Contacts of the strand formed by residues 168 - 174 (chain D) in PDB entry 4F2N
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 168 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D LEU* 5.3 0.4 - - + -
129D ALA* 3.7 39.7 - - + +
130D ILE* 4.0 19.5 - - + +
133D GLN* 3.0 33.8 + - + +
134D PHE* 3.8 18.9 - - + -
159D LEU* 4.1 6.1 - - + -
160D CYS 3.2 13.2 - - - +
161D VAL* 3.7 16.8 - - + -
166D LYS 3.8 2.2 + - - +
167D GLU* 1.3 74.0 - - - +
169D LEU* 1.3 64.1 + - - +
187D ILE* 3.7 27.6 - - + -
225D TYR* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D GLN* 5.4 2.9 - - - +
134D PHE* 4.5 2.0 - - - -
158D TRP 3.6 0.5 - - - +
159D LEU* 3.4 6.2 - - - +
160D CYS* 2.8 37.8 + - + +
162D ASP* 3.8 29.4 - - + +
167D GLU* 4.5 21.1 - - + +
168D LEU* 1.3 82.6 - - - +
170D ILE* 1.3 68.5 + - - +
171D ASP* 3.9 2.0 + - + +
184D LEU* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D PHE* 3.9 19.8 - - + -
140D PHE* 3.8 31.9 - - + -
143D SER* 3.7 30.5 - - - -
144D PHE* 3.7 14.1 - - + +
147D ALA* 3.8 28.7 - - + -
157D THR* 4.2 9.2 - - + -
158D TRP 3.2 11.0 - - - +
159D LEU* 4.6 0.7 - - + -
169D LEU* 1.3 76.5 - - - +
171D ASP* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D THR* 3.5 1.4 - - - +
158D TRP* 2.6 49.0 + - + -
160D CYS* 4.6 4.3 - - - -
169D LEU* 3.9 3.1 + - + +
170D ILE* 1.3 77.1 - - - +
172D SER* 1.3 68.4 + - - +
173D THR* 3.9 9.2 - - - +
179D PRO* 3.4 27.2 - - - +
182D SER* 5.3 1.2 + - - -
184D LEU* 4.2 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D ALA* 3.6 25.7 + - - +
151D ASN* 3.8 22.2 - - - -
156D TRP 3.4 4.7 - - - -
157D THR* 3.3 16.6 + - - -
171D ASP* 1.3 80.7 + - - +
173D THR* 1.3 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ASN* 3.0 23.0 + - - -
155D GLY* 3.3 0.5 - - - -
156D TRP* 2.9 26.6 + - - +
158D TRP* 3.0 24.1 + - - +
171D ASP* 3.9 15.5 - - - +
172D SER* 1.3 78.5 - - - +
174D SER* 1.3 60.8 + - - +
177D GLY* 2.7 37.9 + - - -
178D CYS 3.9 4.3 - - - +
179D PRO* 4.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ASN* 4.5 12.2 + - - -
151D ASN* 4.9 3.8 - - - -
152D PHE 5.2 3.5 + - - -
154D SER 3.6 7.5 + - - -
173D THR* 1.3 75.5 - - - +
175D ASN* 1.3 80.7 + - - +
177D GLY* 3.0 21.2 + - - -
----------------------------------------------------------
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