Contacts of the helix formed by residues 157 - 170 (chain B) in PDB entry 3NJ4
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 THR 157 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASP* 3.5 22.4 - - - +
132B GLY* 3.9 8.7 - - - +
155B GLU* 3.0 8.1 + - - +
156B GLU* 1.3 79.7 - - - +
158B THR* 1.3 65.6 + - - +
159B THR 3.9 0.2 - - - +
160B GLY 3.3 16.1 + - - +
161B VAL* 3.0 24.8 + - - +
181B ASN* 3.2 9.2 - - - +
301B HIS* 4.0 5.2 - - + +
502B NAD 2.7 31.3 + - - +
602B AFX 3.2 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B THR* 1.3 74.8 + - - +
159B THR* 1.3 66.8 + - - +
161B VAL* 3.1 5.7 + - - +
162B HIS* 2.9 25.8 + - + +
181B ASN* 2.9 27.5 + - - +
182B ASP* 5.8 2.9 - - - +
191B ASN* 3.3 3.1 + - - -
502B NAD 2.5 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 5.5 2.9 - - - +
132B GLY 4.6 0.4 - - - +
157B THR* 4.5 0.2 - - - -
158B THR* 1.3 78.3 - - - +
160B GLY* 1.3 64.1 + - - +
162B HIS* 3.1 12.1 - - - +
163B ASN* 3.0 20.8 + - + +
277B GLY* 4.3 13.9 + - - +
301B HIS* 4.1 9.9 - - + +
302B PHE* 3.6 38.4 + - + -
502B NAD 2.9 35.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
132B GLY* 3.8 17.7 - - - -
133B GLY* 4.2 1.9 - - - -
155B GLU* 3.2 30.5 - - - +
157B THR* 3.3 8.3 + - - +
158B THR 3.2 0.8 - - - -
159B THR* 1.3 77.5 - - - +
161B VAL* 1.3 65.3 + - - +
163B ASN* 3.1 8.5 + - - +
164B LEU* 3.1 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU* 3.5 24.0 - - + -
157B THR 3.0 21.2 + - - +
158B THR* 3.7 5.6 - - - +
160B GLY* 1.3 72.6 - - - +
162B HIS* 1.3 65.8 + - - +
164B LEU* 3.1 14.3 + - - +
165B TYR* 3.1 28.8 + - + -
179B ASN* 3.0 52.7 - - + +
181B ASN* 3.7 11.4 - - + +
182B ASP* 3.8 5.8 - - - +
383B VAL* 4.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR 5.1 2.0 - - - -
417A LEU* 3.0 47.7 + - + +
418A GLY 5.2 1.0 + - - -
419A MET* 6.3 1.1 - - - -
158B THR* 2.9 15.9 + - + +
159B THR* 3.1 14.9 + - - +
161B VAL* 1.3 78.1 - - - +
163B ASN* 1.3 63.4 + - - +
165B TYR* 3.1 15.5 + + + +
166B LYS* 3.0 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLY 5.3 3.1 - - - +
133B GLY* 4.8 4.9 - - - -
136B THR* 4.6 3.0 + - - -
137B ASN* 2.7 42.3 + - - +
159B THR* 3.0 12.5 + - + +
160B GLY* 3.3 13.9 + - - +
162B HIS* 1.3 76.5 - - - +
164B LEU* 1.3 57.9 + - - +
166B LYS* 3.3 16.8 + - - +
167B MET* 2.8 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY* 6.5 0.2 - - - -
136B THR* 4.4 17.9 - - + +
153B ILE* 4.7 8.1 - - + -
155B GLU* 3.8 31.4 - - + +
160B GLY 3.1 13.3 + - - +
161B VAL* 3.3 11.0 - - + +
163B ASN* 1.3 75.1 - - - +
165B TYR* 1.3 59.7 + - - +
167B MET* 3.1 10.3 + - - +
168B MET* 2.8 29.8 + - - +
173B LEU* 4.1 27.9 - - + +
177B ALA* 3.8 24.9 - - + -
178B ILE 5.2 2.0 - - - +
179B ASN* 5.3 0.2 - - - -
383B VAL* 4.4 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PRO* 5.9 2.7 - - + -
429A HIS* 3.7 20.4 - + - -
161B VAL* 3.1 36.5 + - + -
162B HIS* 3.1 14.2 + + + +
164B LEU* 1.3 78.1 - - - +
166B LYS* 1.3 59.4 + - - +
168B MET* 3.1 4.1 + - + +
169B ALA* 2.9 31.3 + - - +
179B ASN* 3.0 23.2 + - - -
182B ASP* 4.3 1.1 - - - -
383B VAL* 3.3 39.8 + - + +
385B PHE* 3.4 20.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A GLN 4.8 5.9 + - - -
416A TYR 5.2 7.0 + - - +
417A LEU 6.1 1.1 - - - +
418A GLY* 4.7 17.8 - - - -
162B HIS* 3.0 21.7 + - + +
163B ASN* 3.5 20.0 - - - +
165B TYR* 1.3 75.9 - - - +
167B MET* 1.3 62.5 + - + +
169B ALA* 3.7 7.4 + - - +
170B ASN* 3.3 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 4.4 7.0 - - - +
137B ASN* 3.6 12.1 - - - +
140B HIS* 3.5 49.4 - - + +
163B ASN* 2.8 47.4 + - - +
164B LEU* 3.4 15.7 - - - +
165B TYR 3.1 0.2 - - - -
166B LYS* 1.3 76.7 - - + +
168B MET* 1.3 63.4 + - - +
170B ASN* 3.2 3.2 + - - +
171B GLY 3.0 4.0 + - - -
172B ILE* 2.8 49.6 + - + +
173B LEU* 4.0 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU 2.8 16.0 + - - +
165B TYR* 3.6 9.9 - - + +
167B MET* 1.3 69.9 - - - +
169B ALA* 1.3 61.0 + - - +
171B GLY* 2.7 32.4 + - - -
173B LEU* 4.0 23.9 - - + +
381B VAL* 3.9 13.9 - - + +
382B GLY* 3.7 28.9 - - - -
383B VAL* 4.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B TYR 2.9 16.6 + - - +
166B LYS* 3.7 9.2 - - - +
168B MET* 1.3 78.7 - - - +
170B ASN* 1.3 62.3 + - - +
171B GLY 3.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LYS* 3.3 33.7 + - - +
167B MET* 3.2 2.8 + - - +
169B ALA* 1.3 80.7 - - - +
171B GLY* 1.3 64.8 + - - +
172B ILE* 3.1 30.9 + - + +
----------------------------------------------------------
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