Contacts of the strand formed by residues 24 - 27 (chain 1) in PDB entry 3SDI
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 24 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201 SER* 3.5 1.8 - - - -
211 TYR* 2.8 52.1 + - + +
231 SER* 1.3 78.9 + - - +
251 LEU* 1.3 61.4 + - - +
261 ARG* 3.0 24.7 + - + -
1322 THR* 5.6 4.3 - - + -
1352 TYR* 3.4 34.5 - - + +
133N PHE* 3.9 28.9 - - + -
165N TRP* 3.3 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181 LEU* 3.7 38.4 - - + -
201 SER* 4.2 7.9 - - - +
231 SER 4.3 2.7 - - - +
241 LEU* 1.3 68.5 - - - +
261 ARG* 1.3 60.9 + - - +
271 PHE 3.8 1.3 - - - -
281 ASN* 4.3 8.3 - - - +
1801 ALA 3.9 20.4 - - - +
1811 ARG* 4.6 2.7 - - - -
1821 SER 4.8 5.8 - - - +
19N ARG* 5.7 0.2 - - - +
163N ILE 4.2 0.2 - - - +
164N LYS* 3.5 22.8 - - - +
165N TRP* 3.0 34.8 + - - +
166N ASP 3.9 7.0 - - - +
167N GLY* 4.0 10.3 - - - +
201N MG 3.6 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191 GLY 3.5 11.2 + - - +
211 TYR* 3.5 51.1 - - + -
241 LEU* 3.0 23.4 + - + +
251 LEU* 1.3 73.8 - - - +
271 PHE* 1.3 97.9 + - + +
281 ASN* 4.3 1.5 + - - +
1122 THR* 4.8 7.9 + - - +
1142 PRO* 3.7 18.7 - - - +
1262 ILE 4.0 17.2 + - - -
1272 ALA* 4.3 13.7 - - - +
1352 TYR* 3.5 27.3 + - + +
165N TRP* 4.0 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-31 VAL* 3.9 16.2 - - + -
171 ASN 3.9 0.2 - - - +
181 LEU* 3.3 7.4 - - - +
191 GLY* 2.9 40.0 + - - +
261 ARG* 1.3 121.8 - - + +
281 ASN* 1.3 62.2 + - - +
291 GLY 3.7 0.7 - - - +
301 VAL* 3.9 18.4 - - + -
1122 THR* 3.9 21.8 - - + -
1142 PRO* 4.3 7.4 - - + -
1202 HIS* 3.4 47.8 - + + +
1222 LEU* 4.2 22.4 - - + -
----------------------------------------------------------
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