Contacts of the strand formed by residues 184 - 193 (chain B) in PDB entry 1F11
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B THR* 3.8 27.4 - - + +
146B GLY* 3.9 32.5 - - - +
147B TYR 3.7 13.5 - - - +
148B PHE* 4.1 4.3 - - + -
178B LEU* 3.1 11.6 - - - +
179B GLN* 2.8 40.0 + - - +
180B SER* 5.1 5.2 - - - +
183B ASP* 1.3 89.5 - - - +
185B TYR* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B HIS* 4.9 14.2 + - - -
110B THR* 6.1 2.6 - - + +
146B GLY* 2.8 24.6 + - - -
147B TYR* 2.7 51.6 + - + +
148B PHE* 3.9 24.8 - + - -
149B PRO* 4.4 0.7 - - + -
150B GLU* 3.6 43.8 - - + +
176B ALA* 3.8 15.9 - - + -
177B VAL 3.4 13.7 - - - -
178B LEU* 3.2 33.6 - - + +
184B LEU* 1.3 72.3 - - - +
186B THR* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.9 4.3 - - + -
178A THR* 6.0 4.3 - - + +
143B LEU* 4.1 11.0 - - + -
144B VAL 3.5 5.6 - - - +
145B LYS* 3.2 25.1 - - + -
146B GLY 3.4 2.6 + - - -
147B TYR* 4.1 1.1 - - - -
175B PRO 4.3 0.9 - - - +
176B ALA* 4.1 1.3 - - - -
177B VAL* 2.8 44.3 + - + +
179B GLN* 2.8 40.9 + - - +
185B TYR* 1.3 76.3 + - - +
187B LEU* 1.3 68.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.5 5.1 - - - +
144B VAL* 2.8 38.8 + - + +
147B TYR* 3.4 9.3 - - + +
150B GLU* 4.9 1.6 - - - +
152B VAL* 3.3 39.5 - - + +
154B VAL* 3.9 16.8 - - + -
173B THR* 3.8 17.7 - - + -
174B PHE* 3.6 21.1 - - - +
175B PRO 4.5 2.7 - - - -
176B ALA* 3.7 13.9 - - + +
186B THR* 1.3 75.2 - - - +
188B SER* 1.3 90.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 5.1 4.1 - - - +
135A PHE* 3.8 18.2 - - - -
176A SER* 3.3 23.4 + - - -
178A THR* 5.0 3.4 + - - -
142B CYS 3.4 12.1 - - - -
143B LEU* 3.8 16.6 - - - -
144B VAL 4.5 0.2 - - - +
174B PHE* 3.0 34.4 + - - +
187B LEU* 1.3 85.1 - - - +
189B SER* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 3.8 3.9 - - - -
141B GLY* 3.3 2.3 - - - -
142B CYS* 2.8 35.3 + - - +
154B VAL* 3.9 24.7 - - - +
157B TRP* 3.0 23.1 + - - -
171B VAL* 3.6 1.7 - - - +
172B HIS 3.3 9.3 + - - -
173B THR* 3.4 25.4 + - - -
174B PHE* 4.6 0.2 - - - -
187B LEU* 4.4 0.4 - - - +
188B SER* 1.3 77.0 - - - +
190B SER* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 3.5 34.1 - - - -
137A ASN* 3.8 12.3 + - - -
139B THR* 4.2 6.1 - - - -
140B LEU 3.2 7.9 - - - -
157B TRP* 4.0 2.9 - - - -
169B GLY 4.3 0.8 + - - -
171B VAL* 3.2 4.0 - - - +
172B HIS* 2.9 49.4 + - - +
174B PHE* 4.1 2.6 - - - -
189B SER* 1.3 78.6 + - - +
191B VAL* 1.3 62.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
138B VAL 3.8 1.4 - - - +
139B THR* 3.5 2.1 - - - -
140B LEU* 2.8 40.4 + - + +
157B TRP* 3.6 46.7 - - + +
166B LEU* 4.7 10.1 - - + -
168B SER 4.3 5.2 - - - +
169B GLY 3.5 7.4 - - - -
171B VAL* 4.1 19.1 - - + -
190B SER* 1.3 76.4 - - - +
192B THR* 1.3 66.6 + - - +
193B VAL* 3.8 21.8 + - + -
206B VAL* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASN* 4.3 9.7 + - - -
137B MET* 3.9 36.2 - - + +
138B VAL 3.5 7.0 - - - +
139B THR* 3.2 21.1 + - - +
168B SER 4.2 3.8 - - - +
169B GLY* 3.3 28.0 + - - -
172B HIS* 5.6 0.3 - - - -
191B VAL* 1.3 75.4 - - - +
193B VAL* 1.3 65.0 + - - +
194B PRO* 4.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B MET* 4.2 4.7 - - - -
138B VAL* 2.6 49.4 + - + +
140B LEU* 4.5 9.0 - - + -
166B LEU* 4.5 23.1 - - + -
191B VAL* 4.0 23.8 - - + +
192B THR* 1.3 79.9 - - - +
194B PRO* 1.3 77.2 - - + +
199B PRO* 4.0 15.5 - - + -
200B ARG* 4.3 16.2 - - + +
206B VAL* 5.0 6.1 - - + -
----------------------------------------------------------
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