Contacts of the helix formed by residues 295 - 312 (chain E) in PDB entry 1NBF
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 ASP 295 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E TYR* 3.5 14.9 + - - -
294E HIS* 1.3 77.6 - - - +
296E VAL* 1.3 66.8 + - + +
297E GLN* 2.7 35.8 + - - +
298E GLU* 3.0 36.5 + - - +
299E LEU 3.1 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E TYR* 3.4 48.1 - - + +
228E LEU* 4.6 12.9 - - + +
295E ASP* 1.3 75.0 - - + +
297E GLN* 1.3 65.7 + - + +
299E LEU* 3.8 1.4 - - - +
300E CYS* 3.0 27.7 + - - +
405E GLN* 4.4 12.1 - - + -
454E LEU* 5.1 1.6 - - + -
514E TYR* 3.5 34.1 - - + +
515E MET* 4.2 24.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 297 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E ASP* 2.7 29.5 + - - +
296E VAL* 1.3 81.2 - - + +
298E GLU* 1.3 62.9 + - + +
300E CYS* 3.7 3.9 + - - +
301E ARG* 3.2 33.7 + - - +
349E ASP* 4.2 12.3 - - - +
351E GLN* 3.1 34.9 + - - +
405E GLN* 3.5 46.1 + - + +
407E MET* 4.3 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 298 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285E TRP* 4.8 2.9 - - + -
293E GLN 4.5 0.3 - - - +
294E HIS* 3.1 50.5 + - + +
295E ASP* 3.0 23.4 + - - +
297E GLN* 1.3 74.2 - - + +
299E LEU* 1.3 63.0 + - - +
301E ARG* 3.4 16.8 + - - +
302E VAL* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E TYR* 3.3 37.2 - - + -
225E MET* 3.7 30.7 - - + -
228E LEU* 4.8 9.6 - - + -
283E PHE* 4.4 13.2 - - + -
285E TRP* 3.8 23.5 - - + -
291E PHE* 4.3 3.1 - - + -
295E ASP 3.1 5.0 + - - +
296E VAL* 3.8 6.1 - - - +
298E GLU* 1.3 74.3 - - - +
300E CYS* 1.3 65.8 + - - +
301E ARG 3.2 0.2 + - - -
302E VAL* 3.3 5.8 + - + +
303E LEU* 3.1 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 300 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E LEU* 4.5 13.6 - - + +
232E LEU* 4.4 12.8 - - - -
296E VAL 3.0 18.0 + - - +
297E GLN* 4.0 4.3 - - - +
299E LEU* 1.3 77.0 - - - +
301E ARG* 1.3 59.2 + - + +
303E LEU* 4.0 8.8 - - - +
304E LEU* 3.0 54.9 + - - +
403E HIS* 3.8 31.0 - - - +
405E GLN* 5.9 1.8 - - - +
515E MET* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 301 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E GLN* 3.2 21.8 + - - +
298E GLU* 3.6 18.0 - - - +
299E LEU 3.1 0.6 - - - -
300E CYS* 1.3 76.9 - - + +
302E VAL* 1.3 54.7 + - + +
304E LEU* 3.3 4.5 + - - +
305E ASP* 2.5 52.0 + - - +
348E TYR* 6.2 4.8 - - + +
349E ASP* 3.4 36.8 + - - +
351E GLN* 4.8 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E VAL* 5.9 1.1 - - + -
283E PHE* 4.0 31.0 - - + -
285E TRP* 4.9 13.2 - - + +
298E GLU* 2.9 19.9 + - + +
299E LEU* 3.7 8.3 - - + +
301E ARG* 1.3 78.3 - - + +
303E LEU* 1.3 65.2 - - + +
305E ASP* 3.3 6.3 + - - +
306E ASN* 3.2 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E MET* 6.1 0.4 - - + -
228E LEU* 3.6 11.9 - - + -
229E LEU* 4.6 11.2 - - + -
232E LEU* 3.6 32.1 - - + -
256E VAL* 4.6 11.7 - - + +
260E LEU* 5.0 11.0 - - + -
279E LEU* 4.2 11.9 - - + -
283E PHE* 4.0 27.1 - - + -
299E LEU* 3.1 39.0 + - + +
300E CYS* 4.0 4.3 - - - +
302E VAL* 1.3 79.6 - - + +
304E LEU* 1.3 60.9 + - + +
306E ASN* 4.2 1.9 - - - +
307E VAL* 3.0 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E LEU* 4.6 11.0 - - + -
238E LEU* 3.9 28.0 - - + -
260E LEU* 6.4 1.1 - - + -
300E CYS* 3.0 41.9 + - - +
301E ARG* 3.9 4.5 - - - +
303E LEU* 1.3 81.3 - - + +
305E ASP* 1.3 61.2 + - - +
307E VAL* 3.8 6.1 - - + -
308E GLU* 2.9 34.4 + - - +
320E ILE* 3.4 30.4 - - + +
324E PHE* 4.6 21.8 - - + -
348E TYR* 5.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 305 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301E ARG* 2.5 42.2 + - - +
302E VAL* 3.3 7.8 + - - +
304E LEU* 1.3 73.8 - - - +
306E ASN* 1.3 55.8 + - - +
308E GLU* 4.9 9.1 - - - +
309E ASN* 2.7 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 306 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E LYS 5.4 0.6 + - - -
256E VAL* 3.1 47.1 - - + +
257E PRO* 3.1 12.1 - - + +
302E VAL* 3.2 25.4 + - - +
303E LEU 4.2 0.4 - - - +
305E ASP* 1.3 83.5 - - - +
307E VAL* 1.3 57.4 + - - +
309E ASN* 4.2 5.7 - - - +
310E LYS* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 307 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E LEU* 4.8 3.1 - - + -
242E VAL* 4.5 10.8 - - + -
245E MET* 3.9 25.3 - - + +
256E VAL* 5.6 1.3 - - + -
257E PRO* 4.9 5.6 - - + -
260E LEU* 3.8 26.9 - - + -
303E LEU 3.0 23.4 + - - +
304E LEU* 3.8 7.9 - - + +
305E ASP 3.1 0.6 - - - -
306E ASN* 1.3 75.4 - - + +
308E GLU* 1.3 68.1 + - - +
310E LYS* 3.0 5.4 + - - +
311E MET* 2.9 41.8 + - + +
320E ILE* 3.6 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LYS* 5.8 0.2 + - - -
304E LEU 2.9 15.7 + - - +
305E ASP* 4.2 8.6 - - - +
307E VAL* 1.3 70.9 - - - +
309E ASN* 1.3 58.1 + - - +
311E MET* 2.5 37.2 + - - +
312E LYS* 3.3 19.0 + - + +
317E GLU* 5.3 1.7 - - + +
318E GLY* 4.9 10.3 - - - +
320E ILE* 3.2 27.9 - - + +
321E PRO* 3.2 36.5 - - + +
325E ARG* 4.7 5.5 + - - -
348E TYR* 4.8 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 309 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E ASP 2.7 26.1 + - - +
306E ASN* 4.2 4.9 - - - +
308E GLU* 1.3 73.5 - - - +
310E LYS* 1.3 61.1 + - - +
312E LYS* 3.4 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 310 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E MET* 4.1 15.3 - - + -
246E PRO* 3.0 43.2 + - + +
247E THR* 3.6 17.0 - - - -
250E ASP* 3.3 19.5 + - - +
257E PRO* 3.5 19.1 - - + -
306E ASN 2.9 18.0 + - - +
307E VAL 3.0 7.3 + - - +
309E ASN* 1.3 79.4 - - - +
311E MET* 1.3 59.5 + - - +
312E LYS 3.3 6.0 + - - +
314E THR* 4.0 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E LEU* 5.1 1.6 - - + +
241E ALA* 2.9 52.7 - - + +
242E VAL 4.0 1.1 - - - +
245E MET* 4.4 9.4 - - + -
246E PRO* 5.5 1.3 - - - -
307E VAL* 2.9 38.2 + - + +
308E GLU* 2.5 22.8 + - - +
310E LYS* 1.3 71.5 - - - +
312E LYS* 1.3 61.0 + - - -
314E THR* 2.5 30.0 + - - +
316E VAL* 3.4 13.2 - - + +
317E GLU* 3.0 29.3 - - - +
318E GLY 4.7 0.7 - - - +
319E THR* 3.3 17.0 - - - +
320E ILE* 4.3 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ASP* 4.5 14.1 - - - +
375A GLY* 4.4 23.5 - - - +
388A GLU* 5.9 2.0 - - - -
308E GLU* 3.3 18.3 + - + +
309E ASN* 3.4 40.3 - - - +
310E LYS 3.3 4.6 - - - +
311E MET* 1.3 78.7 - - - +
313E GLY* 1.3 62.2 + - - +
314E THR* 3.5 5.0 + - - +
317E GLU* 3.7 22.6 - - + +
----------------------------------------------------------
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