Contacts of the strand formed by residues 242 - 250 (chain A) in PDB entry 2C10
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 HIS 242 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLY* 3.7 13.7 - - - -
229A LEU 4.2 2.2 - - - -
230A TYR* 3.2 41.9 + + + -
240A LEU 3.7 1.8 - - - -
241A HIS* 1.3 76.2 - - - +
243A VAL* 1.3 62.1 + - - +
244A GLY* 3.1 31.3 + - - -
245A LEU 3.9 5.4 - - - -
246A GLU* 3.1 41.4 + - + -
291A ILE* 3.5 19.1 - - - +
376A SER* 5.6 1.1 - - - -
497A SER* 3.6 13.2 - - - +
498A ALA* 3.9 7.4 - - + +
499A PHE* 3.6 31.9 + - + +
514A HIS* 5.2 1.4 - - - +
515A THR* 5.3 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 5.6 0.2 - - + -
199A CYS* 3.5 26.4 - - + -
208A LEU* 3.9 20.2 - - + -
229A LEU* 2.9 20.2 + - + +
231A TYR* 3.7 51.8 - - + +
242A HIS* 1.3 72.3 - - - +
244A GLY* 1.3 57.1 - - - +
245A LEU* 4.2 18.2 - - + +
266A TYR* 4.0 11.4 - - + -
267A GLN* 4.4 2.6 + - - -
291A ILE* 3.3 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A HIS* 3.1 21.9 + - - -
243A VAL* 1.3 78.4 - - - +
245A LEU* 1.3 59.4 + - - +
246A GLU* 4.6 2.4 - - - +
265A PHE* 3.3 11.3 - - - +
266A TYR* 3.4 2.2 - - - -
267A GLN* 3.0 26.9 + - - -
499A PHE* 3.6 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 3.7 31.4 - - + -
194A LEU* 6.2 0.2 - - + -
195A LEU* 4.2 20.0 - - + -
208A LEU* 5.8 0.7 - - + -
229A LEU* 3.0 51.2 + - + +
242A HIS* 3.9 1.0 - - - -
243A VAL* 3.3 9.5 - - + +
244A GLY* 1.3 76.8 - - - +
246A GLU* 1.3 66.0 + - - +
247A LEU* 4.2 7.4 - - + -
264A VAL* 3.8 29.2 - - + -
265A PHE 3.5 6.1 - - - +
266A TYR* 3.9 21.5 - - + -
274A LEU* 4.5 5.6 - - + -
277A LEU* 4.2 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TRP* 3.9 13.0 - - + -
227A PHE 3.2 11.2 - - - +
228A GLY* 4.2 2.2 - - - -
242A HIS* 3.1 30.6 + - + +
244A GLY 4.6 2.5 - - - +
245A LEU* 1.3 81.4 - - - +
247A LEU* 1.3 65.8 + - - +
264A VAL* 3.7 4.3 - - - +
265A PHE* 2.9 40.2 + - + +
376A SER* 3.6 19.1 - - - -
377A PRO* 3.2 14.7 - - - +
378A ALA* 3.0 42.2 + - + +
498A ALA* 4.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ILE* 4.1 32.5 - - + -
187A GLU* 5.3 0.7 - - + -
188A LEU* 4.3 8.1 - - + -
225A THR 3.3 3.1 - - - +
226A TRP* 3.4 4.7 - - - -
227A PHE* 2.9 34.9 + - + +
229A LEU* 3.9 25.4 - - + -
245A LEU* 4.2 5.2 - - + -
246A GLU* 1.3 82.6 - - - +
248A LEU* 1.3 60.3 + - - +
249A VAL* 3.5 5.5 + - + +
261A ILE* 4.4 17.7 - - + -
263A LYS 3.7 2.7 - - - +
264A VAL* 3.9 26.9 - - + -
274A LEU* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLY* 6.2 0.7 - - - -
224A ALA* 3.8 21.5 - - + +
225A THR 3.5 22.4 - - - -
226A TRP* 3.6 42.5 - - + +
247A LEU* 1.3 70.3 - - - +
249A VAL* 1.3 58.8 + - - +
261A ILE* 3.4 4.8 - - - -
262A GLN* 2.8 62.6 + - + +
263A LYS* 3.0 23.6 + - + +
553B TRP* 4.0 20.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
179A ILE* 4.0 17.0 - - + -
182A MET* 4.2 15.5 - - - -
183A ILE* 4.1 18.6 - - + -
224A ALA* 3.2 2.7 - - - -
225A THR 2.8 39.7 + - - +
227A PHE* 4.0 22.9 - - + -
247A LEU* 4.3 6.1 - - + +
248A LEU* 1.3 69.9 - - - +
250A ASN* 1.3 61.2 + - - +
251A HIS* 3.2 25.4 - - + -
259A TRP* 5.1 0.2 - - + -
260A THR 3.5 7.9 - - - +
261A ILE* 3.8 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ARG 3.6 7.2 + - - +
224A ALA* 4.1 6.5 - - + +
248A LEU 3.7 2.4 + - - -
249A VAL* 1.3 69.6 - - - +
251A HIS* 1.3 63.2 + - - +
252A LYS* 3.2 23.8 + - - +
253A ALA 5.8 0.2 - - - -
259A TRP* 3.4 9.9 - - - +
260A THR* 2.8 48.2 + - - +
262A GLN* 3.2 31.3 + - - +
----------------------------------------------------------
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