Contacts of the helix formed by residues 300 - 317 (chain A) in PDB entry 5NDD
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 PHE 300 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A MET* 4.2 16.4 - - - -
162A SER* 4.1 17.0 - - - -
163A ILE* 3.9 32.1 - - + -
166A LEU* 4.0 5.2 - - + -
251A PHE* 3.6 20.2 - - + -
295A MET* 3.3 33.4 + - + -
296A TYR* 3.4 53.1 + + - +
299A CYS* 1.3 93.2 - - + +
301A THR* 1.3 61.5 + - - +
302A PRO 3.5 0.4 - - - -
303A SER* 3.4 0.9 + - - -
304A ASN* 2.9 37.8 + - - +
333A SER* 5.5 0.4 - - - -
336A ASN* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 3.6 25.9 - - + -
296A TYR* 2.8 33.4 + - - +
297A LEU* 4.4 5.4 - - - -
300A PHE* 1.3 71.2 - - - +
302A PRO* 1.3 69.0 - - + +
305A LEU* 3.1 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU 3.3 22.7 - - - +
298A ILE* 3.2 29.8 - - - +
300A PHE 3.7 1.1 - - - +
301A THR* 1.3 90.9 - - + +
303A SER* 1.3 61.1 + - - +
305A LEU* 4.3 4.7 - - + +
306A LEU* 3.2 35.9 + - + +
329A ALA* 3.6 16.6 - - + +
332A LEU* 6.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A MET* 3.8 19.5 - - - -
299A CYS 2.9 24.5 + - - -
300A PHE 3.4 2.4 + - - -
301A THR 3.2 0.8 - - - -
302A PRO* 1.3 77.3 - - - +
304A ASN* 1.3 63.0 + - - +
306A LEU* 3.4 1.4 + - - +
307A LEU* 2.8 37.3 + - - +
326A TYR* 5.9 0.2 - - - -
329A ALA* 3.2 19.2 + - - -
330A LEU* 4.9 8.2 - - - +
333A SER* 3.1 15.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A MET* 3.9 22.4 - - - -
160A TYR* 3.4 30.4 + - - -
163A ILE* 4.5 3.6 - - - +
243A PHE 4.9 0.3 - - - +
247A ALA* 4.0 15.2 - - + +
251A PHE* 3.8 40.1 - - + +
300A PHE* 2.9 29.6 + - - +
303A SER* 1.3 77.0 - - - +
305A LEU* 1.3 64.4 + - - +
307A LEU* 3.5 9.3 + - - +
308A VAL* 3.3 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 5.4 2.3 - - + -
301A THR* 3.1 29.7 + - + +
302A PRO* 4.3 3.6 - - + +
304A ASN* 1.3 79.5 - - - +
306A LEU* 1.3 63.5 + - + +
308A VAL* 3.3 10.1 + - + +
309A VAL* 3.1 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PRO* 3.2 25.2 + - + +
303A SER 4.0 1.1 - - - +
305A LEU* 1.3 81.5 - - + +
307A LEU* 1.3 57.7 + - - +
308A VAL 3.1 1.6 - - - -
309A VAL* 3.6 15.7 - - + +
310A HIS* 2.5 38.9 + - - +
322A VAL* 4.1 28.7 - - + +
325A LEU* 3.3 45.3 - - + +
326A TYR* 4.5 11.4 - - + -
329A ALA* 3.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 4.0 25.1 - - + +
159A MET* 5.7 4.3 - - + -
160A TYR* 4.5 9.0 - - - +
243A PHE* 3.6 36.3 - - + +
303A SER* 2.8 27.5 + - - +
304A ASN* 3.7 11.2 - - - +
305A LEU 3.3 0.2 - - - -
306A LEU* 1.3 76.9 - - - +
308A VAL* 1.3 61.0 + - - +
310A HIS* 4.0 2.9 - - - +
311A TYR* 3.1 50.8 + - + +
326A TYR* 3.5 27.8 - - + -
330A LEU* 4.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 3.8 27.1 - - + +
243A PHE* 3.7 23.8 - - - +
244A LEU* 3.8 25.6 - - + +
247A ALA* 3.9 10.8 - - + -
304A ASN 3.3 15.9 + - - +
305A LEU* 3.3 9.1 + - + +
306A LEU 3.1 0.4 - - - -
307A LEU* 1.3 75.9 - - - +
309A VAL* 1.3 62.7 + - + +
312A PHE* 3.0 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 3.1 29.6 + - + +
306A LEU* 3.0 16.5 + - + +
308A VAL* 1.3 79.2 - - + +
310A HIS* 1.3 63.1 + - - +
312A PHE* 3.2 7.3 + - + +
313A LEU* 3.1 32.6 + - + +
322A VAL* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ASP 5.4 1.8 + - - -
306A LEU 2.5 20.8 + - - +
307A LEU 4.0 2.9 - - - +
309A VAL* 1.3 75.7 - - - +
311A TYR* 1.3 79.0 + + - +
313A LEU 3.3 5.4 + - - -
314A ILE* 3.2 43.1 + - + +
320A SER* 2.6 32.4 + - - -
322A VAL* 4.0 11.8 - - + +
323A TYR* 3.4 32.2 - + - -
326A TYR* 3.7 44.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 4.9 2.3 + - - -
227A HIS* 4.9 7.3 + - - -
230A LEU* 4.6 19.0 - - + +
236A VAL* 3.4 13.6 - - + +
239A MET* 3.8 30.5 - - + +
240A PHE* 4.0 22.9 - - + +
243A PHE* 3.5 40.0 - + + -
307A LEU* 3.1 38.2 + - + +
308A VAL 4.5 0.7 - - - +
309A VAL 3.5 0.4 - - - -
310A HIS* 1.3 97.4 - + - +
312A PHE* 1.3 59.9 + - - +
314A ILE* 3.9 11.0 - - + -
315A LYS* 3.1 28.2 + - - +
326A TYR* 3.9 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 3.6 31.2 - + + -
308A VAL* 3.0 22.2 + - + +
309A VAL* 3.5 8.3 - - + +
310A HIS 3.1 0.2 - - - -
311A TYR* 1.3 79.3 - - - +
313A LEU* 1.3 76.1 + - + +
315A LYS* 3.5 9.3 + - + +
316A SER* 3.1 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A VAL* 3.1 21.6 + - + +
310A HIS 3.3 0.2 + - - -
312A PHE* 1.3 93.6 - - + +
314A ILE* 1.3 57.7 + - - +
315A LYS 3.1 1.3 - - - -
316A SER* 3.0 9.1 + - - +
317A GLN* 2.6 39.9 + - + +
318A GLY 3.2 2.6 + - - -
319A GLN 3.5 16.3 - - - +
320A SER* 3.5 24.5 - - - -
321A HIS* 3.6 34.8 - - + +
322A VAL* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 5.8 5.6 - - + -
233A GLN* 3.6 25.8 - - - +
236A VAL* 3.6 26.8 - - + +
310A HIS* 3.2 49.5 + - + +
311A TYR* 4.1 10.3 - - + +
312A PHE 3.4 0.2 - - - -
313A LEU* 1.3 76.5 - - - +
315A LYS* 1.3 60.6 + - - +
318A GLY* 3.1 30.6 + - - +
319A GLN* 3.9 3.6 - - - +
320A SER* 4.2 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 3.5 13.2 - - + +
237A GLY* 4.4 17.2 + - - +
240A PHE* 3.8 40.7 - - + -
241A ASN* 4.4 13.5 + - - +
311A TYR 3.1 19.2 + - - +
312A PHE* 3.6 10.3 - - + +
314A ILE* 1.3 79.3 - - - +
316A SER* 1.3 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 3.1 28.9 + - - -
313A LEU* 3.0 20.0 + - - +
315A LYS* 1.3 80.3 - - - +
317A GLN* 1.3 74.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU* 2.6 20.5 + - - +
316A SER* 1.3 88.6 + - - +
318A GLY* 1.3 58.2 + - - +
319A GLN* 3.3 27.5 + - + +
----------------------------------------------------------
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