Contacts of the strand formed by residues 265 - 271 (chain E) in PDB entry 4GDK
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 265 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E ILE* 4.5 7.9 - - + -
186E PRO 2.9 18.7 + - - +
187E PHE* 3.4 5.7 - - + +
188E ARG 3.1 21.0 + - - +
240E ILE* 4.2 16.2 - - + -
251E LEU* 4.1 26.0 - - + -
254E LEU* 4.0 27.4 - - + +
255E SER* 4.4 9.4 - - - +
258E LEU* 3.5 32.3 - - + +
259E SER* 4.2 5.6 - - - +
264E PHE* 1.3 70.1 - - - +
266E HIS* 1.3 63.0 + - - +
267E ILE* 3.5 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 266 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E TYR* 6.2 0.4 - + - -
82E PRO* 4.1 15.5 - - + +
85E LEU* 3.7 18.1 - - + +
128E CYS* 6.2 0.2 - - - -
188E ARG* 3.5 24.0 - - - +
190E TYR* 2.7 36.7 + - + -
240E ILE* 3.7 21.8 - - - +
260E TYR* 3.4 43.4 + + + -
262E ASP* 2.9 25.7 + - - -
264E PHE* 3.5 21.6 + - + +
265E LEU* 1.3 70.7 - - - +
267E ILE* 1.3 59.7 + - - +
268E SER* 4.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187E PHE* 4.6 2.7 - - + -
188E ARG 2.9 10.3 + - - +
189E ILE* 3.5 18.1 - - + +
190E TYR* 2.8 35.0 + - - -
215E LEU* 4.2 21.1 - - + -
218E LEU* 4.2 18.4 - - + -
219E LEU* 5.0 2.9 - - + -
238E VAL* 3.8 28.0 - - + -
239E MET 3.9 5.4 - - - +
240E ILE* 4.2 11.0 - - + -
265E LEU* 3.6 28.3 - - + +
266E HIS* 1.3 78.3 - - - +
268E SER* 1.3 60.9 + - - +
269E ILE* 3.9 12.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 268 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU* 3.6 24.3 + - - +
88E ASP* 3.8 19.3 - - - +
89E LEU* 4.1 16.3 + - - +
190E TYR* 3.8 3.6 - - - -
237E GLN 3.4 1.9 - - - +
239E MET* 2.8 55.1 + - - +
266E HIS 4.3 0.4 + - - -
267E ILE* 1.3 71.6 - - - +
269E ILE* 1.3 66.2 + - - +
270E ILE* 3.8 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E LEU* 4.7 0.5 - - - +
189E ILE* 3.7 26.0 - - + -
190E TYR 2.9 13.4 + - - +
191E GLN* 3.6 41.9 + - + +
192E THR* 4.4 3.3 + - - -
219E LEU* 4.6 8.1 - - + -
223E CYS* 5.0 3.1 - - - -
226E ALA* 3.8 28.7 - - + -
236E ASN* 4.2 13.9 - - + -
237E GLN 3.4 5.8 - - - +
238E VAL* 3.7 31.0 - - + -
267E ILE* 4.2 7.6 - - + -
268E SER* 1.3 79.2 - - - +
270E ILE* 1.3 62.8 + - - +
271E PRO* 4.5 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E ASP 3.6 16.4 - - - +
89E LEU* 4.0 26.9 - - + +
92E SER* 3.5 24.5 - - - +
93E SER* 5.8 2.2 - - - +
192E THR* 5.4 2.2 - - - +
236E ASN* 3.5 4.5 - - - -
237E GLN* 2.5 60.8 + - + +
239E MET* 3.6 28.5 - - + -
268E SER* 4.3 5.8 - - - -
269E ILE* 1.3 79.7 - - - +
271E PRO* 1.3 69.9 - - + +
273E PRO* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 271 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E THR* 4.6 12.3 - - - +
193E THR* 5.8 6.7 - - + -
235E LYS 4.0 1.3 - - - +
236E ASN* 3.8 17.9 - - - +
237E GLN* 4.6 0.2 - - - -
269E ILE 4.5 1.6 - - - +
270E ILE* 1.3 98.0 - - + +
272E GLN* 1.3 67.4 + - - +
273E PRO* 3.4 8.0 - - - +
----------------------------------------------------------
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