Contacts of the strand formed by residues 184 - 194 (chain A) in PDB entry 3IFO
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 184 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA* 4.5 7.0 - - + -
125A LYS 4.8 0.7 - - - +
127A THR* 4.4 16.2 - - + +
154A GLY* 3.7 31.9 - - - +
155A TYR 3.7 4.7 - - - +
156A PHE* 3.9 21.5 - - + -
180A LEU* 3.4 4.7 - - - -
181A GLN* 2.7 42.1 + - - +
182A SER* 4.1 7.2 - - - +
183A ASP* 1.3 88.0 - - + +
185A TYR* 1.3 61.2 + - - +
1L ASP 6.2 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 5.5 3.8 - - - +
120A THR* 3.9 21.8 + - - +
154A GLY 2.9 22.2 + - - -
155A TYR* 2.9 50.7 + - + +
156A PHE* 3.7 26.0 - + - -
157A PRO* 4.3 0.9 - - + -
158A GLU* 3.7 44.1 - - + +
178A ALA* 4.0 14.6 - - + -
179A VAL 3.4 7.9 - - - -
180A LEU* 3.6 33.8 - - + +
184A LEU* 1.3 73.1 - - - +
186A THR* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 3.9 16.3 - - - +
152A VAL 3.1 12.9 + - - -
153A LYS* 3.8 14.6 - - - +
154A GLY 4.2 1.6 - - - -
155A TYR* 4.1 1.6 - - - -
177A PRO 4.5 0.3 - - - +
178A ALA* 3.5 1.5 - - - -
179A VAL* 3.0 48.8 + - + +
181A GLN* 3.9 31.2 - - + +
185A TYR* 1.3 76.2 - - - +
187A LEU* 1.3 62.2 + - - +
165B LEU* 4.7 3.6 - - + -
183B THR* 5.9 1.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 3.8 3.3 - - - +
152A VAL* 2.7 54.9 + - + +
155A TYR* 3.3 22.4 - - + +
158A GLU* 4.9 1.6 - - - +
160A VAL* 3.6 20.2 - - + +
162A VAL* 4.2 14.6 - - + -
175A THR* 4.2 10.1 - - + -
176A PHE 3.5 20.2 - - - +
177A PRO* 4.2 3.1 - - + +
178A ALA* 3.8 12.6 - - + +
186A THR* 1.3 77.4 + - - +
188A SER* 1.3 76.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 4.4 2.8 - - - +
150A CYS 3.4 13.0 + - - -
151A LEU* 3.5 23.4 - - - +
175A THR* 3.7 0.2 - - - -
176A PHE* 3.0 33.3 + - - +
187A LEU* 1.3 81.9 - - - +
189A SER* 1.3 62.7 + - - +
138B VAL* 4.5 5.4 - - - +
140B PHE* 3.9 24.3 - - - -
181B SER* 4.1 12.5 + - - -
183B THR* 4.9 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLY* 3.0 4.0 - - - -
150A CYS* 2.9 35.5 + - - +
152A VAL* 6.0 0.2 - - - -
162A VAL* 3.8 21.9 - - - +
164A TRP* 3.0 24.6 + - - -
173A VAL* 4.0 0.2 - - - +
174A HIS 3.2 6.4 + - - -
175A THR* 2.9 27.3 + - - -
176A PHE* 4.6 0.4 - - - -
187A LEU* 4.5 0.2 - - - +
188A SER* 1.3 77.1 - - - +
190A SER* 1.3 62.1 + - - +
140B PHE* 3.9 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A THR* 4.1 5.8 - - - +
148A LEU 3.2 7.9 - - - -
164A TRP* 4.4 0.2 - - - -
172A GLY 4.2 0.4 + - - -
173A VAL* 3.2 5.9 - - - +
174A HIS* 2.8 47.5 + - - +
176A PHE* 4.3 1.5 - - - -
189A SER* 1.3 74.1 - - - +
191A VAL* 1.3 63.1 + - - +
192A THR* 5.2 0.3 + - - -
140B PHE* 3.3 36.1 - - - -
142B ASN* 3.3 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL 3.8 0.9 - - - +
147A THR* 3.6 1.1 - - - -
148A LEU* 2.9 39.6 + - + +
164A TRP* 3.6 38.6 - - + -
169A LEU* 3.8 25.1 - - + -
171A SER 4.1 5.8 - - - +
172A GLY 3.2 4.9 - - - -
173A VAL* 3.5 24.9 - - + -
190A SER* 1.3 75.2 - - - +
192A THR* 1.3 65.9 + - - +
193A VAL* 4.0 10.3 + - + +
203A VAL* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET* 3.5 35.7 - - + +
146A VAL 3.3 9.6 - - - +
147A THR* 3.0 24.4 + - - +
171A SER 4.2 11.1 - - - +
172A GLY* 2.9 21.3 + - - -
174A HIS* 5.7 1.4 - - - -
190A SER* 5.2 0.3 + - - -
191A VAL* 1.3 73.5 - - - +
193A VAL* 1.3 69.9 + - - +
142B ASN* 4.7 7.8 + - - +
143B ASN* 5.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET* 3.7 6.5 - - - -
146A VAL* 2.6 61.6 + - + +
148A LEU* 4.7 11.9 - - + -
169A LEU* 4.0 25.1 - - + -
191A VAL* 4.0 19.1 - - + +
192A THR* 1.3 82.4 - - - +
194A PRO* 1.3 67.7 - - + +
197A THR* 3.7 13.9 - - - +
198A TRP* 4.3 11.4 - - + -
203A VAL* 4.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A SER 4.0 2.7 - - - +
145A MET* 3.7 24.9 - - + -
146A VAL* 4.4 0.2 - - - -
193A VAL* 1.3 91.8 - - + +
195A SER* 1.3 58.2 + - - +
196A SER* 2.9 17.0 - - - +
197A THR* 2.7 43.6 + - + +
198A TRP 3.6 2.3 + - - -
----------------------------------------------------------
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