Contacts of the strand formed by residues 253 - 259 (chain A) in PDB entry 4GXK
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 ARG 253 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP 4.2 2.2 + - - -
146A PHE* 4.1 5.8 - - - -
148A LYS* 3.6 22.8 + - - +
149A ARG 3.3 26.3 + - - -
150A ILE* 3.6 35.0 - - + +
151A PRO* 3.6 8.7 - - - +
154A GLU* 2.8 29.9 + - - -
158A MET* 3.9 23.3 - - + -
238A VAL* 3.3 5.9 - - - -
239A CYS* 2.8 37.0 + - - +
240A GLN* 5.3 2.0 - - - -
241A LEU* 5.8 1.1 - - + +
250A TYR* 5.9 0.4 - - - +
251A PRO* 3.4 38.8 + - - +
252A HIS* 1.3 84.8 - - - +
254A ARG* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 4.7 8.8 + - - -
146A PHE* 3.9 36.6 - - + -
189A GLY 5.0 4.2 + - - +
190A ASP* 3.4 21.0 - - + +
191A MET* 3.1 23.0 + - - +
228A LEU* 3.7 26.2 - - - +
236A MET* 3.4 20.4 - - - +
237A GLY 3.0 27.7 + - - +
253A ARG* 1.3 77.7 - - - +
255A ILE* 1.3 73.7 + - - +
256A ASP* 2.8 31.2 + - - -
9P G 3.7 1.8 + - - -
10P A 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 4.4 4.7 - - + -
191A MET* 3.1 36.6 - - + +
193A VAL* 4.0 11.7 - - + -
218A LEU* 5.4 2.2 - - + -
223A PHE* 4.1 19.1 - - + -
224A ILE* 4.6 3.6 - - + -
235A PHE* 4.1 11.3 - - + +
236A MET* 3.7 0.9 - - - -
237A GLY 3.0 44.1 + - - +
238A VAL 4.0 2.7 - - - +
239A CYS* 3.6 27.4 - - + -
254A ARG* 1.3 77.7 + - - +
256A ASP* 1.3 65.6 + - - +
257A ILE* 4.1 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASP* 3.2 2.6 - - - +
191A MET 2.8 6.5 + - - +
192A ASP* 3.4 10.8 - - + +
193A VAL* 2.7 33.3 + - - +
234A LYS* 6.4 0.9 - - + -
235A PHE 3.4 6.1 - - - +
236A MET* 3.5 12.7 - - + +
254A ARG* 2.8 37.3 + - - -
255A ILE* 1.3 72.5 - - - +
257A ILE* 1.3 57.5 + - - +
258A ARG* 4.2 12.8 - - + +
401A MN 2.0 34.7 + - - +
10P A 3.9 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 6.2 0.4 - - + -
193A VAL* 3.2 26.2 - - + +
195A LEU* 4.3 18.6 - - + -
211A LEU* 3.8 18.9 - - + +
214A VAL* 4.8 6.3 - - + -
215A VAL* 4.5 9.2 - - + -
218A LEU* 4.1 26.2 - - + -
224A ILE* 4.4 6.3 - - + -
233A THR 3.9 0.5 - - - +
234A LYS* 3.6 4.0 - - - +
235A PHE* 2.9 59.5 + - + +
255A ILE* 4.1 13.9 - - + -
256A ASP* 1.3 77.8 - - - +
258A ARG* 1.3 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A VAL 2.7 11.2 + - - +
194A LEU* 3.5 18.2 - - + +
195A LEU* 2.6 35.5 + - - +
233A THR 3.5 4.7 - - - +
234A LYS* 3.9 34.2 - - + +
236A MET* 6.2 0.8 - - - -
256A ASP* 4.2 11.3 - - + +
257A ILE* 1.3 79.5 - - - +
259A LEU* 1.3 54.9 + - - +
260A ILE* 4.3 5.4 - - + -
272A PHE* 3.2 48.5 - - - -
295A GLU* 5.3 2.8 + - - -
296A TYR* 5.9 1.2 + - - -
9P G 5.5 4.6 - - - +
10P A 4.6 27.7 + - - +
9T G 5.6 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TYR* 5.3 0.4 - - + -
195A LEU* 3.5 39.5 - - + +
196A THR* 4.2 10.5 - - - -
197A HIS* 5.2 0.7 - - + -
200A PHE* 3.8 27.0 - - + -
207A GLN 4.8 5.4 - - - +
210A LEU* 3.7 35.0 - - + -
211A LEU* 4.1 14.3 - - + +
232A GLU 3.7 18.2 - - - +
233A THR* 2.8 39.7 + - + +
257A ILE 4.2 0.4 - - - -
258A ARG* 1.3 72.5 - - - +
260A ILE* 1.3 62.7 + - - +
261A PRO* 4.6 0.7 - - - +
296A TYR* 5.4 2.3 + - - -
----------------------------------------------------------
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