Contacts of the helix formed by residues 303 - 320 (chain B) in PDB entry 1Z10
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 303 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B SER* 4.4 8.3 - - - +
178B VAL* 3.4 8.7 - - + +
179B SER* 3.1 42.6 + - - +
182B ILE* 3.8 4.0 - - - +
202B LEU* 4.0 9.6 - - + -
205B MET* 3.9 20.3 - - - +
299B PHE* 2.8 21.4 + - - -
300B ILE 2.9 4.9 + - - -
301B GLY 3.3 0.2 - - - -
302B GLY* 1.3 79.6 - - - +
304B GLU* 1.3 69.0 + - - +
305B THR 3.4 1.7 + - - -
306B VAL 3.5 1.3 + - - -
307B SER* 3.0 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B SER* 5.2 4.8 - - - -
202B LEU* 4.6 2.4 - - - +
205B MET* 3.6 22.9 - - + +
206B LEU* 3.1 41.2 + - - +
209B PHE* 3.3 49.3 - - + +
300B ILE* 3.0 8.5 + - + +
303B THR* 1.3 89.2 - - - +
305B THR* 1.3 55.9 + - - +
307B SER* 4.4 9.8 + - - -
308B THR* 2.5 45.8 + - - +
311B ARG* 4.6 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 3.8 17.5 - - + -
301B GLY 2.8 25.2 + - - +
304B GLU* 1.3 76.2 - - - +
306B VAL* 1.3 68.2 + - - +
308B THR* 3.4 2.3 + - - -
309B THR* 2.8 29.3 + - - -
365B VAL* 4.0 10.0 - - - +
366B ILE* 4.2 8.1 - - + -
500B HEM 3.2 36.3 - - + +
501B COU 3.8 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL* 3.5 23.1 - - + -
302B GLY 4.6 2.7 - - - +
303B THR 3.5 1.0 + - - +
305B THR* 1.3 81.0 + - - +
307B SER* 1.3 68.2 + - - +
309B THR* 3.2 3.9 + - - -
310B LEU* 3.0 26.8 + - + +
445B ALA* 4.0 20.9 - - + +
448B GLU* 3.5 30.7 - - + +
449B LEU* 4.0 16.2 - - + -
500B HEM 3.7 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B THR* 4.4 2.3 + - - +
174B LEU* 4.4 4.3 - - - +
175B SER* 3.5 39.3 + - - -
178B VAL* 3.9 12.0 - - - +
303B THR 3.0 20.2 + - - -
304B GLU* 4.1 9.7 + - - -
306B VAL* 1.3 78.6 - - - +
308B THR* 1.3 63.1 + - - +
310B LEU* 3.3 4.0 + - - +
311B ARG* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 4.5 5.8 - - + -
304B GLU* 2.5 38.6 + - - +
305B THR* 3.8 4.0 - - - -
306B VAL 3.2 0.2 - - - -
307B SER* 1.3 76.6 - - - +
309B THR* 1.3 56.6 + - - +
311B ARG* 3.3 17.6 + - - +
312B TYR* 2.8 30.5 + - + +
365B VAL* 4.3 15.7 - - + -
481B ALA* 6.1 0.2 - - + -
482B THR 3.6 24.0 - - - +
483B ILE* 4.7 7.4 - - + +
484B PRO* 3.8 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR 2.8 21.2 + - - -
306B VAL* 3.6 4.9 - - - -
308B THR* 1.3 78.3 - - - +
310B LEU* 1.3 53.0 + - - +
312B TYR* 3.3 4.8 + - - +
313B GLY* 2.7 32.2 + - - -
359B ILE* 3.8 20.0 - - + +
360B GLN* 4.1 15.2 + - + -
365B VAL* 3.4 21.7 - - + +
449B LEU* 3.7 30.5 - - + -
453B PHE* 3.8 2.0 - - + -
500B HEM 3.6 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 6.1 0.9 - - + -
174B LEU* 4.0 24.7 - - + +
177B THR* 6.3 0.7 - - + -
178B VAL* 3.6 31.2 - - + -
306B VAL* 3.0 15.3 + - + +
307B SER* 3.7 3.1 - - - +
309B THR* 1.3 75.6 - - - +
311B ARG* 1.3 65.7 + - - +
313B GLY* 3.0 10.7 + - - -
314B PHE* 3.1 25.7 + - + -
449B LEU* 3.8 14.4 - - + +
452B PHE* 4.0 33.4 - - + -
453B PHE* 3.7 40.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASP* 5.1 0.2 - - - -
170B PRO* 4.6 2.7 - - + -
171B THR* 3.3 43.3 + - - +
174B LEU* 3.7 17.7 - - + +
206B LEU* 4.0 22.8 - - - +
304B GLU* 4.6 0.6 + - - -
307B SER* 2.9 24.5 + - - +
308B THR* 3.6 24.1 + - - +
310B LEU* 1.3 78.7 - - - +
312B TYR* 1.3 62.8 + - - +
315B LEU 3.5 4.3 + - - -
476B LYS* 5.8 0.8 - - - +
483B ILE* 3.8 26.5 - - - +
484B PRO* 3.9 20.6 + - + +
485B ARG 5.6 1.0 + - - -
486B ASN* 6.4 0.6 - - - +
487B TYR* 2.6 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B THR* 2.8 21.4 + - + +
309B THR* 3.7 6.7 - - - +
311B ARG* 1.3 74.0 - - - +
313B GLY* 1.3 63.2 + - - +
315B LEU* 3.2 10.0 + - + +
316B LEU* 3.0 40.3 + - + +
359B ILE* 5.2 1.8 - - + -
362B PHE* 4.2 13.5 + + - -
363B GLY* 3.7 35.2 - - - -
365B VAL* 5.4 2.2 - - + -
473B VAL* 2.6 38.0 + - + -
475B PRO* 3.5 20.4 - - - +
482B THR* 3.9 14.8 - - + -
484B PRO* 3.8 40.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR 2.7 19.4 + - - -
310B LEU 3.0 4.4 + - - -
312B TYR* 1.3 73.2 - - - +
314B PHE* 1.3 56.8 + - - +
316B LEU* 3.2 6.4 + - - +
317B LEU* 3.0 31.5 + - - +
359B ILE* 3.7 18.0 - - - +
453B PHE* 3.7 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 3.9 35.7 - - + -
310B LEU* 3.1 26.9 + - + -
313B GLY* 1.3 71.1 - - - +
315B LEU* 1.3 67.5 + - - +
317B LEU* 3.2 10.0 + - + +
318B MET* 3.0 27.8 + - - +
452B PHE* 4.7 0.7 - - + -
453B PHE* 3.9 26.4 - + - -
456B VAL* 3.5 43.3 - - + -
457B MET* 4.0 10.3 - - + -
462B LEU* 3.9 20.2 - - + +
487B TYR* 3.8 12.3 - - - +
489B MET* 4.0 17.9 - - + -
491B PHE* 4.9 9.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG 3.5 4.5 + - - +
312B TYR* 3.2 13.4 + - + +
314B PHE* 1.3 77.9 - - - +
316B LEU* 1.3 63.1 + - - +
318B MET* 3.2 9.7 + - - +
319B LYS* 3.0 21.8 + - - +
466B GLN* 5.5 3.6 - - - +
471B ILE* 3.8 22.7 - - + -
472B ASP 4.0 19.3 - - - +
473B VAL* 4.1 17.0 - - + -
484B PRO* 4.8 13.2 - - + -
485B ARG* 4.6 9.9 - - + +
487B TYR* 3.7 56.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TYR* 3.0 41.5 + - + +
313B GLY* 3.2 11.2 + - - +
315B LEU* 1.3 77.6 - - - +
317B LEU* 1.3 56.7 + - - +
319B LYS* 3.3 3.3 + - - -
320B HIS* 3.0 37.2 + - + +
359B ILE* 4.6 12.3 - - + +
362B PHE* 3.7 35.9 - - + -
363B GLY 5.0 0.2 - - - +
411B PHE* 3.6 43.3 - - + -
473B VAL* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLY 3.0 21.9 + - - +
314B PHE* 3.2 16.8 + - + +
316B LEU* 1.3 75.4 - - + +
318B MET* 1.3 64.8 + - - +
320B HIS* 3.1 22.9 + - - +
321B PRO* 3.4 4.0 - - - +
323B VAL* 3.9 27.4 - - + -
324B GLU* 4.2 24.7 - - + +
327B VAL* 4.8 6.1 - - + -
355B VAL* 4.2 12.3 - - + -
359B ILE* 4.6 13.2 - - + -
411B PHE* 5.5 2.0 - - + -
453B PHE* 4.7 6.3 - - + -
457B MET* 4.2 28.3 - - + -
462B LEU* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PHE 3.0 17.1 + - - +
315B LEU* 3.7 9.6 - - + +
317B LEU* 1.3 77.1 - - - +
319B LYS* 1.3 62.9 + - - +
320B HIS 3.2 0.9 + - - -
321B PRO* 3.4 17.4 - - - +
324B GLU* 6.2 0.7 - - - -
462B LEU* 3.5 15.9 - - + +
463B LYS 3.1 33.2 - - - +
464B SER* 3.4 19.8 + - - +
468B PRO* 3.9 8.8 - - - +
471B ILE* 3.9 14.4 - - + +
487B TYR* 4.9 7.9 - - - -
488B THR 5.1 0.7 - - - +
489B MET* 3.1 54.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU 3.0 13.6 + - - +
316B LEU 3.5 8.7 - - - +
318B MET* 1.3 77.8 - - - +
320B HIS* 1.3 79.6 + - + +
321B PRO* 3.4 6.4 - - - +
468B PRO* 2.9 27.8 + - - +
469B LYS* 2.9 27.5 + - - +
471B ILE* 2.6 46.1 + - + +
473B VAL* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 3.0 29.2 + - + +
317B LEU 3.2 6.2 - - - +
318B MET 3.1 0.6 - - - -
319B LYS* 1.3 101.6 - - + +
321B PRO* 1.3 57.2 - - - +
322B GLU* 3.1 3.6 - - + -
323B VAL* 2.8 47.1 + - + +
324B GLU 3.3 3.5 + - - -
411B PHE* 3.6 49.0 + + + +
473B VAL* 5.5 2.7 - - + -
----------------------------------------------------------
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