Contacts of the helix formed by residues 214 - 227 (chain A) in PDB entry 1NMS
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 TRP 214 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A TRP* 3.2 47.4 + + + +
207A ARG 4.6 0.2 - - - -
208A ASN* 5.2 2.2 - - + +
212A GLY 4.7 2.2 - - - -
213A SER* 1.3 71.8 - - - +
215A PHE* 1.3 61.7 + - - +
217A GLN* 3.6 6.9 - - - +
218A SER* 2.9 29.9 + - - -
243A VAL* 4.2 11.2 - - + -
247A PHE* 3.4 56.3 - + + -
248A GLU* 3.9 7.0 - - - -
249A SER 3.7 12.6 - - - -
259A LYS 3.7 20.6 - - - -
261A GLN* 3.7 46.2 - - + +
1278A 161 2.9 40.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 3.9 17.3 - - + -
160A ILE 4.2 3.8 - - - -
161A GLN* 3.5 13.9 + - + +
196A ALA* 3.5 38.6 - - + -
197A TYR 3.8 12.6 - - - -
198A SER* 3.3 35.0 - - - +
206A TRP 4.9 0.2 + - - -
213A SER* 3.2 1.4 + - - -
214A TRP* 1.3 78.4 - - - +
216A ILE* 1.3 74.6 + - + +
218A SER* 3.1 2.1 + - - -
219A LEU* 2.7 42.2 + - + +
236A LEU* 5.4 3.4 - - + -
239A VAL* 3.9 21.3 - - + -
240A ASN* 5.6 0.2 - - - -
243A VAL* 4.0 7.0 - - + -
261A GLN* 4.3 3.9 - - - +
263A PRO* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 3.5 31.0 - - + +
73A ASN* 4.9 1.3 - - + -
74A LEU* 3.6 36.8 - - + -
117A VAL* 4.6 0.2 - - + -
119A LEU* 4.1 7.2 - - + -
159A ILE* 4.0 20.9 - - + -
161A GLN* 3.8 18.8 - - + -
213A SER* 3.1 20.7 + - - +
215A PHE* 1.3 93.9 - - + +
217A GLN* 1.3 64.3 + - - +
219A LEU* 3.8 8.0 - - + +
220A CYS* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 4.3 1.9 + - - +
73A ASN* 4.2 13.3 + - - +
208A ASN* 4.6 3.1 + - - -
211A ASP* 3.1 44.3 + - - +
212A GLY* 3.3 18.3 - - - +
213A SER 2.8 25.1 + - - +
214A TRP* 3.6 7.2 + - - +
216A ILE* 1.3 79.2 - - - +
218A SER* 1.3 61.1 + - - +
220A CYS* 4.0 2.1 - - - +
221A ALA* 3.2 23.7 + - - +
242A LYS* 4.9 2.2 - - - -
247A PHE* 3.8 29.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A TRP 2.9 17.1 + - - -
215A PHE 3.6 1.1 - - - -
217A GLN* 1.3 76.4 - - - +
219A LEU* 1.3 64.6 + - - +
221A ALA* 3.3 1.9 + - - +
222A MET* 2.9 28.2 + - - +
239A VAL* 4.1 8.3 - - - -
242A LYS* 3.6 26.9 - - - +
243A VAL* 3.5 20.3 - - - +
247A PHE* 3.2 23.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.5 10.5 - - + -
159A ILE* 3.7 42.0 - - + -
196A ALA* 5.9 0.2 - - + -
215A PHE* 2.7 29.4 + - + +
216A ILE* 3.8 13.2 - - + +
218A SER* 1.3 73.7 - - - +
220A CYS* 1.3 58.5 + - - +
222A MET* 3.4 1.6 + - - +
223A LEU* 2.9 52.0 + - + +
232A PHE* 4.9 5.2 - - + -
235A ILE* 5.4 0.9 - - + -
236A LEU* 3.8 28.7 - - + -
239A VAL* 3.6 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 3.4 47.8 - - - +
74A LEU* 3.7 24.5 - - - -
77A THR* 3.4 29.5 + - - +
216A ILE* 3.0 18.5 + - - +
217A GLN 4.0 0.2 - - - +
219A LEU* 1.3 74.3 - - - +
221A ALA* 1.3 62.5 + - - +
223A LEU* 3.3 1.3 + - - +
224A LYS* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN 3.2 16.1 + - - +
218A SER 3.3 4.5 + - - +
220A CYS* 1.3 81.2 - - - +
222A MET* 1.3 70.9 + - + +
224A LYS* 3.3 8.9 + - - +
225A GLN* 3.0 28.6 + - - +
242A LYS* 4.2 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER 2.9 20.0 + - - +
219A LEU 4.0 0.2 - - - +
221A ALA* 1.3 80.7 - - + +
223A LEU* 1.3 60.8 + - - +
225A GLN* 3.6 21.1 - - - +
226A TYR* 2.9 55.1 + - + +
235A ILE* 4.0 12.7 - - + +
238A ARG* 3.8 16.8 - - - +
239A VAL* 3.7 35.0 - - + +
242A LYS* 3.9 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 3.8 24.7 - - + -
78A PHE* 3.9 28.9 - - + -
81A LEU* 4.4 8.7 - - + +
159A ILE* 5.9 0.2 - - + -
219A LEU* 2.9 43.5 + - + +
220A CYS* 4.8 0.9 - - - -
222A MET* 1.3 72.2 - - - +
224A LYS* 1.3 67.8 + - - +
227A ALA* 3.0 33.8 + - + +
232A PHE* 4.2 7.4 - - + -
235A ILE* 4.1 20.2 - - + +
275A PHE* 3.9 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 5.9 3.1 - - - -
76A GLU* 5.9 5.6 - - - +
77A THR* 4.8 10.0 - - + +
80A ASN* 5.8 5.5 - - - +
220A CYS 2.8 19.0 + - - +
221A ALA* 3.6 8.3 - - - +
223A LEU* 1.3 77.0 - - - +
225A GLN* 1.3 63.9 + - + +
227A ALA 4.7 0.5 + - - -
228A ASP* 5.5 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA 3.0 16.1 + - - +
222A MET* 3.6 20.1 - - - +
224A LYS* 1.3 81.9 - - + +
226A TYR* 1.3 98.2 + - + +
227A ALA 3.9 0.2 - - - -
228A ASP* 4.0 3.6 - - - +
229A LYS* 3.7 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A MET* 2.9 39.2 + - + +
225A GLN* 1.3 118.7 + - + +
227A ALA* 1.3 63.5 + - - +
228A ASP* 3.1 3.6 - - - -
229A LYS* 2.9 15.3 + - + +
230A LEU* 2.9 59.0 + - + +
235A ILE* 3.9 10.7 - - + +
238A ARG* 2.7 41.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.6 29.6 - - + -
222A MET 4.1 0.4 + - - -
223A LEU* 3.0 29.6 + - + +
224A LYS 4.7 0.2 + - - -
225A GLN 3.9 0.2 - - - -
226A TYR* 1.3 78.3 - - - +
228A ASP* 1.3 57.1 + - - +
229A LYS 3.2 0.8 + - - -
230A LEU 4.6 2.0 - - - +
235A ILE* 3.8 11.0 - - - +
275A PHE* 4.1 24.2 + - + +
276A TYR* 3.2 19.8 + - - +
----------------------------------------------------------
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