Contacts of the helix formed by residues 157 - 170 (chain B) in PDB entry 3NX4
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 157 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLY 3.1 12.7 + - - -
155B ALA 3.2 0.2 - - - -
156B SER* 1.3 77.6 - - - +
158B GLY* 1.3 59.7 + - - -
159B VAL 3.6 1.8 - - - -
160B GLY 4.0 0.7 - - - -
161B SER* 2.8 32.0 + - - -
315B VAL 5.7 0.4 - - - -
316B GLN* 5.4 0.4 - - - -
317B GLY 3.9 5.2 - - - -
330B NAP 3.2 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ALA* 3.6 9.2 - - - -
157B GLY* 1.3 74.4 - - - +
159B VAL* 1.3 62.0 + - - +
161B SER* 4.0 1.6 - - - -
162B THR* 2.9 26.2 + - - -
317B GLY 3.6 8.7 + - - -
318B ARG* 3.5 27.0 - - - -
330B NAP 2.9 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ALA* 3.5 34.9 - - + +
130B THR* 4.4 2.7 - - + -
131B ALA* 3.6 19.5 - - + +
158B GLY* 1.3 71.5 - - - -
160B GLY* 1.3 63.3 + - - +
162B THR* 3.3 1.8 + - - -
163B ALA* 3.0 20.8 + - - +
216B ILE* 4.9 7.0 - - + -
218B THR* 3.8 21.5 - - + -
240B CYS* 3.9 13.2 - - - -
330B NAP 2.8 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B VAL* 3.8 12.2 - - - +
153B THR 4.4 2.2 - - - -
154B GLY 3.7 15.1 + - - -
155B ALA* 3.0 18.8 - - - -
157B GLY 3.7 3.6 + - - -
158B GLY 3.4 0.4 - - - -
159B VAL* 1.3 79.6 - - - +
161B SER* 1.3 61.4 + - - +
163B ALA* 3.3 2.8 + - - +
164B VAL* 3.0 28.9 + - - +
218B THR* 4.2 3.8 - - - +
330B NAP 4.5 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA 3.0 5.6 + - - -
156B SER 3.3 12.5 + - - -
157B GLY 2.8 26.6 + - - -
158B GLY 4.0 2.7 - - - -
160B GLY* 1.3 73.0 - - - +
162B THR* 1.3 63.0 + - - +
164B VAL* 3.4 3.8 + - - +
165B ALA* 3.2 17.8 + - - +
186B TYR* 2.7 34.6 + - - -
190B LEU* 3.7 13.9 - - - +
290B PHE* 3.7 15.0 - - - -
294B ALA* 4.8 0.4 - - - -
317B GLY* 3.7 5.0 - - - -
318B ARG* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 5.1 1.1 + - + -
128B GLY* 3.6 30.9 + - - +
131B ALA* 3.7 12.1 - - + -
158B GLY 2.9 15.0 + - - -
159B VAL 3.3 6.8 + - - -
161B SER* 1.3 76.8 - - - +
163B ALA* 1.3 58.1 + - - +
165B ALA* 3.3 3.1 + - - +
166B LEU* 2.9 44.7 + - + +
282B LEU* 4.8 1.1 - - + -
286B LEU* 4.3 18.8 - - + -
290B PHE* 3.5 22.4 - - + -
318B ARG* 4.6 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA* 3.7 13.0 - - + +
135B VAL* 5.1 0.4 - - - -
152B VAL* 4.2 8.7 - - + -
159B VAL 3.0 17.5 + - - +
160B GLY 3.7 4.3 - - - +
161B SER 3.3 0.2 - - - -
162B THR* 1.3 74.9 - - - +
164B VAL* 1.3 64.5 + - - +
166B LEU* 3.8 5.3 - - - +
167B LEU* 2.9 32.0 + - - +
216B ILE* 3.8 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B VAL* 4.2 21.8 - - + -
155B ALA* 4.4 13.7 - - + +
160B GLY 3.0 20.9 + - - +
161B SER* 3.7 8.1 - - - +
162B THR 3.3 0.2 - - - -
163B ALA* 1.3 76.2 - - - +
165B ALA* 1.3 56.0 + - - +
167B LEU* 3.9 1.2 - - - +
168B HIS* 2.9 28.4 + - - +
174B VAL* 4.4 15.1 - - + +
176B ALA* 4.5 6.3 - - + -
187B LEU* 4.3 4.0 - - + +
190B LEU* 3.9 19.1 - - + -
191B GLY 4.1 0.4 - - - -
192B ALA* 3.6 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B SER 3.2 5.9 + - - +
162B THR 3.3 4.9 + - - +
164B VAL* 1.3 76.1 - - - +
166B LEU* 1.3 61.0 + - - +
168B HIS* 3.7 1.9 - - - +
169B LYS* 2.9 30.5 + - - +
190B LEU* 3.7 21.1 - - + +
286B LEU* 4.0 9.6 - - + -
287B PRO* 4.5 9.5 - - + +
290B PHE* 3.6 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA* 4.0 6.1 - - + -
132B MSE 3.9 47.3 - - + +
135B VAL* 4.1 14.8 - - + -
162B THR* 2.9 32.0 + - + +
163B ALA 3.4 3.1 + - - +
165B ALA* 1.3 74.8 - - - +
167B LEU* 1.3 58.4 + - - +
169B LYS* 3.3 2.4 + - - +
170B LEU* 3.0 38.7 + - + +
282B LEU* 4.3 4.3 - - + -
285B ASP* 3.7 30.5 - - + +
286B LEU* 3.7 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 4.2 21.3 - - + -
138B LEU* 4.3 16.4 - - + -
150B VAL* 3.6 19.7 - - + -
152B VAL* 3.6 27.6 - - + -
163B ALA 2.9 22.0 + - - +
164B VAL 3.9 0.4 - - - +
166B LEU* 1.3 73.1 - - - +
168B HIS* 1.3 66.5 + - - +
170B LEU* 3.2 2.1 + - - -
171B GLY 3.1 5.5 + - - -
172B TYR* 3.0 55.0 + - + -
174B VAL* 3.5 19.1 - - + -
216B ILE* 4.0 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL 2.9 19.4 + - - +
165B ALA 3.7 4.9 - - - +
167B LEU* 1.3 76.9 - - - +
169B LYS* 1.3 66.8 + - - +
171B GLY* 3.1 13.5 + - - -
172B TYR 4.3 9.9 + - - +
174B VAL* 4.1 3.3 - - + +
190B LEU 4.1 6.5 - - - +
191B GLY* 3.4 40.3 + - - +
193B ASN* 5.0 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA 2.9 18.7 + - - +
166B LEU 3.3 2.4 + - - +
168B HIS* 1.3 82.2 - - + +
170B LEU* 1.3 70.2 + - + +
171B GLY* 3.3 4.0 + - - -
284B LYS* 3.6 19.7 + - - +
285B ASP* 2.9 48.0 + - + +
287B PRO* 4.5 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B MSE 5.2 0.4 - - + -
135B VAL* 3.7 30.1 - - + -
139B GLU* 4.2 7.0 - - - +
145B PRO* 3.5 15.9 - - - +
166B LEU* 3.0 27.1 + - + +
167B LEU* 3.2 1.5 + - - +
168B HIS 3.2 0.2 - - - -
169B LYS* 1.3 84.8 - - + +
171B GLY* 1.3 58.9 + - - +
172B TYR* 3.6 20.2 - - + -
281B ARG* 4.0 14.6 - - - +
285B ASP* 3.7 31.0 - - + +
----------------------------------------------------------
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