Contacts of the strand formed by residues 159 - 165 (chain A) in PDB entry 1SLL
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 ILE 159 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 4.9 4.3 - - + -
152A TYR* 3.3 17.7 - - - +
153A ILE* 4.1 9.6 - - + -
154A THR* 5.0 0.2 - - - +
158A GLY* 1.3 75.5 - - - +
160A GLY* 1.3 64.3 + - - +
175A ASP* 3.1 5.7 - - - +
176A ARG 3.0 29.9 + - - +
179A SER* 3.4 16.6 - - - +
180A VAL* 4.4 3.4 - - + -
193A VAL* 3.4 43.7 - - + -
206A LEU* 4.1 16.0 - - + +
207A PHE 4.5 3.6 - - - +
208A ALA* 4.3 7.6 - - + -
213A LEU* 3.4 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 3.4 6.1 - - - +
152A TYR* 2.9 48.0 + - - +
159A ILE* 1.3 78.3 - - - +
161A ILE* 1.3 64.2 + - - +
174A LEU 3.0 13.9 - - - -
175A ASP* 3.8 0.7 - - - -
206A LEU* 3.6 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 4.2 14.6 - - + -
150A HIS 3.1 14.6 - - - +
151A ILE* 3.8 17.5 - - + -
152A TYR* 3.5 3.4 + - - -
160A GLY* 1.3 79.9 - - - +
162A GLU* 1.3 71.4 + - - +
163A LEU* 5.0 7.2 - - + +
172A TYR* 4.7 9.9 - - + +
173A THR* 3.5 3.6 - - - -
174A LEU* 2.9 45.5 + - + +
195A LEU* 3.6 36.3 - - + -
204A CYS* 4.8 15.3 - - + -
206A LEU* 3.9 9.9 - - + -
216A LEU* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A HIS* 3.6 5.3 + - + +
149A PHE* 3.2 6.9 - - - -
150A HIS* 2.9 60.9 + - + +
152A TYR* 4.0 12.1 - - + +
161A ILE* 1.3 81.3 - - - +
163A LEU* 1.3 60.7 + - - +
164A ARG* 3.9 27.6 + - + +
171A ASN* 4.8 0.3 - - - +
172A TYR 3.4 5.6 - - - -
173A THR* 3.9 19.2 - - + +
246A TYR* 4.0 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A HIS 3.7 0.7 - - - -
149A PHE* 3.9 21.5 - - + -
161A ILE* 5.0 6.0 - - + +
162A GLU* 1.3 71.4 - - - +
164A ARG* 1.3 60.9 + - - +
170A PHE* 3.3 21.3 - - + -
171A ASN* 3.5 0.2 - - - -
172A TYR* 2.8 52.4 + - + +
204A CYS* 5.5 7.0 - - - -
222A LYS* 3.2 40.8 - - + +
223A PHE* 3.8 22.0 - - + -
224A ILE 4.5 0.2 - - - +
227A ILE* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ASP* 3.1 53.3 + - - +
147A ARG* 3.3 1.4 - - - -
148A HIS* 2.8 53.3 + - + +
162A GLU* 4.2 22.6 + - + -
163A LEU* 1.3 83.5 - - - +
165A ASN* 1.3 61.8 + - - +
166A THR 4.4 0.7 - - - +
167A ASP* 3.0 25.2 + - - -
170A PHE* 3.5 10.1 - - - +
171A ASN* 2.9 30.8 + - - +
227A ILE* 3.8 8.3 - - - +
240A ARG* 3.4 16.4 - - - +
246A TYR* 4.7 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ASP 3.5 2.7 - - - -
147A ARG* 2.8 38.9 + - - +
164A ARG* 1.3 72.8 - - - +
166A THR* 1.3 80.3 + - - +
169A VAL* 3.3 20.4 - - + +
170A PHE* 3.2 33.2 + - + -
226A ASP 3.2 12.3 - - - +
227A ILE* 3.8 1.0 - - - +
228A THR* 2.9 39.4 + - - +
----------------------------------------------------------
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