Contacts of the helix formed by residues 305 - 312 (chain A) in PDB entry 2NPP
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 305 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ALA 3.9 9.6 - - - +
265A ASP* 2.7 28.2 + - - +
267A PHE* 3.4 5.9 - - + +
268A THR* 3.4 32.7 + - + +
269A GLU* 2.5 35.1 + - - -
287A PHE* 4.3 12.1 - - + -
301A ALA 3.7 14.6 - - - +
302A ALA* 2.7 17.4 + - - +
303A SER 2.7 0.2 + - - -
304A HIS* 1.3 79.5 - - + +
306A VAL* 1.3 52.3 + - - -
307A LYS 3.5 0.9 - - - -
308A GLU* 3.4 10.4 + - + +
309A PHE* 2.6 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 4.2 17.9 - - + -
291A MET* 4.7 8.7 - - - -
302A ALA 3.4 3.6 + - - +
303A SER* 2.8 37.3 + - - +
304A HIS 3.5 0.2 - - - -
305A LYS* 1.3 70.3 - - - +
307A LYS* 1.3 67.2 + - - +
309A PHE* 3.4 1.8 - - - +
310A CYS* 2.9 23.6 + - - -
326A ILE* 4.3 9.4 - - + -
330A ILE* 4.0 27.6 - - + -
333A LEU* 5.3 0.2 - - + -
345A LEU* 4.5 15.9 - - + -
348A VAL* 4.5 6.5 - - + -
349A ILE* 5.6 3.4 - - - +
352A LEU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LYS 3.5 0.4 - - - -
306A VAL* 1.3 82.2 - - - +
308A GLU* 1.3 69.6 + - - +
310A CYS* 3.1 2.1 + - - +
311A GLU* 2.9 59.5 + - + +
347A SER 5.8 0.2 - - - +
348A VAL* 3.5 40.3 + - + +
351A GLY* 3.8 25.1 - - - -
352A LEU* 4.5 9.9 - - - -
355A ILE* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 3.1 39.4 + - + +
272A LYS* 5.5 2.8 + - - -
304A HIS 5.5 1.8 - - - +
305A LYS* 3.4 12.9 + - + +
307A LYS* 1.3 86.6 - - + +
309A PHE* 1.3 64.0 + - - +
311A GLU* 3.9 10.5 - - - +
312A ASN* 3.2 37.2 + - - +
348A VAL* 5.2 1.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PHE* 3.4 33.4 - + + -
268A THR* 4.1 6.5 - - + +
271A GLN* 2.5 62.9 - - + +
279A THR* 3.8 19.3 - - + -
283A LEU* 4.5 1.1 - - + -
284A VAL* 4.3 21.1 - - + -
287A PHE* 3.6 32.1 - + + -
305A LYS* 2.6 26.7 + - + +
306A VAL* 3.4 3.8 - - - +
308A GLU* 1.3 74.5 - - - +
310A CYS* 1.3 64.3 + - - +
313A LEU* 3.5 15.1 + - + +
326A ILE* 4.4 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 5.9 0.2 - - - -
306A VAL* 2.9 18.9 + - - +
307A LYS 3.8 2.2 - - - +
309A PHE* 1.3 76.7 - - - +
311A GLU* 1.3 65.8 + - - +
312A ASN 3.1 2.0 - - - -
313A LEU* 3.2 26.0 + - - +
318A ARG* 3.9 11.8 + - - +
322A ILE* 3.6 33.2 - - + -
326A ILE* 3.7 35.2 - - - -
352A LEU* 4.0 17.5 - - + -
355A ILE* 4.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LYS* 2.9 64.7 + - + +
308A GLU* 3.9 7.6 - - - +
310A CYS* 1.3 76.0 - - - +
312A ASN* 1.3 60.4 + - - +
318A ARG* 2.9 31.0 + - - +
351A GLY 4.6 4.8 - - - +
355A ILE* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 5.2 0.8 + - - -
271A GLN* 3.3 33.4 - - + +
272A LYS* 3.2 39.9 + - + +
276A PRO* 5.5 5.4 - - - +
279A THR* 6.1 0.2 - - - +
308A GLU* 3.2 30.6 + - - +
310A CYS 3.1 0.8 - - - -
311A GLU* 1.3 81.0 - - - +
313A LEU* 1.3 66.4 + - - +
314A SER* 3.6 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