Contacts of the strand formed by residues 163 - 171 (chain D) in PDB entry 4A12
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 HIS 163 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D HIS* 3.1 29.7 + + + -
159D GLN* 3.4 2.0 - - - +
160D THR* 2.8 46.4 + - - +
162D LYS* 1.3 97.3 - - + +
164D TYR* 1.3 59.5 + - - +
165D TYR* 4.1 18.9 + - + -
183D LYS* 3.5 40.5 - - + -
184D MSE 3.3 4.7 - - - +
185D PHE* 3.7 24.6 - + + +
186D TYR* 3.4 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ASN* 3.4 43.0 + - + +
126D ILE* 3.8 41.3 - - + -
128D GLN* 4.0 10.3 + - + -
156D VAL* 3.7 26.0 - - + -
158D ASN 3.7 2.7 - - - -
159D GLN* 3.1 37.5 + - + -
163D HIS* 1.3 70.8 - - - +
165D TYR* 1.3 61.9 + - - +
166D VAL* 3.8 1.3 + - + -
182D PHE 3.5 1.9 - - - +
183D LYS* 3.8 1.6 - - - -
184D MSE 2.7 38.6 + - + +
186D TYR* 3.4 47.1 - + + -
188D LYS* 5.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D VAL* 3.5 3.6 - - - +
157D VAL* 2.7 40.8 + - + -
158D ASN* 2.7 50.1 + - + +
159D GLN 4.4 0.7 - - - -
160D THR* 3.7 28.8 + - + +
163D HIS* 4.1 17.9 + - + +
164D TYR* 1.3 71.7 - - - +
166D VAL* 1.3 54.5 + - - +
181D ASN* 4.9 10.3 - - - +
182D PHE 3.4 6.7 - - - +
183D LYS* 3.6 47.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D CYS* 3.7 26.2 - - - -
125D LEU* 3.8 7.6 - - + -
126D ILE* 3.8 29.2 - - + -
154D ALA* 3.8 21.8 - - + -
155D ARG 3.4 11.0 - - - +
156D VAL* 4.4 11.2 - - + -
157D VAL* 4.6 0.7 - - - -
164D TYR 4.3 2.7 - - - +
165D TYR* 1.3 77.1 - - - +
167D GLU* 1.3 65.8 + - - +
168D VAL* 5.0 0.2 - - - -
180D GLY 3.7 0.7 - - - +
181D ASN* 3.5 5.4 + - - -
182D PHE* 2.7 40.8 + - + +
184D MSE 4.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D GLU 3.7 1.9 - - - +
154D ALA* 3.4 1.4 - - - -
155D ARG* 2.9 52.8 + - + +
157D VAL* 3.7 34.0 - - + +
166D VAL* 1.3 71.2 - - - +
168D VAL* 1.3 62.3 + - - +
169D LYS* 4.3 10.9 + - + -
179D LYS* 6.5 1.1 - - + -
180D GLY 3.5 5.2 - - - +
181D ASN* 3.6 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ALA* 3.9 26.2 - - + +
121D LEU* 4.7 2.2 - - + -
122D CYS* 3.7 31.0 - - - -
152D ALA* 4.5 6.5 - - + -
153D GLU 3.4 11.7 - - - +
154D ALA* 3.8 11.0 - - + -
166D VAL* 4.3 1.1 - - + -
167D GLU* 1.3 74.8 - - - +
169D LYS* 1.3 67.4 + - - +
170D SER* 4.1 15.0 - - - +
178D PHE* 4.5 2.7 - - + -
179D LYS* 3.4 6.5 - - - +
180D GLY 2.7 39.2 + - - +
182D PHE* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D GLU* 2.9 40.9 + - + +
155D ARG* 3.3 31.2 - - - +
167D GLU* 4.3 12.5 + - + -
168D VAL* 1.3 77.4 - - - +
170D SER* 1.3 61.2 + - - +
171D TYR* 3.4 33.6 + - + +
176D LEU* 3.8 14.4 - - + -
178D PHE 3.6 3.4 - - - -
179D LYS* 4.3 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D LEU* 4.8 3.7 + - - +
117D GLN* 4.4 2.1 + - - -
118D ALA* 5.3 0.7 - - - +
150D VAL* 3.6 22.2 - - - +
151D ARG 3.5 4.0 - - - -
152D ALA* 3.3 21.1 - - - +
168D VAL* 4.1 3.7 - - - +
169D LYS* 1.3 73.3 - - - +
171D TYR* 1.3 58.9 + - - +
176D LEU* 3.6 5.0 - - - +
177D VAL* 3.0 26.7 + - - -
178D PHE* 2.9 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D THR 3.7 0.9 - - - +
150D VAL* 3.5 4.7 - - - -
151D ARG* 2.8 61.0 + - - +
153D GLU* 3.3 22.5 + - - -
155D ARG* 5.6 0.3 + - - -
169D LYS* 3.4 46.7 - - + +
170D SER* 1.3 71.6 - - - +
172D VAL* 1.3 63.4 + - - +
173D LYS 3.8 15.4 + - - +
174D HIS* 4.6 4.0 - - - -
175D THR 3.3 12.3 - - - +
176D LEU* 3.5 39.8 - - + +
177D VAL* 4.1 0.9 - - - -
----------------------------------------------------------
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