Contacts of the strand formed by residues 211 - 215 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F TYR* 4.2 16.4 - - + +
210F HIS* 1.3 77.3 - - - +
212F ILE* 1.4 61.2 + - - +
213F GLN* 3.6 30.2 + - + +
228F THR* 3.7 19.1 - - + +
230F PHE 3.5 3.6 - - - -
231F ARG* 3.5 38.1 - - + -
260F GLN 3.3 2.4 - - - +
261F LEU* 3.3 6.0 - - - -
262F ALA* 2.8 39.2 + - + +
264F PRO* 3.8 25.1 - - + -
27L LEU* 5.3 2.5 - - + +
28L LEU* 4.2 3.6 - - + -
30L ARG* 4.4 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F ILE* 3.5 26.2 - - + -
196F TYR* 3.8 8.7 - - - +
197F GLY* 3.7 30.5 - - - +
210F HIS* 4.6 14.1 - - + +
211F LEU* 1.4 70.6 - - - +
213F GLN* 1.3 57.0 + - - +
228F THR 3.7 0.9 - - - -
229F LEU* 2.7 42.5 + - + +
230F PHE* 2.8 39.1 + - + +
247F SER* 3.8 14.1 - - - +
259F LEU* 5.0 1.6 - - + -
260F GLN 3.5 3.4 - - - +
261F LEU* 4.6 3.4 - - + -
279F PHE* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 213 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F TYR* 5.2 6.6 + - - -
211F LEU* 3.6 35.0 - - + +
212F ILE* 1.3 77.1 - - - +
214F ARG* 1.3 59.7 + - - +
215F LYS 4.2 0.2 - - - -
226F LEU* 3.5 28.0 - - + +
227F VAL 3.1 6.5 - - - +
228F THR* 3.3 23.2 + - - +
229F LEU* 4.7 0.9 - - - -
258F GLU 3.8 0.3 - - - +
259F LEU* 3.3 11.1 - - - +
260F GLN* 2.7 73.1 + - + +
262F ALA* 3.6 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PHE* 5.8 4.0 - - - +
223A GLU* 4.0 18.8 + - - -
213F GLN* 1.3 74.1 - - - +
215F LYS* 1.3 60.2 + - - +
216F LYS* 3.4 30.0 + - - +
225F SER 3.3 5.7 - - - +
226F LEU* 3.4 3.6 - - - -
227F VAL* 2.8 40.8 + - + +
229F LEU* 3.9 24.7 - - + +
252F LYS* 3.8 18.6 + - - +
253F LEU* 3.5 22.7 - - + +
254F GLU* 3.5 24.2 + - - +
257F ASP* 2.8 35.5 + - + +
258F GLU 3.5 6.7 - - - +
259F LEU* 4.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F LYS* 6.5 0.2 - - + -
213F GLN 4.2 0.6 - - - -
214F ARG* 1.3 70.8 - - - +
216F LYS* 1.3 68.6 + - - +
217F VAL 3.5 0.2 + - - -
225F SER* 3.6 33.9 - - - +
226F LEU* 3.8 19.9 - - + +
256F GLY 4.6 0.9 - - - +
257F ASP* 3.4 4.3 - - - -
258F GLU* 2.7 50.9 + - + +
260F GLN* 5.6 5.6 - - + +
----------------------------------------------------------
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