Contacts of the strand formed by residues 198 - 207 (chain F) in PDB entry 3IT8
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 MET 198 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F GLY 4.4 5.4 - - - +
191F ASN 4.1 5.8 - - - +
192F GLU* 3.4 17.0 - - + +
193F LEU 5.5 0.4 - - - -
196F GLY 5.3 0.8 - - - -
197F ASN* 1.3 86.8 - - + +
199F THR* 1.3 69.6 + - - +
200F LEU* 5.0 1.8 - - + -
270F ARG* 4.0 6.8 - - - -
271F THR* 2.9 51.2 + - + +
278F GLN* 3.7 20.6 - - - +
296F SER* 3.8 6.1 - - - -
297F GLU* 3.0 49.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 199 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F GLY* 3.3 4.7 - - - -
191F ASN* 3.1 54.5 + - + +
192F GLU* 3.6 3.1 - - - +
193F LEU* 4.1 28.0 - - + +
198F MET* 1.3 78.2 - - - +
200F LEU* 1.3 60.9 + - - +
268F LEU* 3.8 30.3 - - + +
269F VAL 3.2 15.9 + - - -
270F ARG* 4.6 3.9 - - - +
271F THR* 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F VAL* 3.9 16.2 - - + -
189F THR 3.5 12.8 - - - +
190F GLY* 3.9 2.9 - - - -
198F MET* 5.0 2.0 - - + -
199F THR* 1.3 73.2 - - - +
201F GLU* 1.3 60.2 + - - +
202F CYS 4.2 0.7 - - - -
216F TRP* 3.8 17.9 - - + -
267F ASP 3.9 0.5 - - - +
268F LEU* 3.3 4.9 - - - +
269F VAL* 2.7 43.0 + - + +
271F THR* 3.6 16.3 + - - +
278F GLN* 4.0 4.9 - - + +
279F PRO* 3.4 46.7 - - + +
295F CYS 4.1 0.2 - - - +
296F SER* 2.9 35.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 201 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F LYS 3.6 1.9 - - - +
188F VAL* 3.2 4.4 - - - -
189F THR* 2.7 44.4 + - - +
191F ASN* 3.5 23.4 + - - +
200F LEU* 1.3 74.8 - - - +
202F CYS* 1.3 61.4 + - - +
203F THR* 3.4 21.7 + - + +
266F THR* 3.8 28.2 + - + +
267F ASP 3.4 3.4 - - - +
268F LEU* 3.4 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 202 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186F VAL* 4.0 21.5 - - - -
187F LYS 3.8 2.9 - - - -
188F VAL* 4.1 4.0 - - - +
201F GLU* 1.3 69.7 - - - +
203F THR* 1.3 62.2 + - - +
204F VAL* 4.2 5.4 + - - +
214F THR* 4.2 1.8 - - - -
216F TRP* 3.3 17.5 - - + -
265F LEU* 4.6 0.9 - - - +
266F THR* 3.5 1.0 - - - -
267F ASP* 2.7 45.5 + - + +
281F CYS* 2.0 50.0 - - - -
283F VAL* 4.1 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F THR 3.4 1.4 - - - +
186F VAL* 3.3 5.9 - - - +
187F LYS* 3.0 40.9 + - + +
189F THR* 5.2 4.9 - - - +
201F GLU* 3.4 32.1 - - + +
202F CYS* 1.3 77.7 - - - +
204F VAL* 1.3 60.8 + - - +
205F ASN* 3.6 21.4 + - - -
265F LEU 3.4 10.5 - - - -
266F THR* 4.2 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F PRO* 3.2 35.2 - - + -
185F THR 3.4 2.9 - - - -
186F VAL* 4.2 10.1 - - + -
202F CYS* 4.7 5.2 - - - +
203F THR* 1.3 77.0 - - - +
205F ASN* 1.3 60.7 + - - +
207F PHE* 3.5 18.2 - - + -
212F VAL* 4.9 3.6 - - + -
214F THR* 5.6 0.7 - - - +
264F SER* 3.4 4.3 - - - -
265F LEU* 2.8 56.6 + - + +
283F VAL* 4.0 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 205 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F PRO* 3.0 19.1 - - - +
185F THR* 2.7 31.4 + - - +
187F LYS* 4.2 23.0 - - - +
203F THR* 3.6 21.7 + - - -
204F VAL* 1.3 77.7 + - - +
206F SER* 1.3 77.8 + - - +
207F PHE 3.8 0.9 - - - -
264F SER* 3.8 10.2 + - - +
265F LEU 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 206 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F THR* 3.3 16.8 - - - +
183F THR 3.7 6.8 - - - +
205F ASN* 1.3 79.2 + - - +
207F PHE* 1.3 56.6 + - - +
257F ASP* 3.2 15.5 - - - -
258F LYS* 4.6 9.0 + - - -
262F THR* 2.6 28.8 + - - -
263F TYR 2.8 9.1 + - - -
264F SER* 3.0 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F THR* 3.1 11.7 - - - +
184F PRO* 3.5 17.3 - - + -
204F VAL* 3.5 41.7 - - + -
206F SER* 1.3 72.5 - - - +
208F TYR* 1.3 62.1 + - - +
209F PRO 3.5 13.9 - - - -
210F PRO* 3.6 17.5 - - + -
212F VAL* 3.4 25.8 - - + -
254F ILE* 4.3 6.3 - - + -
262F THR* 3.4 4.5 - - - -
263F TYR* 2.8 55.4 + - + -
264F SER 4.0 1.6 - - - -
265F LEU* 3.7 22.7 - - + -
285F HIS* 3.7 10.8 - - + -
----------------------------------------------------------
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