Contacts of the strand formed by residues 245 - 251 (chain B) in PDB entry 4D2G
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 GLY 245 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 3.0 14.8 - - - -
52B LEU* 4.6 0.4 - - - -
53B ARG* 3.9 18.3 + - - +
240B LYS* 3.8 6.2 - - - +
241B ILE* 3.1 26.8 + - - +
242B ALA 4.9 1.0 - - - +
243B ASP 4.0 0.2 - - - -
244B MET* 1.3 78.9 - - - +
246B HIS* 1.3 67.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLN* 4.3 10.8 + - + +
50B LEU* 3.6 3.5 - - - +
51B THR* 2.7 66.8 + - + +
53B ARG* 4.6 9.0 + - - -
238B GLU* 3.8 25.0 + - + +
239B TYR 3.2 12.6 - - - +
240B LYS* 4.7 2.0 - - + -
241B ILE* 3.9 7.7 - - - +
245B GLY* 1.3 77.1 - - - +
247B LEU* 1.3 60.5 + - - +
248B LYS* 4.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 4.9 2.9 - - - +
18B ALA* 4.0 7.9 - - + -
19B LEU* 3.8 22.0 - - + -
48B VAL* 4.0 5.2 - - + -
49B GLN 3.6 5.4 - - - +
50B LEU* 3.4 36.3 - - + -
218B ALA* 4.0 6.7 - - + -
221B LEU* 3.8 25.1 - - + -
237B VAL 3.7 1.9 - - - +
238B GLU* 3.5 1.6 - - - -
239B TYR* 2.8 48.6 + - + +
241B ILE* 4.1 8.2 - - + +
246B HIS* 1.3 73.4 - - - +
248B LYS* 1.3 59.5 + - - +
249B TYR* 3.4 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU 4.0 0.2 - - - +
48B VAL* 3.3 7.8 - - - +
49B GLN* 2.8 43.0 + - + +
236B VAL* 4.0 17.9 - - + -
237B VAL 3.5 2.9 - - - -
238B GLU* 3.5 39.8 + - + -
246B HIS* 4.0 27.5 + - + +
247B LEU* 1.3 74.1 - - - +
249B TYR* 1.3 62.4 + - - +
250B TYR* 3.3 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA* 3.3 20.9 + - - +
19B LEU* 4.4 1.2 - - + +
22B LEU* 3.6 23.1 - - + -
47B LEU 3.4 4.5 - - - -
48B VAL* 3.7 19.1 - - + -
214B PHE 4.6 0.6 + - - -
215B PHE* 3.2 62.7 + + + -
218B ALA* 3.6 10.8 + - + +
235B LEU 3.5 0.7 - - - +
236B VAL* 3.4 6.2 - - - +
237B VAL* 2.9 44.9 + - + +
239B TYR* 3.9 22.7 - + - -
247B LEU* 3.4 30.3 - - + +
248B LYS* 1.3 76.1 - - - +
250B TYR* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 3.2 29.9 - - - -
47B LEU* 2.7 36.3 + - + +
49B GLN* 4.2 8.8 - - + +
128B ILE* 3.5 44.3 - - + +
133B TYR* 5.0 2.9 - - - -
215B PHE* 4.6 0.6 - - - -
234B PRO* 4.4 2.9 - - + -
235B LEU 3.4 5.4 - - - +
236B VAL* 3.6 34.8 - - + -
248B LYS* 3.3 41.1 - - + +
249B TYR* 1.3 74.7 - - - +
251B LEU* 1.3 59.9 + - - +
65E ILE* 3.7 19.9 - - + +
69E PHE* 3.8 19.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.7 32.1 - - + +
46B SER* 4.8 1.1 - - - -
207B PHE* 3.5 22.1 - - + -
208B ALA 4.2 7.4 - - - +
211B TYR* 3.9 27.8 - - + -
212B LEU* 3.9 23.3 - - + -
215B PHE* 3.9 12.8 - - + -
234B PRO* 4.0 2.0 - - - -
235B LEU* 2.8 41.7 + - + +
249B TYR 4.3 0.2 + - - -
250B TYR* 1.3 76.0 - - - +
252B ALA* 1.3 67.3 + - - +
62E GLN* 3.8 18.6 - - - +
65E ILE* 4.1 1.9 - - - +
----------------------------------------------------------
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