Contacts of the strand formed by residues 173 - 183 (chain A) in PDB entry 2D2I
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 173 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 3.4 33.9 - - + +
167A LEU* 4.2 9.9 - - + -
168A HIS* 2.7 36.7 + - + +
172A GLY* 1.3 72.9 - - - -
174A ILE* 1.3 61.5 + - - +
175A LYS* 4.0 15.3 - - - +
226A LEU* 3.8 25.4 - - + -
229A LYS* 2.8 28.1 + - + +
230A LEU* 4.5 9.2 - - + -
247A LEU* 5.9 0.7 - - + -
249A VAL* 3.9 33.2 - - + -
250A GLN 3.9 2.9 - - - -
251A VAL* 4.9 2.5 - - + +
252A GLU* 5.8 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
172A GLY 4.1 0.2 - - - +
173A ILE* 1.3 75.2 - - - +
175A LYS* 1.3 74.5 + - - +
229A LYS* 3.3 29.1 - - - +
250A GLN* 2.9 44.4 + - + +
251A VAL 3.5 27.6 - - - +
252A GLU* 3.8 32.5 - - - +
306B ASP* 5.4 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 3.6 5.3 - - - -
174A ILE* 1.3 86.8 - - - +
176A GLY* 1.3 61.6 + - - +
229A LYS* 3.1 15.3 - - - +
249A VAL* 3.6 2.1 - - - +
250A GLN* 2.7 59.8 + - + +
305B MET* 3.6 28.5 - - + +
306B ASP* 2.9 40.7 + - + -
308B ASP* 3.0 24.8 + - - -
309B LEU* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LYS* 1.3 78.4 - - - +
177A THR* 1.3 63.4 + - - -
229A LYS 2.7 16.5 + - - +
230A LEU* 3.4 17.7 - - - +
231A ASN 3.4 13.3 + - - -
248A VAL 3.1 12.6 - - - -
249A VAL* 3.9 2.9 - - - -
305B MET* 3.5 11.1 - - - +
309B LEU* 5.3 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLY* 1.3 75.8 - - - -
178A MET* 1.3 63.4 + - - +
230A LEU* 4.5 0.8 - - - +
231A ASN* 3.3 22.7 + - - -
246A ASP 4.0 0.3 - - - +
247A LEU* 3.7 2.4 - - - +
248A VAL* 2.7 40.4 + - + +
248B VAL* 3.5 41.1 - - + -
303B LEU* 4.6 1.5 - - - +
305B MET* 5.2 0.9 - - - -
309B LEU* 4.1 13.9 - - + +
311B LYS* 3.2 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR* 3.2 34.8 - - + -
160A LEU* 3.2 34.1 - - + -
177A THR* 1.3 78.4 + - - +
179A THR* 1.3 77.8 + - - +
180A THR* 3.9 5.6 - - - -
213A THR* 4.9 6.7 - - + -
215A ALA* 4.2 6.5 - - + -
216A ALA* 4.6 5.4 - - + +
230A LEU* 6.2 1.3 - - + -
231A ASN 2.8 13.2 + - - +
232A GLY* 2.8 31.5 - - - -
233A ILE 2.9 9.1 + - - +
245A VAL* 4.1 18.6 - - + -
246A ASP 3.2 12.8 - - - +
247A LEU* 4.2 11.4 - - + -
311B LYS* 3.8 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A MET* 1.3 74.6 - - - +
180A THR* 1.3 66.0 + - - +
181A THR* 4.2 4.7 + - - +
233A ILE* 3.2 21.9 - - + +
235A LEU* 4.1 28.0 - - + -
244A VAL 4.2 0.5 - - - +
246A ASP* 2.9 40.8 + - + +
246B ASP* 2.4 29.7 + - - +
311B LYS* 3.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR* 4.0 25.1 - - + +
178A MET* 4.4 2.7 - - - -
179A THR* 1.3 75.0 - - - +
181A THR* 1.3 57.5 + - - +
182A HIS* 3.4 15.3 + - + +
213A THR* 4.8 4.7 - - - +
233A ILE 3.1 5.9 + - - +
234A ALA* 3.3 26.2 - - + +
235A LEU* 2.8 32.1 + - - +
244A VAL 3.4 9.6 + - - -
245A VAL* 4.3 4.7 - - - +
316A TYR* 2.8 25.6 + - - -
1339A SO4 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A THR* 4.2 5.2 + - - +
180A THR* 1.3 70.2 - - - +
182A HIS* 1.3 58.9 + - - +
235A LEU* 3.3 11.3 - - + +
237A VAL* 3.8 33.2 - - + -
243A SER* 3.4 4.3 - - - -
244A VAL* 3.0 41.4 + - + +
246A ASP* 6.1 0.5 - - - +
181B THR* 3.9 14.8 + - + -
208B ILE* 4.1 13.0 - - + +
235B LEU* 3.7 19.5 - - + +
237B VAL* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A CYS* 3.5 25.5 - - - -
156A THR* 3.7 8.5 - - - -
180A THR* 3.4 14.1 + - + +
181A THR* 1.3 75.1 - - - +
183A SER* 1.3 87.9 + - - +
185A THR* 4.0 13.7 - - + -
234A ALA* 5.3 0.4 - - + -
235A LEU 2.8 9.8 + - - +
236A ARG* 3.1 31.9 + - - +
237A VAL* 2.9 30.9 + - - -
243A SER* 3.2 14.3 + - - -
316A TYR* 3.3 21.5 - - - -
318A ASN* 3.7 24.9 - - + +
1339A SO4 5.9 1.1 - - - -
1340A SO4 5.2 1.1 - - - -
1341A NAP 4.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A HIS* 1.3 101.5 + - - +
184A TYR* 1.3 63.3 + - - +
236A ARG* 3.2 4.9 + - - -
237A VAL 3.9 1.3 - - - -
239A THR* 2.8 32.8 + - - -
240A PRO 3.7 2.7 - - - -
241A ASN* 2.9 28.2 + - - -
242A VAL 2.7 25.3 + - - -
243A SER* 3.2 7.2 + - - -
318A ASN* 4.2 5.6 - - - -
208B ILE* 5.3 0.2 - - - +
----------------------------------------------------------
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