Contacts of the strand formed by residues 183 - 192 (chain B) in PDB entry 5DK3
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 TYR 183 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASP* 2.8 29.3 + - - -
152B TYR* 2.8 49.3 + - + +
153B PHE* 3.8 28.9 - + - -
154B PRO 4.5 0.2 - - - -
155B GLU* 3.6 46.0 - - + +
175B ALA* 4.0 7.9 - - + -
176B VAL 3.3 19.3 - - - -
177B LEU* 3.8 36.1 - - + +
178B GLN* 3.7 0.7 - - - -
182B LEU* 1.3 74.1 - - - +
184B SER* 1.3 55.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.8 9.5 - - - +
149B VAL 3.2 8.3 - - - -
150B LYS* 3.4 24.1 + - - +
152B TYR* 4.0 2.9 - - - -
175B ALA* 3.2 3.4 - - - -
176B VAL* 2.8 49.0 + - - +
178B GLN* 3.2 23.0 + - - -
183B TYR* 1.3 69.5 - - - +
185B LEU* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 3.7 2.5 - - - +
149B VAL* 2.7 50.2 + - + +
152B TYR* 3.9 7.7 - - - +
155B GLU* 5.4 0.9 - - - +
157B VAL* 3.7 33.7 - - + +
159B VAL* 3.9 24.7 - - + -
172B THR* 4.1 13.7 - - + -
173B PHE 3.4 20.9 - - - +
174B PRO* 5.0 1.1 - - + -
175B ALA* 3.8 14.1 - - + +
176B VAL* 5.8 0.2 - - - -
184B SER* 1.3 76.0 - - - +
186B SER* 1.3 79.2 + - - +
187B SER 4.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.8 2.4 - - - +
180A SER* 4.0 23.3 + - - -
182A THR* 4.6 6.6 + - - -
131B LEU* 4.8 10.7 - - - +
147B CYS 3.5 6.8 + - - -
148B LEU* 3.6 20.1 - - - +
173B PHE* 2.8 46.2 + - - +
185B LEU* 1.3 80.6 - - - +
187B SER* 1.3 55.5 + - - +
188B VAL* 5.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 4.4 0.2 - - - +
146B GLY* 3.1 2.9 - - - -
147B CYS* 2.8 37.0 + - - +
149B VAL* 5.9 0.2 - - - -
159B VAL* 3.7 27.2 - - - +
161B TRP* 3.0 24.6 + - - -
170B VAL* 4.2 0.9 - - - +
171B HIS 3.4 5.2 + - - -
172B THR* 2.8 26.1 + - - -
185B LEU* 4.2 0.6 - - - +
186B SER* 1.3 72.6 - - - +
188B VAL* 1.3 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 4.8 6.5 - - + -
137A VAL* 6.0 0.4 - - + -
139A LEU* 3.7 37.7 - - + -
141A ASN* 4.8 0.4 - - - +
180A SER* 5.1 4.9 - - - +
131B LEU* 4.4 12.8 - - + -
145B LEU 3.3 11.9 - - - +
146B GLY* 4.0 4.3 - - - -
161B TRP* 4.5 2.5 - - - -
170B VAL* 3.3 7.4 - - - +
171B HIS* 2.8 52.6 + - + +
173B PHE* 3.8 22.2 - - + -
186B SER* 5.2 1.3 - - - -
187B SER* 1.3 80.6 + - - +
189B VAL* 1.3 66.4 + - - +
190B THR* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA 4.0 0.2 - - - +
144B ALA* 3.4 2.4 - - - +
145B LEU* 2.8 66.7 + - + +
161B TRP* 4.0 19.7 - - + -
166B LEU* 3.9 19.1 - - + -
168B SER 3.8 11.9 - - - +
169B GLY 3.3 7.4 - - - +
170B VAL* 3.7 26.9 - - + -
188B VAL* 1.3 79.3 - - - +
190B THR* 1.3 71.1 + - - +
191B VAL* 4.1 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 4.3 7.6 - - + -
139A LEU* 4.8 2.9 - - + -
141A ASN* 3.4 33.2 + - - +
142A ASN* 5.3 1.7 + - - -
142B THR* 3.9 18.4 - - + -
143B ALA 3.3 6.5 - - - +
144B ALA* 4.0 19.3 - - + -
168B SER 4.4 2.1 - - - +
169B GLY* 3.2 26.1 + - - +
171B HIS* 6.2 0.2 - - + -
188B VAL* 5.9 0.7 - - + -
189B VAL* 1.3 76.4 - - - +
191B VAL* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR* 3.5 5.7 - - - -
143B ALA* 2.8 39.3 + - + +
145B LEU* 4.4 7.9 - - + -
166B LEU* 4.7 4.9 - - + -
189B VAL* 4.1 19.3 - - + -
190B THR* 1.3 81.4 - - - +
192B PRO* 1.3 82.6 - - + +
196B LEU* 3.9 24.2 - - + -
201B TYR* 3.8 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER 3.4 10.3 - - - +
142B THR* 4.5 2.2 - - - +
191B VAL* 1.3 94.6 - - + +
193B SER* 1.3 65.2 + - - +
194B SER* 3.6 17.7 - - - +
195B SER* 3.0 34.5 + - - +
196B LEU 3.9 1.0 + - - -
201B TYR* 5.1 0.7 - - - +
----------------------------------------------------------
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