Contacts of the helix formed by residues 300 - 309 (chain B) in PDB entry 3NA0
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 300 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 5.0 0.4 - - - -
213B VAL 3.4 12.8 - - - -
214B ILE 3.9 4.5 - - - -
216B GLY* 4.5 2.9 - - - -
298B TYR* 3.1 23.6 - - - -
299B ARG* 1.3 80.8 - - - +
301B ILE* 1.3 65.5 + - - -
302B LEU 3.5 1.6 - - - -
303B TYR* 3.7 3.7 - - - +
304B ARG* 3.4 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 5.7 0.7 - - + -
157B GLU* 3.9 23.6 - - + +
158B VAL* 3.8 17.5 - - + -
167B PHE* 3.8 24.2 - - + -
213B VAL* 2.9 39.9 + - + +
214B ILE* 3.4 14.9 + - + +
298B TYR* 3.7 11.4 - - - +
300B GLY* 1.3 69.0 - - - -
302B LEU* 1.3 67.1 + - - +
304B ARG* 3.0 9.7 + - - +
305B LEU* 3.0 39.0 + - + +
320B VAL* 6.5 0.7 - - + -
323B MET* 4.2 14.4 - - + -
467B ILE* 4.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ILE* 3.0 23.4 + - + +
215B PHE* 3.5 27.6 - - + -
281B THR* 4.2 17.9 - - + +
284B PHE* 3.5 36.1 - - + -
301B ILE* 1.3 76.3 - - - +
303B TYR* 1.3 55.1 + - - +
305B LEU* 3.2 5.7 + - - -
306B LEU* 2.8 51.1 + - + +
316B ILE* 3.5 31.6 - - + -
320B VAL* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 3.8 19.3 - + + -
288B LEU* 3.5 32.2 - - + +
293B SER 4.2 5.2 + - - -
294B VAL* 4.3 3.1 - - - +
295B HIS* 3.4 42.8 + + + +
297B ASP 5.8 0.2 - - - -
298B TYR* 6.5 0.2 - + - -
299B ARG* 3.5 46.0 - - + -
300B GLY 3.7 9.8 - - - +
302B LEU* 1.3 77.7 - - - +
304B ARG* 1.3 68.3 + - + +
306B LEU* 4.2 2.3 - - - +
307B GLY* 2.9 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLN 5.1 0.4 + - - -
157B GLU* 2.8 57.5 + - - +
162B GLU 4.9 3.2 + - - -
163B ALA* 4.1 14.6 - - - +
166B ASN* 3.2 26.7 - - - +
298B TYR* 3.7 21.2 - - + +
300B GLY 3.4 14.1 + - - +
301B ILE* 3.0 10.3 + - - +
303B TYR* 1.3 87.9 - - + +
305B LEU* 1.3 58.1 + - - +
307B GLY* 5.1 0.2 - - - -
308B ASP* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA 4.1 13.2 - - - +
154B LEU* 4.0 22.4 - - + -
157B GLU* 3.8 22.9 - - + -
301B ILE* 3.0 36.3 + - + +
302B LEU* 3.7 7.4 - - + +
304B ARG* 1.3 75.4 - - - +
306B LEU* 1.3 62.9 + - - +
309B SER* 2.8 46.7 + - - +
311B MET* 4.9 4.4 - - - +
316B ILE* 3.6 35.9 - - + +
319B ASN* 6.2 0.7 - - + -
320B VAL* 5.2 6.7 - - + -
323B MET* 5.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B THR 5.4 0.2 - - - +
284B PHE* 3.7 35.9 - - + -
285B TYR* 4.2 23.3 - - + -
288B LEU* 4.2 18.8 - - + -
302B LEU* 2.8 36.2 + - + +
303B TYR 4.2 2.0 - - - +
305B LEU* 1.3 74.0 - - - +
307B GLY* 1.3 60.4 + - - +
309B SER 5.2 0.2 + - - -
313B PHE* 3.8 31.4 - - + -
316B ILE* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 5.5 3.3 - - - +
303B TYR* 2.9 21.4 + - - -
304B ARG* 4.0 0.4 - - - -
306B LEU* 1.3 78.6 - - - +
308B ASP* 1.3 62.4 + - - +
309B SER 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B GLN* 4.6 13.8 + - - -
157B GLU* 5.4 1.2 - - - +
304B ARG* 2.9 16.2 + - - +
307B GLY* 1.3 79.7 - - - +
309B SER* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA* 4.0 7.4 + - - +
156B GLN* 6.1 0.7 - - - +
305B LEU* 2.8 46.7 + - - +
307B GLY 4.1 0.2 - - - -
308B ASP* 1.3 78.0 - - - +
310B LYS* 1.3 63.9 + - - +
311B MET* 3.0 32.8 + - - +
316B ILE* 4.4 1.6 - - - -
----------------------------------------------------------
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