Contacts of the strand formed by residues 278 - 283 (chain I) in PDB entry 1QDU
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 LYS 278 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230I PHE* 3.6 9.9 - - + +
265I PHE* 2.8 35.4 - - + +
266I THR 4.3 7.0 - - - -
267I GLY* 4.9 0.9 - - - +
273I LEU* 3.2 37.4 + - + -
274I ALA* 4.2 1.8 - - - +
275I GLY 4.1 5.3 - - - +
276I LYS 2.7 30.1 + - - +
277I PRO* 1.3 73.4 - - - +
279I VAL* 1.3 61.3 + - - +
280I PHE* 3.9 9.3 - - + -
323J ASP 5.5 0.7 - - - -
325J ALA 4.0 11.8 + - - -
326J ASP* 2.8 12.0 + - - +
327J PHE* 3.4 38.0 - - + -
328J LEU 3.0 22.6 + - - +
394J LEU* 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 279 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I CYS* 4.7 6.7 - - - -
230I PHE 2.9 12.4 + - - +
231I ILE* 3.3 14.2 - - + -
232I CYS 2.8 25.3 + - - -
277I PRO* 4.7 2.7 - - + -
278I LYS* 1.3 77.0 - - - +
280I PHE* 1.3 70.6 + - - +
281I PHE* 3.4 41.7 - - + -
328J LEU* 3.5 24.5 - - + +
366J ILE* 6.2 0.7 - - + -
394J LEU* 5.7 0.2 - - + -
398J LEU* 4.1 26.5 - - + -
400J PHE* 5.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 280 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I LEU* 5.2 0.9 - - + -
230I PHE* 4.3 6.1 - + - -
232I CYS* 3.2 36.8 - - + -
234I ILE* 5.4 1.1 - - + -
261I LEU* 4.1 12.8 - - + -
262I THR* 4.0 31.9 - - - +
265I PHE* 3.7 30.5 - + - -
278I LYS* 3.9 17.0 - - + -
279I VAL* 1.3 82.0 - - - +
281I PHE* 1.3 66.9 + - - +
282I ILE* 3.8 20.6 - - + -
327J PHE* 4.1 21.8 - + - -
328J LEU 2.9 11.5 + - - +
329J LEU* 4.2 8.3 - - + -
330J GLY 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 281 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I LEU* 5.9 0.7 - - + -
193I PHE* 3.8 27.1 - + - -
231I ILE* 3.9 18.8 - - + -
232I CYS 3.0 9.3 + - - -
233I CYS* 3.8 17.0 - - + +
234I ILE 3.1 20.6 + - - +
235I LEU* 4.6 3.1 - - - +
279I VAL* 3.4 28.3 - - + -
280I PHE* 1.3 78.1 - - - +
282I ILE* 1.3 64.0 + - - +
283I GLN* 3.6 1.4 + - - +
328J LEU* 5.5 1.3 - - + -
330J GLY* 3.8 8.7 - - - +
349J TYR* 3.8 18.6 - - + -
350J ILE* 5.0 5.5 - - + +
353J LEU* 3.5 40.6 - - + -
357J LEU* 5.8 0.7 - - + -
366J ILE* 4.7 12.6 - - + -
370J LEU* 4.6 14.8 - - + -
400J PHE* 6.1 2.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234I ILE* 3.6 24.5 - - + -
243I ILE* 3.3 33.0 - - + -
258I ILE* 3.5 29.6 - - + -
261I LEU* 5.7 1.1 - - + -
280I PHE* 3.8 31.8 + - + -
281I PHE* 1.3 76.0 - - - +
283I GLN* 1.3 61.6 + - - +
284I ALA* 4.0 5.8 + - + +
329J LEU* 3.9 9.6 - - + -
330J GLY 3.3 9.5 + - - +
331J MET* 3.8 20.6 - - + -
332J ALA* 3.3 23.6 + - - +
349J TYR* 4.0 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179I ARG* 4.0 13.2 + - - +
185I ASP* 4.3 1.6 - - - +
234I ILE 2.7 14.8 + - - +
235I LEU* 3.5 4.7 - - + -
236I SER 3.1 22.7 + - - +
282I ILE* 1.3 73.8 - - - +
284I ALA* 1.3 62.6 + - - +
332J ALA* 3.5 12.3 - - - +
339J SER* 3.0 17.2 + - - -
340J TYR 4.0 5.1 + - - -
347J THR* 2.8 42.0 + - - +
349J TYR* 4.2 11.5 - - + +
350J ILE* 3.8 31.4 - - + -
385J GLN* 5.3 0.2 - - - +
4503X ASP* 3.5 9.5 + - - +
----------------------------------------------------------
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