Contacts of the strand formed by residues 275 - 281 (chain A) in PDB entry 1CEC
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 LYS 275 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TRP* 3.1 31.1 - - + -
191A ASP 5.3 0.2 + - - -
193A ILE 4.5 6.1 + - - +
194A VAL* 3.8 29.0 - - + -
195A TYR* 2.9 30.8 + - - +
269A ARG* 5.0 0.4 - - - +
274A CYS* 1.3 77.5 - - - +
276A LEU* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 5.5 1.0 + - - -
182A LEU* 3.9 27.8 - - + -
194A VAL* 4.1 3.3 - - - +
195A TYR* 3.3 14.1 - - + +
197A PHE* 4.4 4.7 - - + -
265A ALA* 3.4 33.7 - - + +
266A ILE* 4.4 1.3 - - + +
268A PHE* 4.2 8.7 - - + -
269A ARG* 3.7 32.5 - - + +
274A CYS* 4.0 2.2 + - - -
275A LYS* 1.3 80.0 - - - +
277A TYR* 1.3 61.9 + - - +
307A ASP 5.2 0.9 + - - +
308A ILE* 3.7 43.9 - - + +
309A GLY* 3.9 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.8 14.1 - - + -
44A HIS* 2.7 35.0 + + - -
46A ARG* 4.0 12.4 - - - +
86A VAL* 4.0 7.7 - - + +
136A GLU* 4.4 3.8 - - - -
170A TYR* 3.4 34.5 - + + -
194A VAL* 3.6 18.2 - - + -
195A TYR 2.7 10.1 + - - +
196A ASN* 3.1 23.7 - - - +
197A PHE* 3.0 30.3 + - - -
276A LEU* 1.3 76.8 - - - +
278A CYS* 1.3 58.1 + - - +
279A GLY* 3.4 21.3 - - - -
308A ILE* 4.1 0.2 - - - -
309A GLY* 3.4 18.6 - - - -
310A GLY* 3.7 13.5 - - - -
311A ALA* 3.4 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 3.2 30.5 - - + -
199A PHE* 3.9 8.7 - - - -
277A TYR* 1.3 71.4 - - - +
279A GLY* 1.3 59.0 + - - +
280A GLU 3.3 19.5 + - - -
281A PHE* 3.7 17.0 - - + -
299A TYR* 3.4 23.3 - - - +
303A LEU* 4.4 10.3 - - + -
308A ILE* 4.1 0.8 - - + +
309A GLY 2.9 14.0 + - - +
310A GLY* 3.0 2.6 - - - -
311A ALA 2.9 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASN* 3.0 22.2 + - - -
46A ARG* 3.3 17.0 - - - -
196A ASN* 2.9 24.9 + - - -
197A PHE 3.2 3.4 + - - -
198A HIS* 4.1 2.0 - - - -
277A TYR* 3.4 18.6 - - - -
278A CYS* 1.3 72.9 - - - +
280A GLU* 1.3 60.9 + - - +
311A ALA* 3.1 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASN* 4.1 1.1 - - - +
46A ARG* 3.0 39.3 + - - +
48A PRO* 6.0 0.2 - - - +
90A HIS* 5.1 5.9 + - - -
139A ASN* 3.5 9.0 - - - +
198A HIS* 3.3 28.3 + - + +
199A PHE 2.8 25.6 + - - +
200A TYR* 2.8 34.1 + - + +
278A CYS* 3.3 3.0 + - - -
279A GLY* 1.3 75.5 - - - +
281A PHE* 1.3 61.8 - - - +
311A ALA 3.5 4.3 - - - -
313A TRP* 3.9 28.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY 5.5 0.7 - - - -
199A PHE 3.1 20.4 - - - +
200A TYR* 4.0 7.3 - - - -
278A CYS* 3.7 19.3 - - - -
280A GLU* 1.3 72.9 - - - +
282A GLY* 1.3 59.3 + - - +
295A TRP* 4.0 9.9 - + + -
296A HIS* 4.3 4.0 - + - -
299A TYR* 3.6 30.5 - + + -
300A ILE* 3.9 30.3 - - + -
303A LEU* 4.2 10.1 - - + -
310A GLY 4.0 5.2 - - - -
311A ALA 3.5 31.8 + - - -
312A VAL* 3.5 28.1 - - + +
313A TRP 2.9 22.2 + - - +
338A LEU* 4.2 9.2 - - + -
340A ARG* 5.8 0.4 - - - -
----------------------------------------------------------
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