Contacts of the strand formed by residues 240 - 246 (chain A) in PDB entry 1PH3
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 THR 240 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 3.0 25.6 + - + -
237A ASP* 2.6 33.0 + - - +
239A TYR* 1.3 83.8 - - - +
241A ASN* 1.3 70.7 + - - +
256A LEU* 3.9 35.2 - - + -
257A SER 4.1 5.2 - - - +
258A LEU* 4.5 10.1 - - + -
259A LYS* 4.3 1.3 - - - +
145B LYS* 3.0 20.9 + - - +
10D G 3.4 8.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A VAL* 4.0 15.1 - - + +
234A HIS 3.6 1.8 - - - +
235A GLU* 3.6 19.8 - - - +
236A LEU* 4.8 0.7 - - - -
240A THR* 1.3 76.5 - - - +
242A GLU* 1.3 60.0 + - - +
243A LEU* 3.9 14.8 - - + -
255A THR 3.8 0.2 - - - +
256A LEU* 3.3 6.7 - - - +
257A SER* 2.7 47.7 + - - +
259A LYS* 3.7 31.9 - - - +
262A PHE 5.0 0.8 + - - -
263A PRO* 6.1 0.4 - - - +
265A VAL* 3.9 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A GLN* 3.6 3.3 - - - +
234A HIS* 2.7 65.8 + - + +
236A LEU* 4.5 9.7 - - + +
241A ASN* 1.3 74.0 - - - +
243A LEU* 1.3 62.7 + - - +
244A LYS* 3.9 0.7 + - - +
254A TYR* 3.5 30.9 - - + -
255A THR 3.5 5.4 - - - +
256A LEU* 3.8 9.0 - - + -
285A LYS* 2.8 25.8 + - - -
332A ALA* 4.6 8.1 + - - +
142B ASP* 2.7 30.2 - - - +
146B THR* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 4.4 18.4 - - + -
232A GLN 3.4 5.8 - - - +
233A VAL* 4.3 13.0 - - + -
241A ASN* 4.0 13.5 - - + -
242A GLU* 1.3 77.2 - - - +
244A LYS* 1.3 60.2 + - - +
245A LEU* 3.8 14.7 + - + +
253A PHE 3.6 0.7 - - - +
254A TYR* 3.1 9.8 - - - -
255A THR* 2.8 47.9 + - + +
257A SER* 3.9 20.6 - - - -
265A VAL* 3.8 29.4 - - + -
271A VAL* 5.9 0.2 - - + -
273A ILE* 5.6 0.7 - - + -
296A ILE* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 3.7 2.3 - - - -
231A LEU* 2.8 43.0 + - + +
232A GLN* 2.9 41.2 + - + +
242A GLU 3.9 0.6 + - - +
243A LEU* 1.3 72.2 - - - +
245A LEU* 1.3 60.6 + - - +
252A VAL* 4.2 21.1 - - + -
253A PHE 3.6 2.5 - - - -
254A TYR* 3.5 36.1 - - + +
315A ASP* 4.2 6.9 + - - -
316A ASP 2.6 30.5 + - - -
317A HIS* 4.4 2.0 - - - -
319A VAL* 5.0 3.4 - - - -
320A GLU* 2.8 30.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
214A LEU* 4.7 3.1 - - + -
226A VAL* 5.3 1.8 - - + -
228A ALA* 4.1 14.4 - - + -
229A LYS 3.5 7.2 - - - +
230A ILE* 4.1 22.9 - - + -
231A LEU* 5.0 0.4 - - - -
243A LEU* 4.1 25.1 - - + +
244A LYS* 1.3 76.2 - - - +
246A LYS* 1.3 63.2 + - - +
251A GLN 4.4 0.2 - - - -
252A VAL* 3.1 9.1 - - - +
253A PHE* 2.5 47.0 + - + +
255A THR* 3.9 17.7 - - + -
271A VAL* 4.9 4.5 - - + -
273A ILE* 3.5 31.2 - - + -
288A LEU* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 4.4 0.2 - - - -
228A ALA* 3.5 3.3 - - - +
229A LYS 3.0 26.1 + - - +
231A LEU* 3.6 28.3 - - + -
245A LEU* 1.3 79.1 - - - +
247A ASP* 1.3 67.8 + - - +
250A GLY* 3.7 26.0 - - - +
251A GLN 3.3 13.9 - - - +
252A VAL* 3.9 6.1 - - + -
313A ILE* 3.3 17.7 - - + +
314A GLN* 2.9 30.4 + - - +
315A ASP 4.1 1.2 + - - -
316A ASP* 3.2 29.1 + - + +
----------------------------------------------------------
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