Contacts of the strand formed by residues 213 - 219 (chain B) in PDB entry 4U7D
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 PHE 213 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.7 28.5 - + + -
135B LEU* 3.9 14.1 - - + -
204B LEU* 3.8 26.2 - - + -
207B ALA* 3.4 2.3 + - + -
208B TYR* 3.7 50.1 - + + +
211B ARG* 3.3 1.9 - - - -
212B ARG* 1.3 80.1 - - - +
214B THR* 1.3 63.6 + - - +
215B ARG 3.1 33.2 - - - -
216B ILE* 3.5 25.1 - - + -
241B LEU* 5.8 0.2 - - + -
245B PHE* 3.7 29.8 - + + -
247B ASN 5.8 0.2 - - - -
248B ALA* 4.2 3.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
130B SER* 3.1 27.2 + - - +
131B ASP 4.3 4.9 + - - +
133B PHE 4.1 5.7 + - - -
211B ARG* 4.0 21.8 - - + +
212B ARG 4.9 0.4 - - - -
213B PHE* 1.3 79.2 - - - +
215B ARG* 1.3 78.5 + - - +
247B ASN 4.2 5.9 - - - +
248B ALA* 3.4 9.7 - - - +
249B SER* 3.0 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B THR* 2.9 45.3 + - + -
104B MET* 4.0 26.4 + - - +
106B GLY* 4.7 2.8 - - - -
123B TYR* 5.4 1.8 - - - +
126B PRO* 3.8 20.2 + - - +
129B CYS 5.3 0.2 + - - -
130B SER* 3.7 24.9 + - - -
133B PHE 4.5 0.8 + - - -
134B THR* 3.4 29.3 + - + +
135B LEU 2.9 25.2 + - - -
213B PHE* 3.1 11.5 - - - -
214B THR* 1.3 90.5 + - - +
216B ILE* 1.3 64.8 + - - +
249B SER* 3.1 23.9 + - - +
251B ILE* 6.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 4.7 1.1 - - - -
135B LEU* 3.4 7.0 - - + +
137B ILE* 4.0 21.8 - - + -
213B PHE* 3.5 26.5 - - + -
215B ARG* 1.3 73.3 - - - +
217B ALA* 1.3 62.0 + - - +
218B VAL* 4.2 6.7 - - + -
241B LEU* 4.0 37.9 - - + +
242B LYS* 4.8 1.6 - - + -
245B PHE* 4.6 2.0 - - + +
248B ALA* 3.8 25.8 - - + +
249B SER 2.7 12.0 + - - +
250B LEU* 3.3 28.1 - - + +
251B ILE* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 3.8 32.3 - - + -
134B THR* 4.3 3.3 - - + +
135B LEU 2.5 17.3 + - - +
136B VAL* 3.2 9.9 - - + +
137B ILE* 2.5 36.7 + - - +
215B ARG 4.2 0.2 - - - -
216B ILE* 1.3 74.7 - - - +
218B VAL* 1.3 56.2 + - - +
219B ASP 3.9 0.2 - - - -
251B ILE* 3.5 19.1 - - + -
253B LEU* 4.6 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 3.7 13.5 - - + -
216B ILE* 4.2 6.5 - - + -
217B ALA* 1.3 75.0 - - - +
219B ASP* 1.3 60.9 + - - +
220B GLU 3.7 0.2 + - - -
221B VAL* 4.0 19.4 + - + -
235B TYR* 3.7 30.5 - - + +
238B LEU* 4.6 8.7 - - + -
241B LEU* 5.1 2.9 - - + -
250B LEU* 4.1 27.1 - - + -
251B ILE 2.9 12.7 + - - +
252B GLY* 3.7 4.6 - - - -
253B LEU* 3.2 25.2 + - - -
269B LEU* 4.7 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS* 5.4 5.2 - - - +
120B SER* 5.4 1.4 + - - -
123B TYR* 3.8 19.8 + - - -
136B VAL* 4.9 5.8 - - + +
137B ILE 2.6 18.7 + - - +
138B CYS* 4.3 19.3 - - + +
139B PRO* 4.2 0.2 - - - +
143B LEU* 5.8 0.3 - - - +
147B GLN* 4.8 5.2 - - - +
188B TYR* 5.7 1.0 - - - -
217B ALA 3.9 1.8 + - - -
218B VAL* 1.3 72.6 - - - +
220B GLU* 1.3 87.5 + - + +
235B TYR* 2.5 30.8 + - - -
253B LEU* 3.8 21.7 - - + +
----------------------------------------------------------
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