Contacts of the strand formed by residues 274 - 278 (chain A) in PDB entry 4H1S
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 274 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP 4.7 0.9 - - - +
266A ILE* 3.9 22.4 - - + -
267A VAL 3.6 2.0 - - - -
268A THR* 2.9 35.0 + - - +
272A GLY 5.7 2.9 - - - +
273A ARG* 1.3 76.0 + - - +
275A VAL* 1.3 60.9 + - - +
276A PRO* 3.5 9.2 - - - +
300A VAL* 4.6 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ALA* 3.6 41.5 - - + +
236A VAL 3.7 18.8 - - - +
237A ASP 3.6 19.1 - - - +
238A VAL* 4.1 3.1 - - - +
239A VAL* 4.3 4.7 - - + -
265A PHE 3.6 0.3 - - - +
266A ILE* 4.3 2.6 - - - +
267A VAL* 2.8 41.2 + - - +
269A SER* 4.1 5.4 - - - -
273A ARG* 3.9 22.0 - - - +
274A LYS* 1.3 74.0 - - - +
276A PRO* 1.3 73.8 - - - +
277A VAL* 3.6 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP 3.3 18.4 - - - +
238A VAL* 3.6 17.0 - - + +
239A VAL 3.0 24.4 + - - +
264A PRO* 3.6 22.4 - - + -
265A PHE 3.5 5.4 - - - +
266A ILE* 4.0 8.1 - - + -
274A LYS 3.5 9.2 - - - +
275A VAL* 1.3 85.6 - - - +
277A VAL* 1.3 60.1 + - - +
278A VAL* 4.2 0.4 - - - -
290A LEU* 4.3 6.7 - - + -
292A ILE* 4.2 7.6 - - + -
300A VAL* 4.9 7.0 - - + -
303A SER* 3.7 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PHE* 3.9 21.8 - - + -
226A ASP* 3.8 31.6 - - + +
227A LYS* 4.5 1.1 - - + -
230A ALA* 3.7 19.3 - - + -
239A VAL* 3.5 9.9 - - + +
248A LEU* 3.5 7.8 - - - +
265A PHE* 2.7 40.4 + - + +
267A VAL* 3.7 29.6 - - + -
275A VAL 3.9 0.9 - - - +
276A PRO* 1.3 76.6 - - - +
278A VAL* 1.3 69.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 5.9 0.2 - - + -
33A HIS* 3.6 25.8 - - + +
239A VAL 2.9 13.5 + - - +
240A VAL* 3.7 17.7 - - + -
241A GLY* 2.9 26.9 + - - -
248A LEU* 4.1 4.3 - - - -
263A TYR* 3.5 26.7 - - + +
264A PRO* 3.6 21.3 - - + -
277A VAL* 1.3 85.2 - - - +
279A GLN* 1.3 64.1 + - - +
290A LEU* 3.8 20.0 - - + -
----------------------------------------------------------
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