Contacts of the strand formed by residues 173 - 179 (chain X) 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 VAL 173 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2X ILE* 4.6 9.9 - - + -
4X LEU* 5.5 0.2 - - + -
15X ALA* 4.1 8.1 - - + -
16X SER* 3.1 27.6 - - - +
17X SER* 4.0 2.2 - - - +
18X LYS* 4.0 11.3 - - - +
159X VAL* 3.6 35.0 - - + +
170X PHE* 4.1 12.1 - - + -
172X GLY* 1.3 76.4 - - - +
174X ILE* 1.3 62.2 + - - +
175X VAL* 3.9 12.7 + - + +
190X PHE* 3.8 32.7 - - + +
191X GLN* 5.5 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14X LEU 3.4 1.7 - - - +
15X ALA* 3.2 4.5 - - - -
16X SER* 2.8 37.0 + - - +
18X LYS* 3.7 23.8 - - + +
30X SER 4.4 5.8 - - - +
31X ASP 3.6 24.9 - - - +
32X ASP* 4.1 22.2 - - + +
173X VAL* 1.3 73.2 - - - +
175X VAL* 1.3 62.8 + - - +
176X LYS* 4.0 30.7 - - + -
186X GLN* 4.2 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13X ILE* 3.3 28.9 - - + -
14X LEU 3.2 4.0 - - - +
15X ALA* 4.0 1.1 - - + -
152X LEU* 4.0 16.6 - - + -
155X LEU* 4.0 12.3 - - + -
173X VAL* 3.9 15.2 + - + +
174X ILE* 1.3 77.1 - - - +
176X LYS* 1.3 71.2 + - - +
186X GLN* 3.6 5.4 - - - +
187X VAL* 3.1 41.2 + - + +
190X PHE* 3.7 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X VAL 3.7 1.0 - - - +
13X ILE* 3.4 4.0 - - - -
14X LEU* 2.9 36.6 + - + +
32X ASP* 2.9 30.4 + - - -
34X THR* 3.1 22.9 - - + +
42X LEU* 3.7 33.6 - - + +
174X ILE* 4.0 10.3 - - + -
175X VAL* 1.3 80.6 - - - +
177X ILE* 1.3 64.9 + - - +
178X VAL* 4.9 1.0 - - - +
184X ILE* 4.6 10.0 - - + +
185X ARG 3.3 10.8 - - - +
186X GLN* 3.7 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X SER* 3.5 31.0 - - - +
12X VAL 3.5 4.9 - - - +
13X ILE* 4.5 12.6 - - + -
148X THR* 3.7 19.1 - - + -
152X LEU* 4.4 8.7 - - + -
176X LYS* 1.3 76.4 - - - +
178X VAL* 1.3 63.7 + - - +
179X ASP* 4.0 12.3 - - - +
183X GLY 3.4 1.2 - - - +
184X ILE* 3.2 7.3 - - - +
185X ARG* 2.9 67.0 + - + +
187X VAL* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11X SER* 3.2 4.9 - - - -
12X VAL* 2.9 45.1 + - + +
14X LEU* 5.5 2.5 - - + -
40X HIS* 3.3 33.9 - - - +
42X LEU* 4.0 18.4 - - + -
102X GLY* 3.8 17.5 - - - +
103X GLY* 3.8 3.4 - - - -
104X TYR* 3.6 17.3 - - + +
176X LYS 4.9 1.3 - - - +
177X ILE* 1.3 77.3 - - - +
179X ASP* 1.3 61.4 + - - +
183X GLY 3.2 7.6 - - - +
184X ILE* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10X ASP* 3.5 16.4 - - + +
11X SER* 3.8 6.6 - - - -
40X HIS* 3.7 3.1 - - - -
104X TYR* 3.6 22.8 - - - +
148X THR* 5.3 2.0 + - - +
177X ILE* 4.1 6.0 - - - +
178X VAL* 1.3 74.0 - - - +
180X LYS* 1.3 67.6 - - + +
181X ASP* 2.9 35.3 + - - +
183X GLY* 2.9 22.2 + - - +
185X ARG* 2.8 31.6 + - - -
----------------------------------------------------------
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