Contacts of the strand formed by residues 168 - 177 (chain A) in PDB entry 1SMN
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 SER 168 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU* 2.9 10.3 + - - +
150A TYR* 4.5 0.8 - - - +
151A GLU* 2.9 34.3 + - - +
152A ARG* 3.8 39.7 + - - -
154A MET* 3.8 5.2 - - - -
166A ILE 3.7 0.6 + - - -
167A PRO* 1.3 70.8 - - - +
169A ALA* 1.3 57.6 + - - +
191A ASP* 3.4 9.2 - - - +
192A GLN* 2.8 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PRO* 3.4 5.0 - - - +
149A LEU* 2.9 39.0 + - + +
151A GLU* 5.4 1.8 - - - +
167A PRO* 3.5 3.1 - - - +
168A SER* 1.3 82.2 + - - +
170A TYR* 1.3 71.5 + - - +
189A LEU* 4.0 14.8 - - + -
190A PHE 3.1 18.2 - - - +
191A ASP* 3.8 9.4 - - - +
192A GLN* 3.9 3.3 - - - +
213A ARG* 5.7 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLN* 5.0 6.7 - - + -
112A THR* 2.6 33.6 + - + -
113A PRO 3.2 19.6 + - - -
114A GLN* 3.5 26.5 - - + -
118A LEU* 3.7 14.4 - - + -
123A TRP* 3.6 25.6 - + + -
147A GLY 3.3 16.2 - - - +
148A PRO* 4.2 5.8 - - + -
167A PRO* 3.5 24.1 - - + +
169A ALA* 1.3 78.9 - - - +
171A TRP* 1.3 62.0 + - - +
189A LEU* 3.2 4.8 - - - +
190A PHE* 2.8 35.1 + - + +
192A GLN* 3.3 30.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASN 4.0 4.5 - - - -
41A TRP* 4.2 1.6 - - + -
123A TRP* 3.9 3.9 - - - -
145A VAL* 3.4 43.5 - - + -
146A THR* 2.7 37.1 + - - -
147A GLY* 2.9 39.1 + - - -
148A PRO 3.3 21.7 + - - -
149A LEU* 4.0 19.1 - - + -
170A TYR* 1.3 75.9 - - - +
172A LYS* 1.3 58.5 + - - +
173A VAL* 4.0 7.9 - - + -
188A PHE 3.2 13.9 - - - +
189A LEU* 3.8 8.7 - - + -
210A ILE* 3.5 31.4 - - + -
214A THR* 3.5 9.6 - - + +
216A LEU* 3.8 24.9 - - + -
218A ILE* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 3.3 15.7 + - - -
90A GLN 4.8 3.8 + - - -
92A PRO* 4.9 0.6 - - - +
123A TRP* 3.8 29.1 + - + -
126A LEU* 4.0 26.9 - - + +
127A GLU* 3.6 27.1 + - - +
130A GLU* 2.9 29.4 + - - +
144A THR* 3.4 22.4 - - + -
145A VAL 3.5 4.7 - - - +
146A THR* 4.0 7.6 - - - -
171A TRP* 1.3 76.4 - - - +
173A VAL* 1.3 62.2 + - - +
174A ILE* 3.9 11.2 - - + -
186A ALA 4.1 0.2 - - - +
187A ALA* 3.3 2.9 - - - -
188A PHE* 2.9 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR 4.0 0.3 - - - +
144A THR* 3.3 4.2 - - - +
145A VAL* 2.9 37.0 + - + +
171A TRP* 4.0 12.6 - - + -
172A LYS* 1.3 71.0 - - - +
174A ILE* 1.3 61.9 + - - +
186A ALA 3.3 5.4 - - - +
187A ALA* 4.2 5.4 - - + -
207A VAL* 3.9 16.4 - - + -
210A ILE* 3.6 30.3 - - + -
218A ILE* 4.0 18.2 - - + -
219A TRP* 3.3 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 4.3 9.4 - - + -
130A GLU* 4.5 10.1 - - + +
133A LEU* 4.7 3.8 - - + -
142A VAL* 3.5 30.1 - - + -
143A TYR 3.5 4.3 - - - -
144A THR* 3.6 10.8 - - - +
172A LYS* 3.9 27.8 - - + -
173A VAL* 1.3 80.4 - - - +
175A PHE* 1.3 67.8 + - - +
185A TYR* 3.1 6.5 - - - +
186A ALA* 2.8 34.9 + - + +
188A PHE* 4.2 24.5 - - + -
219A TRP* 4.3 1.9 - - - -
237A LEU* 3.7 21.5 - - + -
241A MET* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A CYS 3.9 12.3 - - - -
10A ALA* 4.1 6.1 - - + -
11A VAL* 4.0 10.3 - - + -
142A VAL* 3.7 3.3 - - - +
143A TYR* 2.9 79.8 + + + +
174A ILE* 1.3 76.7 - - - +
176A ILE* 1.3 74.9 + - - +
178A ASN 3.5 21.5 - - - -
179A SER* 3.6 5.6 - - - -
180A PRO* 3.6 29.2 - - + -
184A HIS 3.4 14.1 - - - +
185A TYR* 3.8 10.3 - - + +
219A TRP* 3.5 29.6 - + + -
237A LEU* 4.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LEU* 4.3 10.1 - - + -
139A ILE* 3.9 40.8 - - + -
141A SER 3.4 7.4 - - - +
142A VAL* 4.4 4.0 - - + -
143A TYR* 5.3 0.2 - - - -
175A PHE* 1.3 84.8 - - - +
177A ASN* 1.3 62.2 - - - +
178A ASN 3.1 5.0 + - - -
183A ASN* 3.1 29.5 - - + +
184A HIS* 3.3 19.4 + - + +
237A LEU* 3.9 30.1 - - + -
240A LEU* 5.0 0.2 - - + -
181B ALA 4.5 0.7 - - - +
182B VAL* 4.0 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP 3.0 22.0 + - - -
139A ILE* 3.4 6.6 - - - +
140A SER* 2.9 35.5 + - - +
141A SER* 2.9 19.6 + - - -
143A TYR* 3.5 23.3 - - - -
176A ILE* 1.3 73.6 - - - +
178A ASN* 1.3 73.6 + - - +
183A ASN* 3.7 11.8 - - - +
182B VAL* 3.9 24.4 - - - +
----------------------------------------------------------
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