Contacts of the strand formed by residues 260 - 264 (chain B) in PDB entry 5H15
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 LEU 260 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B MET* 4.4 5.8 - - + -
253B SER 3.2 7.9 - - - +
254B CYS* 3.7 20.2 - - + -
258B HIS 5.0 1.8 - - - +
259B SER* 1.3 77.2 - - - +
261B LYS* 1.3 61.7 + - - +
299B PHE* 5.0 0.9 - - - -
300B SER* 3.4 3.1 + - - -
301B THR* 3.0 36.5 + - + +
302B ARG* 6.4 0.2 - - - -
304B ILE* 4.0 21.1 - - + +
305B HIS* 4.1 9.9 - - + -
309B VAL* 4.0 4.7 - - + -
312B VAL* 3.7 18.2 - - + -
321B SER* 3.6 32.1 - - - +
331B TRP* 3.6 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLU 3.8 18.9 + - - +
234B GLY 3.6 6.5 + - - -
235B HIS* 3.6 35.4 - - + +
252B MET* 3.3 6.8 - - - -
253B SER* 2.8 36.7 + - - +
257B ASP* 4.2 2.5 + - - -
259B SER* 3.3 21.7 + - - +
260B LEU* 1.3 73.8 - - - +
262B LEU* 1.4 59.4 + - - +
263B TRP* 3.6 31.3 - - + +
297B PRO* 3.9 7.9 - - + -
299B PHE 3.3 6.7 - - - +
300B SER* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LYS* 3.9 13.7 - - + -
251B ILE 3.4 8.3 - - - +
252B MET* 3.6 13.3 - - + -
261B LYS* 1.4 71.6 - - - +
263B TRP* 1.3 57.1 + - - +
264B ARG* 3.8 37.5 - - + +
297B PRO* 3.2 8.8 - - - +
298B ASP* 2.7 39.5 + - + -
299B PHE* 2.9 31.7 + - + +
314B TRP* 3.5 38.4 - - + -
333B PRO* 5.7 0.2 - - + -
340B ILE* 4.7 6.7 - - + -
343B ILE* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.6 22.4 - - + +
229B PHE* 3.6 45.3 - + + -
230B GLY 4.1 0.4 - - - -
233B GLU 4.8 0.2 - - - -
234B GLY* 3.9 24.2 - - - -
235B HIS* 4.6 2.9 - + - -
250B LYS* 3.6 1.2 - - - -
251B ILE* 2.7 51.2 + - + +
253B SER* 2.8 26.8 + - - -
261B LYS* 3.6 37.5 + - + +
262B LEU* 1.3 72.9 - - - +
264B ARG* 1.3 64.9 + - - +
265B ILE* 3.6 4.0 + - - +
294B ILE* 3.7 22.7 - - + -
295B HIS 5.0 0.2 - - - -
296B PHE 3.8 6.3 - - - -
297B PRO* 3.7 34.8 - - + -
298B ASP* 4.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B PHE* 5.0 2.1 - - - -
249B GLU 3.9 4.3 - - - +
250B LYS* 4.0 14.6 - - + +
262B LEU* 3.8 19.8 - - + +
263B TRP* 1.3 71.3 - - - +
265B ILE* 1.3 61.5 + - - +
266B ASN* 3.6 21.7 - - - +
267B SER* 3.9 14.7 + - - +
270B MET* 3.7 14.6 - - - +
298B ASP* 2.9 43.2 + - + +
340B ILE 2.8 24.4 + - - -
341B ASP* 3.3 35.3 + - - +
343B ILE* 3.5 28.1 + - - +
----------------------------------------------------------
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