Contacts of the helix formed by residues 241 - 253 (chain A) in PDB entry 3N4U
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 GLY 241 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU 3.5 1.8 + - - -
234A MET 3.2 24.5 + - - -
235A GLU 4.0 0.4 + - - -
236A ASP* 3.9 17.3 - - - -
239A GLU 3.6 1.2 - - - -
240A TYR* 1.3 81.8 - - - +
242A MET* 1.3 65.8 + - - -
243A GLU 3.4 2.8 + - - -
244A PHE 3.5 0.9 + - - -
245A VAL* 3.1 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A MET* 3.6 44.0 - - + +
236A ASP* 4.7 8.0 + - - +
241A GLY* 1.3 70.5 - - - -
243A GLU* 1.3 59.4 + - - +
245A VAL* 3.8 5.8 - - + +
246A SER* 2.6 48.5 + - - +
249A LEU* 5.1 3.4 - - + -
261A LEU* 3.6 30.3 - - + -
264A TYR* 5.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 5.0 10.2 + - - -
241A GLY 3.4 1.0 - - - -
242A MET* 1.3 79.6 - - - +
244A PHE* 1.3 67.0 + - - +
246A SER* 3.8 4.8 - - - -
247A LYS* 3.3 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 5.3 1.3 - - + -
108A LEU* 3.6 30.3 - - + -
116A GLN* 3.3 29.4 - - + -
119A ALA* 3.9 10.3 - - + -
120A ALA* 3.5 30.5 - - + -
123A LEU* 3.8 21.3 - - + -
240A TYR* 3.5 47.5 + + + +
241A GLY 3.5 3.1 + - - +
242A MET 3.3 0.2 - - - -
243A GLU* 1.3 82.9 + - - +
245A VAL* 1.3 66.3 + - + +
247A LYS* 3.2 22.8 + - + +
248A ILE* 3.2 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 4.0 13.7 - - + +
233A LEU* 3.5 44.2 - - + +
234A MET* 3.5 37.2 - - + -
240A TYR* 4.5 4.5 - - + -
241A GLY 3.1 19.0 + - - +
242A MET* 4.4 4.0 - - + +
244A PHE* 1.3 76.7 - - - +
246A SER* 1.3 58.1 + - - +
248A ILE* 3.2 10.5 + - + +
249A LEU* 2.9 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A MET* 2.6 37.3 + - - +
243A GLU* 3.8 7.2 - - - -
245A VAL* 1.3 77.7 - - - +
247A LYS* 1.3 62.1 + - - +
249A LEU* 3.3 11.9 + - - +
250A ASN* 3.0 35.0 + - - +
257A ILE* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LYS* 5.9 2.0 - - - +
116A GLN* 5.3 2.0 - - - +
117A ASN* 3.4 30.5 - - - +
120A ALA* 3.7 18.6 - - + -
243A GLU* 3.3 43.2 + - - +
244A PHE* 3.2 17.4 + - + +
246A SER* 1.3 75.8 - - - +
248A ILE* 1.3 61.2 + - - +
250A ASN* 3.3 6.3 + - - +
251A HIS* 2.7 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 3.7 25.8 - - - +
123A LEU* 3.8 18.6 - - + -
124A ALA* 3.4 20.8 - - - +
127A LEU* 4.7 5.8 - - + -
230A PHE* 3.7 26.5 - - + -
233A LEU* 4.0 20.2 - - + -
244A PHE* 3.4 37.7 - - + +
245A VAL* 3.2 11.9 + - + +
247A LYS* 1.3 77.3 - - - +
249A LEU* 1.3 56.6 + - - +
251A HIS 3.3 1.2 + - - -
252A TYR* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 3.4 36.1 - - + -
234A MET* 4.2 12.3 - - + -
242A MET* 5.1 4.5 - - + -
245A VAL* 2.9 32.0 + - + +
246A SER* 3.3 12.5 + - - +
248A ILE* 1.3 74.9 - - - +
250A ASN* 1.3 59.5 + - - +
252A TYR* 3.5 4.2 + - - +
253A LYS 3.1 20.3 + - - -
254A HIS* 3.1 38.8 + - + +
257A ILE* 4.1 33.4 - - + -
260A VAL* 4.7 9.0 - - + -
261A LEU* 5.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 3.0 26.5 + - - +
247A LYS* 3.9 6.1 - - - +
249A LEU* 1.3 74.4 + - - +
251A HIS* 1.3 68.3 + - + +
253A LYS* 3.0 19.2 + - - +
254A HIS 5.7 1.0 + - - -
257A ILE* 3.6 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 4.7 6.1 - - + -
121A LYS* 3.4 55.1 + - + +
124A ALA* 3.6 20.2 - - + +
247A LYS* 2.7 41.8 + - + +
250A ASN* 1.3 77.5 - - + +
252A TYR* 1.3 60.4 + - - +
253A LYS* 3.4 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ALA* 3.6 26.6 - - + +
127A LEU* 3.8 2.5 - - + -
128A SER* 3.5 36.7 + - - -
131A HIS* 2.7 35.4 + - - +
226A PRO* 4.2 8.1 - - - +
230A PHE* 3.4 36.3 - + + -
248A ILE 2.9 16.6 + - - +
249A LEU 3.7 3.4 - - - +
250A ASN 3.2 0.2 - - - -
251A HIS* 1.3 75.3 - - - +
253A LYS* 1.3 68.4 + - - +
254A HIS* 3.8 27.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU 3.1 1.6 + - - -
250A ASN* 3.0 21.0 + - - +
251A HIS 3.9 8.3 - - - +
252A TYR* 1.3 84.0 - - - +
254A HIS* 1.3 67.8 + - - +
255A LYS* 3.3 28.0 + - - +
----------------------------------------------------------
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