Contacts of the strand formed by residues 245 - 249 (chain A) in PDB entry 4HXG
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 245 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU 3.7 0.2 - - - +
232A TYR* 3.5 4.3 - - - -
233A GLY 2.8 38.2 + - - +
234A LYS* 4.6 10.8 - - - +
243A HIS* 4.0 14.8 - - - +
244A ASP* 1.3 76.6 - - - +
246A ILE* 1.3 68.0 + - - +
247A TYR* 3.8 17.9 - - + +
257A LEU* 3.9 28.0 - - + -
258A ASP* 5.2 5.2 - - - +
260A ILE 3.2 25.8 - - - +
261A ASP* 4.7 6.5 - - - +
262A ARG 3.8 19.5 - - - +
264A VAL* 4.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ILE* 4.6 2.7 - - + -
230A LEU* 4.1 7.2 - - + -
231A LEU 3.1 8.3 - - - +
232A TYR* 4.2 9.2 - - + -
245A LYS* 1.3 80.0 - - - +
247A TYR* 1.3 70.5 + - - +
255A GLY* 3.7 1.9 - - - -
256A ILE* 3.4 48.4 + - + -
257A LEU* 4.4 8.6 + - + +
264A VAL* 4.1 17.9 - - + +
267A ALA* 3.7 22.0 - - + -
274A VAL* 3.6 21.5 - - + -
276A PHE* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 3.9 11.4 - + - -
229A ILE 3.4 1.4 - - - +
230A LEU* 3.4 7.5 - - - +
231A LEU* 2.7 53.2 + - + +
233A GLY 2.9 29.8 + - - -
234A LYS* 3.7 9.5 - - - +
235A PRO* 3.1 32.3 - - + +
245A LYS* 3.8 19.2 - - + +
246A ILE* 1.3 77.3 - - - +
248A ILE* 1.3 64.1 + - - +
253A VAL* 3.8 27.1 - - + -
254A LYS 3.6 3.6 - - - +
255A GLY* 3.5 27.4 - - - -
256A ILE* 5.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ARG* 3.7 36.6 - - + -
229A ILE 3.7 2.7 - - - +
230A LEU* 4.5 1.6 - - + -
247A TYR* 1.3 74.6 - - - +
249A TYR* 1.3 64.2 + - - +
250A ASP* 4.7 4.9 - - + +
252A GLU 3.2 4.5 - - - +
253A VAL* 3.5 1.3 - - - -
254A LYS* 2.9 42.0 + - + +
256A ILE* 4.2 14.8 - - + -
269A ILE* 4.2 9.9 - - + -
272A GLY 4.6 3.8 - - - +
274A VAL* 4.1 22.9 - - + -
289A TRP* 3.7 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A HIS* 5.8 0.2 - - - -
213A LEU* 4.0 27.0 + - + +
214A PHE* 3.3 37.7 - + - -
227A GLU 4.5 0.5 - - - +
228A ARG* 3.6 4.9 - - - -
229A ILE* 2.9 54.9 + - + +
231A LEU* 4.2 16.4 - - + -
247A TYR 3.9 0.2 + - - -
248A ILE* 1.3 75.1 - - - +
250A ASP* 1.3 58.6 + - - +
251A GLY* 3.4 36.3 + - - -
252A GLU* 3.5 3.1 - - - -
253A VAL* 3.7 17.7 - - + -
----------------------------------------------------------
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