Contacts of the strand formed by residues 255 - 260 (chain A) in PDB entry 1DG6
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 ARG 255 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LYS* 5.1 0.4 - - - +
173A GLU* 2.6 52.2 + - + +
174A LEU 3.3 4.7 - - - +
175A VAL* 4.2 16.6 - - + -
211A TYR 3.9 0.2 - - - +
212A LYS* 3.3 3.6 - - - -
213A TYR* 2.7 83.3 + - + +
214A THR 5.9 0.2 + - - -
253A ASN 3.7 11.0 - - - +
254A ASP* 1.3 79.2 - - - +
256A ILE* 1.3 62.5 + - - +
257A PHE* 4.7 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 3.2 5.4 - - - -
174A LEU* 2.8 40.6 + - + +
176A ILE* 4.4 8.3 - - + -
184A ILE* 4.1 16.6 - - + -
210A ILE* 3.8 17.7 - - + -
211A TYR 3.2 12.3 - - - +
212A LYS* 3.8 16.6 - - + -
222A LEU* 4.5 1.3 - - + -
250A LEU* 3.7 42.8 - - + -
254A ASP* 4.8 1.3 - - + -
255A ARG* 1.3 84.4 - - - +
257A PHE* 1.3 61.3 + - - +
275A PHE* 3.5 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 4.2 16.8 - - + -
150A LYS* 3.5 40.4 - - + -
172A GLY 4.1 7.0 - - - +
173A GLU* 4.1 22.2 - - + -
210A ILE* 3.4 5.4 - - - +
211A TYR* 2.9 72.8 + + + +
212A LYS 5.0 0.7 - - - -
213A TYR* 3.6 32.8 - + - -
219A PRO* 4.2 7.0 - - + -
255A ARG 4.7 1.6 - - - -
256A ILE* 1.3 80.5 - - - +
258A VAL* 1.3 69.1 + - - +
259A SER* 4.5 4.3 - - - -
275A PHE* 3.8 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LYS* 3.5 4.9 - - - +
151A ILE* 2.8 48.2 + - + +
154A TRP* 4.1 13.1 - - + +
172A GLY 5.1 0.2 + - - -
186A SER* 3.7 24.5 - - - +
188A THR* 4.1 0.9 - - + -
208A GLN* 3.8 19.7 - - + +
209A TYR 3.3 10.1 - - - +
210A ILE* 4.4 4.5 - - + -
257A PHE* 1.3 77.3 - - - +
259A SER* 1.3 58.3 + - - +
275A PHE* 3.5 44.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU 2.8 27.9 + - - -
149A ARG 3.2 19.7 - - - -
150A LYS* 3.8 4.3 - - - -
151A ILE* 4.3 0.7 - - - +
208A GLN* 3.6 0.2 - - - -
209A TYR* 2.8 50.7 + - - +
211A TYR* 3.6 4.2 - - - -
257A PHE* 4.3 11.6 - - - -
258A VAL* 1.3 75.1 - - - +
260A VAL* 1.3 68.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLY* 3.3 5.4 - - - -
149A ARG* 2.8 34.3 + - - +
151A ILE* 4.0 16.4 - - + -
188A THR* 4.0 29.4 - - + +
190A PHE* 4.0 12.8 - - + -
207A VAL 3.2 12.1 - - - +
208A GLN* 4.2 4.0 - - + -
209A TYR* 4.6 0.4 - - - -
259A SER* 1.3 82.2 - - - +
261A THR* 1.3 71.8 + - - +
263A GLU* 3.8 25.1 + - + -
266A ILE* 3.9 11.0 - - + -
----------------------------------------------------------
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