Contacts of the strand formed by residues 257 - 264 (chain A) in PDB entry 3A8X
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 ALA 257 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ARG* 3.4 9.4 - - - +
254A GLY* 3.0 29.9 + - - +
255A SER 3.8 0.4 - - - -
256A TYR* 1.3 89.4 - - + +
258A LYS* 1.3 59.9 + - - +
259A VAL* 5.1 2.2 - - + -
274A LYS* 3.6 39.5 - - + -
275A VAL 3.3 11.4 - - - +
276A VAL* 4.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A VAL* 4.0 25.1 - - + -
252A GLY 3.7 7.0 - - - +
253A ARG* 3.5 29.5 - - - +
257A ALA* 1.3 73.9 - - - +
259A VAL* 1.3 62.6 + - - +
260A LEU* 4.0 16.6 - - + -
273A MET 3.5 1.6 - - - +
274A LYS* 3.7 1.0 - - - -
275A VAL* 2.8 42.0 + - + +
550A GLU* 4.2 2.4 + - - -
551A PRO 4.7 0.6 + - - -
553A GLN* 2.6 40.1 + - - +
554A LEU* 4.8 5.2 - - + -
555A TPO 2.7 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A VAL* 3.6 4.3 - - - +
251A ILE* 2.7 51.0 + - + -
252A GLY* 2.8 33.4 + - - +
253A ARG* 4.6 2.5 - - - +
254A GLY 5.7 0.7 - - - +
257A ALA* 5.1 3.8 - - + -
258A LYS* 1.3 76.6 - - - +
260A LEU* 1.3 59.6 + - - +
272A ALA* 4.0 15.5 - - + -
273A MET 3.4 10.3 - - - +
274A LYS* 4.3 20.2 - - + +
323A ILE* 5.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 5.1 8.7 - - + -
249A ARG 3.1 10.1 - - - +
250A VAL* 3.3 35.2 - - + -
251A ILE* 4.0 4.7 - - - -
258A LYS* 4.0 22.9 - - + -
259A VAL* 1.3 78.8 - - - +
261A LEU* 1.3 61.3 + - - +
262A VAL* 4.1 15.9 - - + -
272A ALA* 3.3 5.4 - - - +
273A MET* 2.7 41.8 + - + +
275A VAL* 3.7 30.3 - - + -
552A VAL* 4.7 7.9 - - + -
553A GLN 5.0 4.5 - - - +
554A LEU* 4.4 9.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
247A LEU* 4.0 0.3 - - - -
248A LEU* 2.7 43.6 + - + -
249A ARG* 2.8 25.2 + - + +
251A ILE* 4.0 15.8 - - + +
260A LEU* 1.3 72.3 - - - +
262A VAL* 1.3 58.9 + - - +
270A ILE* 3.0 31.9 - - + -
271A TYR 3.4 11.2 - - - +
325A TYR* 3.9 26.7 - - + +
538A PHE* 3.4 50.5 - - + -
540A LEU* 4.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.7 26.5 - - + -
246A ASP 3.2 8.7 - - - +
247A LEU* 3.8 15.5 - - + -
248A LEU* 4.1 5.1 - - - +
260A LEU* 4.1 4.7 - - + -
261A LEU* 1.3 79.7 - - - +
263A ARG* 1.3 62.1 + - - +
270A ILE* 3.3 10.2 - - - +
271A TYR* 2.9 53.1 + - + +
272A ALA 4.4 0.2 - - - +
273A MET* 3.7 46.9 - - + -
322A VAL* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE* 3.2 7.5 - - - -
246A ASP* 2.8 71.2 + - + +
248A LEU* 4.0 32.9 - - + +
262A VAL* 1.3 76.0 - - - +
264A LEU* 1.3 73.2 + - - +
265A LYS* 3.3 3.3 + - - +
268A ASP* 3.1 32.8 + - - +
269A ARG 3.3 12.6 - - - +
270A ILE* 4.7 7.6 - - + +
538A PHE* 5.4 3.8 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
240A LEU* 4.0 21.1 - - + -
244A ASP* 3.2 33.2 - - + +
245A PHE* 3.8 22.8 - - + -
263A ARG* 1.3 68.5 - - - +
265A LYS* 1.3 57.6 + - - +
266A LYS* 3.3 15.1 + - + +
267A THR* 3.7 16.8 - - - +
268A ASP* 2.7 34.5 + - - -
269A ARG 2.9 12.4 + - - +
271A TYR* 4.1 7.8 - - + -
310A HIS* 3.6 31.9 - - + +
578B PRO* 3.8 14.4 - - + +
----------------------------------------------------------
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