Contacts of the strand formed by residues 272 - 277 (chain B) in PDB entry 3DC1
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 272 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.4 5.9 - - - +
114B THR* 2.5 44.0 + - - +
116B GLY 3.6 1.0 - - - +
117B SER* 4.0 13.0 - - - -
259B ASP 3.6 11.2 - - - -
260B SER* 4.6 4.0 - - - -
261B PHE 4.7 0.4 - - - -
271B ILE* 1.3 74.5 - - - +
273B PHE* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 3.6 42.6 - - + -
90B LEU* 4.4 12.6 - - + -
91B GLN* 3.9 15.9 - - + -
111B LEU* 3.6 24.7 - - + -
112B CYS 3.2 11.4 - - - +
113B VAL* 4.0 6.1 - - - -
114B THR* 3.7 4.9 + - - -
117B SER* 4.6 1.7 - - - -
235B PHE* 5.7 2.5 - + - -
257B ARG 4.1 0.3 - - - +
258B ALA* 3.7 3.1 - - - +
259B ASP* 3.0 67.1 + - + +
261B PHE* 3.7 27.6 - + - -
271B ILE* 6.1 0.7 - - + -
272B GLY* 1.3 82.9 - - - +
274B LEU* 1.3 61.2 + - - +
275B THR* 4.0 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASP 3.8 0.5 - - - +
111B LEU* 3.1 5.6 - - - -
112B CYS* 2.8 39.5 + - + +
114B THR* 4.1 9.4 - - + -
120B GLY* 3.5 38.6 - - - +
121B LEU* 4.8 2.5 - - + +
124B VAL* 3.7 14.8 - - + -
256B ILE* 3.4 21.3 - - + -
257B ARG 3.4 18.4 - - - +
258B ALA* 4.3 12.1 - - + -
273B PHE* 1.3 73.6 - - - +
275B THR* 1.3 61.1 + - - +
281B ILE* 3.9 15.7 - - + +
284B VAL* 3.9 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLN* 2.9 28.6 + - + +
109B MET* 3.7 31.6 - - + -
110B ASP 3.4 5.8 - - - +
111B LEU* 3.1 20.9 - - + +
247B LEU* 3.7 25.2 - - + +
255B VAL 3.9 0.5 - - - +
256B ILE* 3.4 4.0 - - - +
257B ARG* 2.7 42.2 + - - +
259B ASP* 4.5 0.2 + - - -
273B PHE* 4.0 3.2 - - - -
274B LEU* 1.3 71.1 - - - +
276B GLY* 1.3 60.5 + - - +
281B ILE* 4.0 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLN 4.4 0.2 - - - -
109B MET* 4.5 4.7 - - - -
110B ASP 2.7 39.3 + - - +
247B LEU* 5.6 2.5 - - - -
255B VAL 3.6 7.9 - - - -
256B ILE* 4.5 2.2 - - - -
275B THR* 1.3 78.2 - - - +
277B PRO* 1.4 73.1 - - - +
281B ILE* 3.3 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.1 28.9 - - + +
107B GLY* 3.7 11.0 - - - +
108B GLN 3.4 8.5 - - - +
250B ASP* 5.2 0.4 - - - +
253B GLY* 3.1 34.8 - - - +
255B VAL 3.6 13.2 - - - +
256B ILE* 4.4 11.2 - - + -
276B GLY* 1.4 81.8 - - - +
278B LYS* 1.3 66.6 - - - +
279B PRO* 3.3 1.8 - - + -
280B LEU* 3.0 12.8 + - + +
281B ILE* 2.9 21.8 + - - +
----------------------------------------------------------
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