Contacts of the strand formed by residues 211 - 215 (chain B) in PDB entry 3V56
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 211 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TYR* 4.3 14.6 - - + +
210B HIS* 1.3 81.0 - - - +
212B ILE* 1.4 60.6 + - - +
213B GLN* 3.6 29.5 + - + +
228B THR* 3.7 21.1 - - + +
230B PHE 3.5 3.6 - - - -
231B ARG* 3.6 34.8 - - + -
260B GLN 3.3 2.4 - - - +
261B LEU* 3.3 5.4 - - - -
262B ALA* 2.8 32.9 + - + +
264B PRO* 3.8 28.7 - - + -
27H LEU* 5.4 4.7 - - + +
28H LEU* 4.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ILE* 3.6 24.9 - - + -
196B TYR* 3.8 9.9 - - - +
197B GLY* 3.7 30.1 - - - +
210B HIS* 4.6 14.1 - - + +
211B LEU* 1.4 71.4 - - - +
213B GLN* 1.3 56.2 + - - +
228B THR* 3.7 0.5 - - - -
229B LEU* 2.8 41.8 + - + +
230B PHE* 2.8 40.3 + - + +
247B SER* 3.8 14.6 - - - +
259B LEU* 5.0 2.2 - - + -
260B GLN 3.5 2.9 - - - -
261B LEU* 4.6 3.6 - - + -
279B PHE* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TYR* 5.4 5.1 + - - -
211B LEU* 3.7 34.0 - - + +
212B ILE* 1.3 76.4 - - - +
214B ARG* 1.3 60.1 + - - +
226B LEU* 3.6 27.5 - - + +
227B VAL 3.2 8.5 - - - +
228B THR* 3.4 22.2 + - - +
229B LEU* 4.7 0.7 - - - -
258B GLU 3.8 0.5 - - - +
259B LEU* 3.3 11.0 - - - +
260B GLN* 2.7 73.2 + - + +
262B ALA* 3.6 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE 4.4 0.2 + - - -
213B GLN* 1.3 72.3 - - - +
215B LYS* 1.4 60.8 + - - +
216B LYS* 3.4 35.9 + - - +
225B SER 3.3 5.9 - - - +
226B LEU* 3.4 3.8 - - - -
227B VAL* 2.8 47.8 + - + +
229B LEU* 3.8 20.9 - - + +
252B LYS 3.9 21.4 + - - -
253B LEU* 3.7 19.5 - - + +
254B GLU* 3.5 24.4 + - - +
257B ASP* 2.8 34.3 + - + +
258B GLU 3.4 6.5 - - - +
259B LEU* 4.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLN 4.2 0.6 - - - -
214B ARG* 1.4 70.3 - - - +
216B LYS* 1.3 69.2 + - - +
217B VAL* 4.6 0.5 - - - -
225B SER* 3.6 12.6 - - - +
226B LEU* 3.8 19.7 - - + +
256B GLY 4.6 0.7 - - - +
257B ASP* 3.4 4.3 - - - -
258B GLU* 2.7 49.6 + - + +
260B GLN* 6.0 2.9 - - + +
----------------------------------------------------------
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