245A GLU* 1.3 73.8 - - - +
247A SER* 1.3 62.4 + - - +
248A ALA* 4.1 1.2 + - - -
252A ALA* 4.1 12.6 - - + -
254A PHE* 3.4 23.6 - - + -
277A ARG* 3.2 35.8 + - - +
298A ALA* 3.5 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 3.1 26.5 + - - -
224A PRO* 3.5 0.3 - - - +
225A TYR* 2.8 60.4 + - - -
227A SER* 3.9 6.1 - - - -
246A ALA* 1.3 72.5 - - - +
248A ALA* 1.3 59.4 + - - +
277A ARG* 3.4 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 3.7 11.6 + - - -
224A PRO* 3.5 20.9 - - + -
246A ALA 4.1 1.4 + - - -
247A SER* 1.3 77.7 + - - +
249A VAL* 1.3 70.5 + - - +
250A PRO 3.4 9.9 - - - +
251A MET* 3.6 22.6 + - - +
252A ALA* 4.0 15.2 - - + +
277A ARG* 5.4 0.8 - - - +
300A ASN* 3.5 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A THR* 5.1 9.4 - - - +
220A VAL 3.2 28.5 - - - +
221A ASN* 3.1 16.9 - - - +
222A TYR* 3.0 48.7 + - + +
248A ALA* 1.3 80.9 - - - +
250A PRO* 1.3 66.5 - - + +
251A MET* 5.2 5.4 - - + -
300A ASN* 3.6 2.2 + - - -
302A LEU* 4.2 0.2 - - - +
----------------------------------------------------------
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