Contacts of the helix formed by residues 257 - 267 (chain A) in PDB entry 5CYP
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 GLU 257 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS* 2.4 37.8 + - - -
219A MET* 3.5 33.9 - - + +
222A PHE* 3.6 9.1 - - + -
223A ALA* 2.7 42.8 + - + +
224A VAL* 5.0 0.9 - - - -
253A THR 5.0 2.7 - - - +
256A CYS* 1.3 76.7 - - - +
258A PHE* 1.3 63.3 + - - +
259A ALA 3.3 2.7 - - - -
260A TYR* 3.4 11.8 + - + +
261A LEU* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.6 39.5 - - + -
42A THR* 3.7 24.9 - - + -
43A LEU* 3.6 43.1 - - + -
46A SER* 4.9 1.6 - - - -
223A ALA 3.9 1.2 + - - -
224A VAL* 4.4 16.8 - - + -
225A VAL 4.5 4.7 - - - +
250A VAL* 3.8 22.0 - - + +
251A GLU* 5.2 2.2 - - - -
256A CYS* 3.5 10.8 - - - -
257A GLU* 1.3 76.3 - - - +
259A ALA* 1.3 62.2 + - - +
261A LEU* 3.3 9.5 + - + +
262A ARG* 3.0 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A VAL 4.0 2.4 + - - +
251A GLU* 3.3 32.8 - - - +
252A ASN 4.6 2.0 - - - -
253A THR* 4.1 19.3 - - + -
256A CYS* 5.1 0.4 + - - -
257A GLU 3.3 0.4 - - - -
258A PHE* 1.3 83.8 - - - +
260A TYR* 1.3 61.5 + - - +
262A ARG* 3.9 17.4 + - - +
263A ASP* 3.3 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET* 3.5 34.1 - - + -
222A PHE* 4.7 1.1 - - + -
253A THR* 3.6 48.2 + - + +
257A GLU* 3.4 15.5 + - + +
258A PHE 3.3 0.2 - - - -
259A ALA* 1.3 77.8 - - - +
261A LEU* 1.3 63.9 + - - +
263A ASP* 3.4 5.4 + - + +
264A LEU* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 5.2 0.7 - - + -
137A LEU* 4.2 19.5 - - + -
165A VAL* 3.9 9.0 - - + -
167A VAL* 3.8 26.9 - - + -
216A PHE* 4.6 1.1 - - + -
222A PHE* 3.5 45.3 - - + -
224A VAL* 3.8 13.0 - - + -
257A GLU 3.1 12.5 + - - +
258A PHE* 3.3 12.8 + - + +
260A TYR* 1.3 76.8 - - - +
262A ARG* 1.3 63.8 + - - +
264A LEU* 3.9 1.2 - - - +
265A LEU* 3.0 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 4.7 20.4 - - + -
46A SER* 2.0 45.1 + - - -
47A LYS* 3.9 22.9 - - - +
251A GLU* 5.1 13.3 + - - +
258A PHE* 3.0 37.1 + - + +
259A ALA* 3.9 19.8 + - - +
261A LEU* 1.3 77.9 - - - +
263A ASP* 1.3 83.2 + - - +
265A LEU* 3.8 2.4 - - - -
266A ILE* 2.9 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS* 5.0 4.7 + - - -
259A ALA* 3.3 20.4 + - - +
260A TYR* 4.0 4.8 - - + +
262A ARG* 1.3 104.7 + - - +
264A LEU* 1.3 60.0 + - + +
266A ILE* 4.9 1.8 - - - -
267A ARG* 2.8 34.7 + - + +
268A THR* 3.1 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A VAL* 6.0 0.4 - - + +
215A LYS* 5.3 6.1 - - + +
216A PHE* 3.5 39.3 - - + -
219A MET* 5.0 4.5 - - + -
222A PHE* 3.9 18.4 - - + -
260A TYR* 2.9 34.9 + - + +
261A LEU 3.9 2.5 - - - +
263A ASP* 1.3 77.6 - - + +
265A LEU* 1.3 57.7 + - - +
268A THR* 3.9 18.8 - - + +
269A HIS* 2.5 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.4 18.3 - - + -
26A ILE* 4.7 11.0 - - + -
135A CYS* 3.9 16.4 - - - -
137A LEU* 3.8 23.1 - - + -
165A VAL* 4.3 4.0 - - + -
216A PHE* 4.0 23.8 - - + -
261A LEU* 3.0 43.3 + - + +
262A ARG* 3.9 3.1 - - - +
264A LEU* 1.3 76.3 - - - +
266A ILE* 1.3 63.7 + - + +
269A HIS* 4.2 2.2 - - + -
270A MET* 3.3 24.6 - - - +
273A ILE* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.9 26.9 - - + -
26A ILE* 4.1 14.8 - - + -
43A LEU* 5.5 3.6 - - + -
47A LYS* 5.1 9.6 - - + +
74A ILE* 4.7 16.2 - - + -
76A GLU* 4.9 16.4 - - + -
81A MET* 5.7 6.7 - - + -
83A LEU* 4.1 19.3 - - + -
262A ARG* 2.9 34.0 + - + +
263A ASP* 4.6 1.6 - - - +
265A LEU* 1.3 79.6 - - + +
267A ARG* 1.3 61.6 + - + +
270A MET* 3.2 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ASP* 2.8 18.8 + - + +
266A ILE* 1.3 83.5 - - + +
268A THR* 1.3 69.9 + - - +
269A HIS 3.6 0.2 - - - -
270A MET* 3.9 8.4 + - - +
271A GLN 5.2 0.5 + - - -
----------------------------------------------------------
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