Contacts of the strand formed by residues 201 - 208 (chain B) in PDB entry 4N41
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 201 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG* 4.2 14.1 - - + -
193B VAL 3.4 16.2 - - - +
194B ARG* 4.1 8.8 - - - +
199B ARG 3.5 8.0 + - - -
200B ARG* 1.3 76.1 + - - +
202B TRP* 1.3 84.0 + - - +
246B ASP* 5.2 4.3 - - - +
247B PRO* 5.4 2.8 - - - +
264B VAL* 4.3 7.7 - - + +
10E A 4.0 18.4 + - - +
11E G 3.3 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG* 3.4 9.0 - - - +
193B VAL* 2.8 38.4 + - + +
195B ASN* 2.8 35.9 + - - +
200B ARG* 4.5 8.4 + - + -
201B THR* 1.3 84.5 - - - +
203B GLU* 1.3 59.7 + - - +
204B LEU 3.8 0.2 - - - -
244B VAL* 3.6 35.0 - - + -
245B ALA 3.7 13.9 - - - -
246B ASP* 3.9 28.9 - - + +
247B PRO* 5.5 1.8 - - - -
254B ILE* 3.9 24.7 - - + -
256B HIS* 4.0 8.8 - + - -
261B LEU* 4.3 12.3 - - + -
20E G 4.1 21.1 - - - -
21E T 4.0 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B LYS 3.9 8.7 - - - +
192B ARG* 4.7 1.1 - - - +
202B TRP* 1.3 72.1 - - - +
204B LEU* 1.3 64.7 + - - +
205B LEU* 3.2 2.1 + - - -
244B VAL* 4.5 1.1 - - - -
245B ALA* 2.9 49.2 + - + +
246B ASP 5.5 0.2 - - - -
247B PRO* 5.1 11.7 - - + +
250B PRO* 6.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 3.7 33.7 - - + -
183B LEU* 5.0 2.5 - - + -
189B LEU* 4.2 14.1 - - + +
190B PRO* 3.7 32.5 - - + +
191B LYS* 3.4 13.9 + - - +
193B VAL* 4.7 12.1 - - + -
202B TRP 3.7 3.2 + - - -
203B GLU* 1.3 68.1 - - - +
205B LEU* 1.3 61.8 + - - +
206B ARG* 3.9 14.6 - - - +
207B LEU* 5.5 2.7 - - + -
242B ALA* 3.9 19.7 - - + -
243B TRP 3.3 19.3 - - - +
244B VAL* 4.2 10.1 - - + +
261B LEU* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU 3.2 7.0 + - - +
204B LEU* 1.3 74.7 - - - +
206B ARG* 1.3 63.0 + - + +
243B TRP* 2.9 21.6 + - + +
244B VAL 4.7 6.1 - - - +
245B ALA* 4.9 6.3 - - + -
253B PRO* 6.0 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 3.8 8.5 - - - +
205B LEU* 1.3 84.0 - - + +
207B LEU* 1.3 68.1 + - - +
242B ALA* 3.7 2.9 - - - -
243B TRP* 2.7 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 5.3 0.9 - - + -
183B LEU* 4.2 26.7 - - + -
189B LEU* 6.0 2.7 - - + -
204B LEU* 5.5 2.9 - - + -
206B ARG* 1.3 85.6 - - - +
208B GLY* 1.3 58.2 + - - +
240B ARG* 5.7 2.7 - - + -
241B VAL 3.6 15.7 - - - +
242B ALA* 4.2 9.2 - - + -
243B TRP* 3.5 13.0 - - - -
258B THR* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 1.3 78.8 - - - +
209B GLU* 1.3 59.1 + - - -
210B GLU* 3.1 12.0 + - - +
240B ARG* 4.4 6.8 - - - +
241B VAL* 3.1 34.0 + - - +
243B TRP* 3.9 17.7 - - - -
----------------------------------------------------------
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