Contacts of the strand formed by residues 150 - 159 (chain B) in PDB entry 1NSX
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 LYS 150 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B SER 3.6 1.6 - - - +
145B PHE* 3.4 6.6 - - - -
146B ASP* 3.0 42.5 + - - +
148B ASP* 4.0 24.5 + - - +
149B ASN* 1.3 79.8 - - - +
151B TRP* 1.3 61.1 + - - +
152B LYS* 3.8 4.0 + - + +
333B ILE* 4.2 20.2 - - + -
334B TYR 3.8 3.6 - - - -
335B SER* 3.9 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.9 17.9 - - + -
27B PHE* 3.6 13.9 - + - -
34B ILE* 3.6 48.2 - - + -
37B TRP* 3.7 20.6 - + + -
143B HIS* 3.1 27.3 + + - -
144B SER 3.3 13.0 - - - -
145B PHE* 4.0 5.2 - - + -
149B ASN 3.9 0.8 + - - -
150B LYS* 1.3 73.3 - - - +
152B LYS* 1.3 66.4 + - - +
153B ILE* 3.7 22.3 - - + +
171B VAL* 3.9 25.4 - - + -
173B PHE* 4.5 0.9 - + - -
332B THR 4.1 0.3 - - - +
333B ILE* 3.5 2.7 - - - -
334B TYR* 2.9 73.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLU* 4.8 11.8 + - - -
142B THR 3.4 1.1 - - - +
143B HIS* 3.3 5.4 - - - -
144B SER* 2.7 51.9 + - - +
150B LYS* 3.8 4.8 + - + +
151B TRP* 1.3 77.0 - - - +
153B ILE* 1.3 73.2 - - - +
154B HIS* 4.4 10.1 - - + +
331B THR* 3.9 19.3 - - + -
332B THR 3.6 3.4 - - - +
333B ILE* 3.8 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 5.7 0.2 - - - +
141B VAL* 3.5 29.2 - - + -
142B THR 3.5 1.3 - - - +
143B HIS* 3.7 22.2 - - + +
151B TRP* 3.7 26.9 - - + +
152B LYS* 1.3 77.4 - - - +
154B HIS* 1.3 62.8 + - - +
155B TYR* 3.6 32.5 - - + +
169B GLY* 4.9 10.1 - - - -
171B VAL* 6.1 0.2 - - + -
330B ALA 3.8 0.5 - - - +
331B THR* 3.3 5.2 - - - +
332B THR* 2.9 42.8 + - + +
334B TYR* 4.0 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER* 3.8 1.2 + - - +
141B VAL* 3.5 3.2 - - - -
142B THR* 2.8 49.7 + - - +
152B LYS* 4.8 11.0 - - + -
153B ILE* 1.3 76.5 - - - +
155B TYR* 1.3 70.5 + - - +
156B GLU* 3.4 28.0 + - + +
329B GLN* 2.9 34.4 + - + -
330B ALA 3.2 4.8 + - - -
331B THR* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 4.2 15.6 + - + -
140B SER 3.5 3.6 - - - +
141B VAL* 3.9 26.5 - - + -
153B ILE* 3.6 34.3 - - + +
154B HIS* 1.3 75.6 - - - +
156B GLU* 1.3 68.3 + - - +
165B PHE* 5.5 2.0 - + + -
167B PRO* 3.8 27.6 - - + -
168B THR* 3.2 8.5 - - - -
169B GLY* 3.1 31.7 + - - -
305B CYS 6.0 1.3 - - - -
328B TYR* 3.8 19.3 - - + -
329B GLN* 3.1 22.8 - - - -
330B ALA* 2.9 30.7 + - + +
332B THR* 5.0 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LYS* 4.7 10.0 + - - -
139B MET* 3.5 1.6 - - - +
140B SER* 2.9 49.9 + - - +
142B THR* 4.9 3.3 + - - -
154B HIS* 3.4 26.3 + - + +
155B TYR* 1.3 81.8 - - - +
157B ALA* 1.3 66.7 + - - +
165B PHE* 5.0 1.1 - - - -
327B LYS* 3.5 30.2 + - + -
328B TYR* 3.2 7.0 - - - +
329B GLN* 3.7 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 4.1 9.9 - - + -
138B GLU 3.2 12.3 - - - +
139B MET* 4.4 0.9 - - - -
156B GLU* 1.3 79.6 - - - +
158B ILE* 1.3 68.3 + - - +
165B PHE* 3.5 39.5 - - + -
322B LEU* 4.5 3.1 - - + +
326B GLU 3.6 1.4 - - - +
327B LYS* 3.5 1.5 - - - +
328B TYR* 2.7 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS 3.9 0.9 - - - +
137B ILE* 3.5 3.5 - - - -
138B GLU* 2.8 46.1 + - + +
157B ALA* 1.3 79.3 - - - +
159B SER* 1.4 68.6 + - - +
160B ASP* 5.7 0.2 - - - +
322B LEU* 5.0 0.2 - - - -
325B GLY* 4.1 23.8 - - - +
326B GLU 4.1 3.4 - - - -
327B LYS* 3.8 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLY* 3.7 8.0 - - - -
136B LYS 3.3 11.0 + - - -
137B ILE* 4.3 5.8 - - - +
158B ILE* 1.4 76.4 - - - +
160B ASP* 1.3 63.9 + - - +
161B LYS* 2.5 30.6 + - - -
163B THR* 3.6 21.8 - - - +
322B LEU* 4.5 12.5 - - - +
323B LYS 5.1 0.6 + - - -
324B ALA* 3.5 2.2 - - - -
325B GLY* 2.9 30.6 + - - +
326B GLU 4.7 0.8 + - - -
----------------------------------------------------------
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