Contacts of the strand formed by residues 210 - 216 (chain B) in PDB entry 3SDI
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 210 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 5.5 0.9 - - + -
50B ALA 3.3 17.9 - - - +
51B GLU* 4.5 1.1 - - - -
52B ARG* 3.6 5.8 + - - +
61B GLN* 3.4 22.9 + - - -
194B LEU* 3.8 24.9 - - + -
197B LEU* 3.8 26.0 - - + -
205B LEU* 4.1 22.4 - - + -
206B THR 4.0 7.2 - - - +
207B TYR 3.3 7.4 + - - +
208B ASP 3.6 0.8 - - - -
209B ARG* 1.3 85.3 - - - +
211B GLU* 1.3 64.9 + - - +
212B PHE* 5.5 1.8 - - + -
229B ILE* 3.5 23.6 - - + +
233B LEU* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.4 4.0 - - - -
50B ALA* 2.9 38.2 + - + +
52B ARG* 3.9 29.1 - - - +
61B GLN* 5.4 0.4 - - - +
63B SER 4.4 2.1 - - - +
64B THR* 3.6 8.8 - - - -
65B GLU* 3.1 28.7 + - - +
66B LYS* 3.1 33.5 + - - +
67B LEU* 3.3 28.4 + - + +
210B LEU* 1.3 73.9 - - - +
212B PHE* 1.3 65.0 + - - +
223B ILE* 6.3 2.5 - - + -
229B ILE* 4.3 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.6 23.6 - - + -
48B LEU 3.4 2.9 - - - -
49B ALA* 3.4 30.1 - - + -
67B LEU* 3.5 5.7 - - - +
190B ILE* 3.6 39.7 - - + -
193B ALA* 4.8 0.7 - - + -
194B LEU* 3.6 31.4 - - + -
210B LEU* 5.5 3.8 - - + -
211B GLU* 1.3 76.5 - - - +
213B ALA* 1.3 66.9 + - - +
214B THR* 4.6 2.0 - - + -
223B ILE* 3.8 2.6 - - - +
224B PHE* 2.9 72.4 + + + +
229B ILE* 4.0 17.6 - - + +
232B ILE* 4.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.7 1.6 - - - +
48B LEU* 2.8 43.5 + - + +
67B LEU* 3.7 18.2 - - + -
75B ALA* 6.1 3.8 - - + -
212B PHE* 1.3 79.1 - - - +
214B THR* 1.3 68.2 + - - +
215B ILE* 6.4 0.4 - - + -
222B LYS 3.1 13.7 - - - +
223B ILE* 4.1 15.3 - - + -
224B PHE* 3.7 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE 3.3 10.3 - - - +
47B VAL* 4.3 10.5 - - + -
186B VAL* 4.5 5.6 - - + -
190B ILE* 4.1 23.6 - - + -
212B PHE* 4.6 2.0 - - + -
213B ALA* 1.3 80.3 - - - +
215B ILE* 1.3 69.3 + - - +
216B ARG* 4.0 19.0 + - + +
221B GLN* 3.4 0.9 - - - +
222B LYS* 2.9 47.3 + - - +
224B PHE* 3.6 18.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY* 2.9 27.7 - - - -
46B ILE* 3.0 15.9 + - + +
48B LEU* 5.8 0.4 - - + -
73B LYS 4.3 9.6 - - - +
75B ALA* 4.4 10.3 - - + +
139B ALA* 3.3 44.4 - - + +
141B TYR* 4.7 7.4 - - + +
146B TYR* 3.6 13.7 - - + -
213B ALA* 6.4 0.7 - - + -
214B THR* 1.3 79.9 - - - +
216B ARG* 1.3 58.8 + - - +
218B VAL* 3.5 26.0 - - - +
220B TYR 3.5 3.1 - - - +
221B GLN* 3.8 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASP* 4.0 16.2 + - - +
146B TYR* 3.7 2.7 - - - -
185B LYS* 3.5 18.2 - - - +
186B VAL* 3.9 22.3 - - + +
187B ASP* 2.7 32.3 + - - -
190B ILE* 4.8 8.3 - - - +
214B THR* 4.0 17.3 + - - +
215B ILE* 1.3 78.0 - - - +
216B LYS* 1.3 66.3 + - - +
218B VAL* 3.6 2.4 + - - -
220B TYR* 2.8 48.4 + - + +
----------------------------------------------------------
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