Contacts of the strand formed by residues 206 - 209 (chain B) in PDB entry 3SZB
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 VAL 206 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A MET* 4.7 5.2 - - + -
409A MET* 5.4 0.8 - - - -
182B HIS* 3.9 4.6 - - - -
183B ILE* 3.2 18.6 - - + +
195B ILE* 4.5 6.7 - - + -
196B MET* 4.2 18.6 - - + -
199B ALA* 3.5 29.6 - - + -
204B THR 3.8 0.7 - - - +
205B PRO* 1.3 79.1 - - - +
207B THR* 1.3 62.8 + - - +
208B LEU* 3.8 27.8 + - + -
409B MET* 3.9 27.6 - - - +
410B GLY* 5.0 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B HIS* 2.8 26.8 + - - -
183B ILE 2.9 7.3 + - - +
184B LEU* 3.3 30.0 - - + -
185B TYR 2.9 27.0 + - - +
206B VAL* 1.3 70.8 + - - +
208B LEU* 1.3 62.6 + - - +
209B GLU* 4.1 15.3 - - + +
409B MET 3.6 5.4 - - - +
410B GLY* 4.1 4.6 - - - -
411B SER 3.9 27.1 - - - +
420B THR* 3.4 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 3.9 19.7 - - + -
183B ILE 5.3 0.4 - - - +
185B TYR* 3.6 20.9 - - + -
192B GLY* 3.9 22.2 - - - +
195B ILE* 4.0 22.9 - - + -
196B MET* 4.2 5.8 - - + +
206B VAL* 3.8 28.0 - - + -
207B THR* 1.3 80.0 - - - +
209B GLU* 1.3 64.1 + - - +
210B LEU* 3.8 15.5 - - + -
403B GLY 5.0 1.7 + - - -
408B GLY* 3.1 6.6 - - - -
409B MET* 2.9 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 4.9 2.5 - - + -
185B TYR 2.8 14.4 + - - +
186B THR* 3.3 22.9 - - + +
187B GLY 3.0 24.9 + - - +
207B THR* 4.1 10.2 - - + +
208B LEU* 1.3 73.2 - - - +
210B LEU* 1.3 63.0 + - - +
361B LEU* 4.3 5.7 - - + +
401B PHE* 2.7 44.1 - - + +
402B GLY* 3.4 21.6 - - - -
403B GLY 5.6 0.2 - - - +
407B SER 4.2 1.3 - - - -
410B GLY 4.2 0.6 - - - +
411B SER* 3.9 6.4 - - - -
412B TYR* 3.2 32.1 - - + -
1001B I1E 6.3 0.4 - - + -
----------------------------------------------------------
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