Contacts of the strand formed by residues 198 - 206 (chain D) in PDB entry 1P4A
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 ASN 198 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D GLU* 3.2 41.0 - - - +
131D ILE* 3.7 1.7 - - - -
132D ASP* 2.6 52.7 + - - +
133D VAL 3.4 7.1 + - - +
196D GLY 4.4 4.2 + - - -
197D SER* 1.3 69.8 - - - +
199D VAL* 1.3 60.7 + - - +
225D ASN* 3.1 31.8 + - - +
227D ALA* 4.2 6.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D VAL* 3.5 23.1 - - + +
135D MET* 3.4 33.2 - - + +
193D MET* 4.0 10.5 - - + -
197D SER 3.8 12.3 - - - +
198D ASN* 1.3 77.8 - - - +
200D LEU* 1.3 66.0 + - - +
201D ILE* 3.7 5.2 + - + +
219D LEU* 3.8 36.8 - - + -
224D ALA* 4.1 0.9 - - + -
225D ASN 2.7 14.1 + - - +
226D VAL* 3.6 4.3 - - - +
227D ALA* 2.8 28.3 + - - +
228D GLY 3.6 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D PHE* 5.1 0.9 - - + +
126D PHE* 3.7 36.1 - - + -
131D ILE* 4.0 22.3 - - + +
133D VAL 2.9 13.8 + - - +
134D VAL* 3.3 11.7 - - + +
135D MET 2.8 30.8 + - - -
148D ALA* 5.1 2.5 - - + -
152D LEU* 4.0 26.7 - - + -
198D ASN 4.0 0.6 + - - -
199D VAL* 1.3 71.9 - - - +
201D ILE* 1.3 63.4 + - - +
202D ILE* 3.7 22.7 + - + -
228D GLY* 3.4 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D MET* 3.5 9.0 - - + -
199D VAL* 3.7 15.2 + - + +
200D LEU* 1.3 73.3 - - - +
202D ILE* 1.3 60.1 + - - +
203D ASP 5.0 0.2 - - - +
212D ILE* 4.2 18.2 - - + +
215D MET* 3.9 44.0 - - + -
216D ILE* 3.9 27.1 - - + -
219D LEU* 4.2 14.6 - - + -
226D VAL* 4.5 8.7 - - + -
228D GLY 2.9 14.1 + - - +
229D ILE* 3.3 12.4 - - + -
230D GLY 2.7 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D PHE* 3.6 45.5 - - + -
134D VAL* 3.6 28.0 - - + -
135D MET 2.9 8.2 + - - +
136D THR* 2.7 31.4 + - - -
141D GLY 5.1 0.9 - - - +
144D LEU* 4.3 11.7 - - + +
145D ALA* 4.1 23.6 - - + +
148D ALA* 4.4 5.8 - - + -
200D LEU* 3.8 22.9 - - + -
201D ILE* 1.3 84.9 - - - +
203D ASP* 1.3 63.8 + - - +
215D MET* 4.9 0.5 - - - +
230D GLY* 3.2 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D THR* 4.2 4.8 + - - -
137D VAL* 4.2 10.8 - - - +
141D GLY* 5.2 1.5 - - - -
144D LEU* 3.9 10.4 - - - +
201D ILE* 5.3 0.2 - - + -
202D ILE* 1.3 77.3 - - - +
204D ASP* 1.3 76.1 + - - +
205D PHE 3.7 6.5 - - - +
211D THR* 4.5 4.0 - - - +
212D ILE* 4.2 31.5 - - + +
215D MET* 4.7 10.3 - - + -
230D GLY 2.8 9.6 + - - +
231D VAL* 3.3 8.6 - - + -
232D LEU 3.1 21.8 + - - -
607D PCP 3.0 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LEU* 4.5 3.8 - - + +
109D LEU* 3.8 43.1 - - + +
140D LYS* 3.9 4.7 - - - +
141D GLY* 4.0 16.1 + - - -
144D LEU* 4.0 9.4 - - + +
203D ASP* 1.3 77.2 - - - +
205D PHE* 1.3 72.5 + - + +
206D MET 4.3 0.4 - - - -
232D LEU* 3.1 7.7 - - - +
233D VAL* 2.9 29.1 + - - +
607D PCP 2.7 42.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D GLY 3.9 16.8 - - - -
102D TYR* 3.8 37.0 - + - -
103D VAL* 4.8 4.3 - - + -
105D LEU* 4.2 13.9 - - + -
203D ASP* 3.6 4.0 - - - -
204D ASP* 1.3 95.3 + - - +
206D MET* 1.3 58.6 + - - +
207D LYS* 3.6 23.3 + - + -
233D VAL* 3.2 37.7 - - + -
235D ALA* 3.9 24.2 - - + -
252D LEU* 3.9 16.2 - - + -
607D PCP 3.0 32.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ASP* 4.9 1.1 - - - -
205D PHE* 1.3 73.2 - - - +
207D LYS* 1.3 60.5 + - - +
209D GLY* 4.2 16.4 - - - -
212D ILE* 3.7 28.7 - - + -
231D VAL* 4.0 16.6 - - + +
233D VAL 2.9 8.7 + - - +
234D GLU* 3.4 13.7 - - + +
235D ALA 2.9 26.0 + - - -
238D VAL* 4.1 18.8 - - + +
243D VAL* 4.0 21.1 - - - -
246D TYR* 3.3 48.5 - - + +
607D PCP 3.5 4.5 - - - +
----------------------------------------------------------
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