Contacts of the strand formed by residues 185 - 192 (chain M) 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 ASN 185 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M ASP* 3.6 2.9 - - - +
17M ASN* 3.0 36.4 + - - +
28M ASN* 4.7 10.9 + - - +
183M SER* 3.2 19.4 + - - -
184M ARG* 1.3 80.7 - - - +
186M PHE* 1.3 63.6 + - - +
202M ASN* 5.0 7.2 - - - +
203M LEU 3.1 14.1 - - - +
204M GLN* 3.6 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 186 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ALA* 4.3 0.9 - - + -
15M ALA 3.3 16.2 - - - +
16M ASP* 3.4 11.2 - - + +
17M ASN* 3.5 8.2 - - - +
169M VAL* 4.6 18.6 - - + -
172M MET* 3.8 37.0 - - + -
183M SER 5.4 0.7 - - - +
184M ARG 3.7 10.5 - - - -
185M ASN* 1.3 74.7 - - - +
187M SER* 1.3 74.7 + - - +
188M LEU* 4.2 15.0 - - + -
202M ASN 3.9 2.6 + - - -
203M LEU* 3.0 69.3 + - + +
204M GLN 3.9 20.6 - - - -
205M VAL* 4.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ALA* 3.4 6.2 - - - +
15M ALA 2.9 31.8 + - - +
17M ASN* 3.2 15.1 + - - -
31M GLU* 2.8 37.1 + - - -
33M LEU* 3.7 10.3 - - - -
186M PHE* 1.3 77.9 + - - +
188M LEU* 1.3 61.5 + - - +
199M PHE* 4.5 4.3 - - - -
200M LYS 3.4 12.0 + - - -
201M LYS* 4.4 6.8 - - - +
202M ASN 4.8 0.3 + - - -
203M LEU* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M ILE* 3.9 13.9 - - + -
13M ILE 3.5 6.7 - - - +
14M ALA* 4.0 3.6 - - + -
33M LEU* 3.9 2.9 - - - -
165M GLU* 3.9 20.2 - - + +
168M ILE* 3.5 33.0 - - + -
169M VAL* 4.3 13.5 - - + -
186M PHE* 4.2 11.4 - - + -
187M SER* 1.3 76.4 - - - +
189M ALA* 1.3 61.6 + - - +
190M ILE* 3.8 25.8 - - + -
198M THR 4.1 0.2 - - - +
199M PHE* 3.7 1.3 - - - -
200M LYS* 2.7 44.1 + - + +
203M LEU* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M VAL 3.9 0.7 - - - +
12M ILE* 3.4 4.7 - - - +
13M ILE* 2.9 42.2 + - + +
33M LEU* 3.8 5.6 - - + +
41M VAL* 3.9 22.0 - - + -
188M LEU* 1.3 76.5 - - - +
190M ILE* 1.3 64.7 + - - +
191M ILE* 4.3 1.2 + - + +
197M LEU* 5.7 1.1 - - + -
198M THR 3.3 9.4 - - - +
199M PHE* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 190 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M TYR* 3.1 33.9 - - + +
11M VAL 3.5 5.4 - - - +
12M ILE* 4.4 9.4 - - + -
161M VAL* 4.3 17.9 - - + -
165M GLU* 4.1 23.8 - - - +
188M LEU* 3.8 13.0 - - + -
189M ALA* 1.3 77.7 - - - +
191M ILE* 1.3 62.7 + - - +
192M ASP* 4.6 4.9 - - + +
196M GLY 3.6 1.2 - - - +
197M LEU* 3.5 3.6 - - - +
198M THR* 2.9 46.1 + - - +
200M LYS* 4.2 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 191 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M TYR* 3.7 1.7 + - - -
10M GLY* 3.1 5.4 - - - -
11M VAL* 2.9 60.0 + - + +
13M ILE* 4.9 1.1 - - + -
38M ASP 4.8 3.4 - - - +
39M ASN* 3.9 29.4 - - - +
41M VAL* 3.8 28.7 - - + +
108M ALA* 3.7 22.7 - - + +
109M GLY* 4.4 0.2 - - - -
110M VAL* 3.6 22.5 - - + +
189M ALA* 4.9 5.4 - - + +
190M ILE* 1.3 75.7 - - - +
192M ASP* 1.3 61.8 + - - +
196M GLY 3.5 6.7 - - - +
197M LEU* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 192 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7M TYR* 3.1 21.1 + - - +
9M ASN* 3.2 24.9 - - - +
110M VAL* 4.2 5.1 - - - +
161M VAL* 4.8 4.5 - - - +
190M ILE* 4.7 5.2 - - + -
191M ILE* 1.3 75.6 - - - +
193M LYS* 1.3 60.5 + - - +
194M ASN* 2.8 17.2 + - - +
195M THR* 2.7 42.2 + - - +
196M GLY* 2.7 38.8 + - - +
----------------------------------------------------------
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