Contacts of the strand formed by residues 300 - 305 (chain A) in PDB entry 3I5Y
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 300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE 5.0 3.1 + - - +
142A SER 3.2 16.6 + - - -
143A SER* 4.1 6.3 + - - +
144A GLU 2.8 30.6 + - - -
145A ASP* 3.9 15.9 - - - +
146A HIS* 3.5 23.0 + - + +
147A ASP* 3.6 4.5 - - - -
262A ASP 3.0 13.0 + - - +
263A TYR* 3.4 36.5 + - + +
264A LYS 3.0 25.3 + - - +
298A ASN 3.4 2.6 + - - +
299A ILE* 1.3 76.1 - - - +
301A THR* 1.3 60.5 + - - +
302A LEU* 5.3 2.5 - - + -
322A LYS* 3.5 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ASP* 2.8 21.7 + - - +
148A VAL 3.0 26.0 + - - +
264A LYS* 2.7 48.2 + - + +
266A LEU* 4.3 2.5 - - + -
299A ILE* 4.4 1.9 + - - +
300A LYS* 1.3 73.7 - - - +
302A LEU* 1.3 65.5 + - - +
303A LEU* 3.5 25.4 - - + -
319A ILE* 3.3 6.8 + - + +
320A MET* 3.7 20.5 - - - +
321A ASN 5.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE* 3.8 36.3 - - + -
146A HIS 5.8 0.2 - - - +
147A ASP* 5.4 0.2 - - - -
148A VAL* 3.4 30.7 - - + +
162A PHE* 4.6 8.3 - - + +
166A ILE* 5.2 4.7 - - + -
263A TYR* 4.0 22.9 - - + -
264A LYS 2.9 10.5 + - - +
265A VAL* 3.5 31.1 - - + +
266A LEU 2.8 29.3 + - - +
300A LYS* 5.2 2.2 - - + -
301A THR* 1.3 83.4 - - - +
303A LEU* 1.3 63.7 + - - +
304A PHE* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL 2.9 12.9 + - - +
149A ILE* 3.5 20.7 - - + -
150A ALA* 2.9 27.8 + - - +
266A LEU* 3.7 28.9 - - + -
269A ALA* 3.6 15.3 - - + -
273A LEU* 4.4 7.4 - - + -
301A THR* 3.5 23.1 - - + -
302A LEU* 1.3 80.7 - - - +
304A PHE* 1.3 64.4 + - - +
308A LEU* 4.7 2.2 - - + -
312A VAL* 4.9 7.0 - - + +
316A ALA* 3.7 28.7 - - + -
319A ILE* 4.8 2.0 - - + -
320A MET* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 4.2 7.4 - - + -
136A THR* 4.3 2.5 - - + -
140A ILE* 4.1 23.1 - - + -
148A VAL* 5.3 3.4 - - + -
150A ALA* 3.3 32.5 - - + -
158A LYS* 4.1 24.5 - - + -
161A ALA* 4.0 26.2 - - + -
162A PHE* 3.9 31.2 - + + -
265A VAL* 4.7 2.2 - - + -
266A LEU 3.1 9.0 + - - +
267A ASP* 4.1 14.6 - - - +
268A GLU 3.0 12.0 + - - -
269A ALA* 3.0 23.2 + - - +
302A LEU* 4.2 22.4 - - + -
303A LEU* 1.3 79.1 - - - +
305A SER* 1.3 59.8 + - - +
308A LEU* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ALA 3.3 5.5 + - - +
151A ARG* 3.3 26.7 - - - +
152A ALA 3.4 2.8 + - - -
158A LYS* 4.0 13.9 - - - +
267A ASP* 5.4 0.4 - - - -
268A GLU* 4.0 6.3 + - - +
269A ALA 4.0 3.4 - - - -
270A ASP* 2.6 30.0 + - - -
304A PHE* 1.3 77.3 - - - +
306A ALA* 1.3 68.9 + - - +
307A THR* 3.1 18.3 + - - -
308A LEU* 3.9 13.3 - - - +
438A ARG* 3.8 6.1 + - - -
462A HIS* 3.9 1.2 - - - -
----------------------------------------------------------
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