Contacts of the helix formed by residues 311 - 326 (chain B) in PDB entry 1B43
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 GLU 311 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 4.2 11.7 - - + -
304B CYS* 3.5 24.4 - - + +
305B ASP* 5.3 3.5 - - - +
309B PHE 3.0 7.0 + - - +
310B SER* 1.3 70.9 + - - +
312B GLU* 1.3 57.1 + - - +
315B LYS* 2.9 72.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B SER* 3.1 8.3 + - - +
311B GLU* 1.3 79.9 - - - +
313B ARG* 1.3 57.1 + - - +
315B LYS* 3.9 6.8 - - - +
316B ASN* 3.0 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR* 3.7 31.6 + - + +
310B SER* 2.9 39.0 + - - +
312B GLU* 1.3 78.8 - - + +
314B VAL* 1.3 59.5 + - - +
316B ASN* 3.3 14.0 - - + +
317B GLY* 2.9 23.7 + - - -
320B ARG* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 3.8 23.6 - - + -
62B TYR* 3.7 9.4 - - - +
299B ILE* 4.0 18.4 - - + -
300B LEU* 3.7 18.8 - - + -
303B LEU* 4.5 4.5 - - + -
304B CYS* 3.6 15.5 - - - -
309B PHE* 3.6 31.4 - - + -
310B SER 2.7 21.9 + - - +
311B GLU 4.0 1.3 - - - +
313B ARG* 1.3 69.7 - - - +
315B LYS* 1.3 60.1 + - - +
317B GLY* 3.0 2.3 + - - -
318B LEU* 2.8 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 3.7 26.2 - - + -
311B GLU* 2.9 60.5 + - + +
312B GLU* 3.9 6.5 - - - +
314B VAL* 1.3 75.2 - - - +
316B ASN* 1.3 61.5 + - - +
318B LEU* 3.4 9.7 + - + +
319B GLU* 3.1 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLU* 3.0 18.5 + - + +
313B ARG* 3.3 14.4 - - - +
315B LYS* 1.3 75.3 - - - +
317B GLY* 1.3 65.8 + - - +
319B GLU* 3.2 10.3 + - - +
320B ARG* 3.1 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 4.4 3.8 - - - -
62B TYR* 5.6 0.9 - - - -
65B ILE* 3.6 18.3 - - - +
313B ARG 2.9 15.7 + - - -
314B VAL 3.0 3.7 + - - -
316B ASN* 1.3 77.2 + - - +
318B LEU* 1.3 49.7 + - - +
320B ARG* 2.9 24.9 + - - +
321B LEU* 2.7 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 4.1 9.0 - - + -
294B PRO* 4.1 12.3 - - + -
296B GLU* 3.5 50.5 - - + +
299B ILE* 3.5 36.3 - - + -
300B LEU* 4.0 16.4 - - + -
314B VAL* 2.8 25.1 + - + +
315B LYS* 3.6 9.6 - - + +
317B GLY* 1.3 75.1 - - - +
319B GLU* 1.3 58.3 + - - +
321B LEU* 3.5 6.6 - - + +
322B LYS* 2.9 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLU* 3.5 19.9 - - - +
315B LYS* 3.1 23.9 + - - +
316B ASN* 3.2 10.1 + - - +
318B LEU* 1.3 77.8 - - - +
320B ARG* 1.3 59.2 + - + +
322B LYS* 3.9 18.1 + - - +
323B LYS* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR* 4.8 10.7 + - - -
65B ILE* 3.5 36.4 - - + +
66B ASN* 3.2 22.8 - - - +
69B GLU* 2.7 46.3 + - + +
316B ASN* 3.1 41.4 + - - +
317B GLY* 2.9 16.9 + - - +
319B GLU* 1.3 75.7 - - + +
321B LEU* 1.3 58.9 + - - +
323B LYS* 3.4 11.6 + - + +
324B ALA* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.1 20.8 - - + +
68B MET* 3.3 39.0 - - + -
141B MET* 3.8 33.7 - - + +
143B ILE* 4.6 4.3 - - + -
294B PRO* 3.8 26.5 - - + -
317B GLY 2.7 18.8 + - - +
318B LEU* 3.2 13.4 + - + +
320B ARG* 1.3 72.5 - - - +
322B LYS* 1.3 58.3 + - - +
324B ALA* 3.1 5.9 + - - +
325B ILE* 2.9 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PRO* 3.5 24.2 - - + -
296B GLU* 2.8 46.5 + - - +
318B LEU 2.9 23.1 + - - +
319B GLU* 3.9 18.8 + - - +
321B LEU* 1.3 74.8 - - - +
323B LYS* 1.3 62.2 + - - +
325B ILE* 3.4 10.7 + - - +
326B LYS* 3.3 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLU 3.0 20.4 + - - +
320B ARG* 3.6 11.9 - - + +
321B LEU 3.2 0.2 - - - -
322B LYS* 1.3 77.0 - - - +
324B ALA* 1.3 57.4 + - - +
326B LYS* 3.6 5.7 + - - +
327B SER* 2.8 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE 5.5 0.4 - - - +
68B MET* 3.6 43.9 - - + +
69B GLU* 4.1 6.3 - - - +
320B ARG 2.9 18.2 + - - +
321B LEU* 3.1 5.8 + - - +
323B LYS* 1.3 75.2 - - - +
325B ILE* 1.3 64.9 + - - +
327B SER* 3.1 10.5 - - - -
328B GLY* 3.1 18.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 4.2 19.7 - - + -
141B MET 4.6 1.6 - - - +
143B ILE* 6.4 0.2 - - + -
291B TRP* 4.1 22.4 - - + +
292B ARG 3.3 25.8 - - - +
293B ASP* 4.2 13.0 - - - +
294B PRO* 3.8 22.0 - - + -
321B LEU* 2.9 28.2 + - + +
322B LYS* 3.4 8.7 + - - +
324B ALA* 1.3 74.3 - - - +
326B LYS* 1.3 59.6 + - - +
328B GLY* 3.1 22.5 - - - -
329B LYS* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LYS 3.3 13.2 + - - +
323B LYS* 4.0 4.5 - - - +
325B ILE* 1.3 79.5 - - + +
327B SER* 1.3 64.3 + - - +
328B GLY* 3.3 1.4 + - - -
329B LYS* 3.4 24.7 + - + +
330B GLN* 5.4 0.5 - - - +
----------------------------------------------------------
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