Contacts of the helix formed by residues 233 - 247 (chain A) in PDB entry 2NUP
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 233 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 3.9 26.7 - - + +
158A LEU* 4.2 16.2 - - + +
159A PRO 3.6 20.9 - - - +
160A PRO* 3.7 3.9 + - + +
162A ALA* 2.7 29.8 + - + +
164A VAL* 3.9 30.3 - - + -
231A GLN 3.3 1.7 + - - -
232A PRO* 1.3 71.7 - - - +
234A GLN* 1.3 61.1 + - - +
235A LYS 3.0 0.2 + - - -
237A ASP* 2.6 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PRO* 3.3 40.1 + - + +
161A THR* 4.8 3.2 - - - +
232A PRO* 4.4 7.3 - - + +
233A VAL* 1.3 79.9 - - - +
235A LYS* 1.3 82.8 + - + +
237A ASP* 3.9 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PRO* 6.3 0.8 - - - +
231A GLN* 5.5 4.5 - - - +
232A PRO* 3.1 27.0 + - + +
234A GLN* 1.3 98.8 - - + +
236A ILE* 1.3 67.4 + - + +
237A ASP* 3.7 1.9 - - - +
238A MET* 5.2 0.9 + - - +
239A ASN* 4.7 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL* 3.7 29.8 - - + -
178A LEU* 3.7 17.3 - - + -
179A GLY* 3.6 31.4 - - - +
231A GLN* 3.5 34.5 - - + +
232A PRO 3.0 11.8 + - - +
235A LYS* 1.3 81.4 - - + +
237A ASP* 1.3 65.1 + - - +
238A MET 3.3 2.7 - - - -
239A ASN* 3.1 20.3 + - + -
240A LEU* 3.0 25.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 3.8 20.1 - - + +
233A VAL* 2.6 38.7 + - + +
234A GLN* 3.9 16.4 - - - +
235A LYS 4.8 0.9 - - - -
236A ILE* 1.3 74.5 + - - +
238A MET* 1.3 85.8 + - - +
241A THR* 3.0 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LYS 5.2 1.1 + - - +
236A ILE 3.1 1.4 + - - -
237A ASP* 1.3 92.8 + - - +
239A ASN* 1.3 68.1 + - - +
241A THR* 2.7 29.2 - - + +
242A ASP* 3.0 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 6.5 0.2 - - + -
179A GLY* 2.9 36.2 + - - +
181A GLU* 5.1 3.8 - - - +
235A LYS 4.7 6.3 - - - +
236A ILE* 3.1 23.5 + - + +
238A MET* 1.3 81.1 + - - +
240A LEU* 1.3 54.3 - - - +
242A ASP* 3.1 7.8 + - - +
243A LEU* 2.7 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 4.9 10.5 - - + -
155A LEU* 3.5 28.0 - - + -
164A VAL* 4.1 27.8 - - + -
165A GLY 5.7 1.1 - - - +
166A LEU* 4.2 27.6 - - + -
178A LEU* 4.5 18.8 - - + +
236A ILE* 3.0 23.7 + - + +
239A ASN* 1.3 72.9 - - - +
241A THR* 1.3 61.5 + - - +
243A LEU* 4.4 4.3 - - + +
244A LEU* 2.8 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN* 2.8 44.5 + - - +
155A LEU* 3.8 12.0 - - - +
237A ASP 3.0 19.9 + - - +
238A MET* 2.7 34.8 - - + +
240A LEU* 1.3 76.7 - - - +
242A ASP* 1.3 70.7 + - - +
244A LEU* 3.8 3.5 - - - +
245A GLY* 3.1 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A MET* 3.0 27.0 + - - +
239A ASN* 3.1 6.6 + - - +
241A THR* 1.3 88.3 - - - +
243A LEU* 1.3 60.4 + - - +
245A GLY* 2.8 17.3 + - - -
246A GLU* 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.4 28.5 - - + -
176A HIS* 3.6 34.8 - - + +
178A LEU* 5.1 7.2 - - + -
184A SER* 5.7 9.6 - - - -
239A ASN 2.7 19.7 + - - +
240A LEU* 3.9 9.4 - - + +
242A ASP* 1.3 70.7 - - - +
244A LEU* 1.3 64.4 + - - +
246A GLU* 2.9 19.9 + - + +
247A LEU* 3.1 19.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 5.2 6.7 - - + -
148A LYS* 3.1 34.0 - - - +
151A MET* 4.1 49.4 - - + +
152A GLN* 4.0 15.7 - - + +
155A LEU* 4.6 4.3 - - + -
166A LEU* 4.0 30.7 - - + -
240A LEU* 2.8 42.7 + - + +
241A THR 3.8 4.5 - - - +
243A LEU* 1.3 78.0 - - - +
245A GLY* 1.3 56.4 + - - +
247A LEU* 3.7 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LYS* 2.9 21.3 + - - -
152A GLN* 3.5 17.9 - - - -
241A THR 3.1 6.8 + - - -
242A ASP* 2.8 11.5 + - - -
244A LEU* 1.3 79.6 - - - +
246A GLU* 1.3 59.5 + - - +
247A LEU 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LYS* 4.0 1.5 + - - +
242A ASP* 3.0 15.8 + - - +
243A LEU* 2.9 13.9 + - + +
245A GLY* 1.3 77.4 - - - +
247A LEU* 1.3 67.4 + - - +
248A GLN* 3.2 12.8 + - - +
561B SER 5.0 4.3 - - - +
562B LEU* 3.3 28.3 - - + +
563B SER* 2.8 51.1 + - - -
564B GLN* 4.9 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 4.4 16.8 - - + -
137A THR* 4.6 10.8 - - + -
144A LEU* 4.2 6.7 - - + +
148A LYS* 2.9 34.9 + - + +
151A MET* 4.8 4.3 - - + -
166A LEU* 4.8 1.1 - - + -
168A THR* 3.4 42.0 - - + +
176A HIS* 4.9 3.4 - - + +
243A LEU* 3.1 27.6 + - + +
244A LEU* 3.8 33.0 - - + +
245A GLY 3.4 1.8 - - - -
246A GLU* 1.3 74.2 - - - +
248A GLN* 1.3 63.1 + - - +
----------------------------------------------------------
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