Contacts of the helix formed by residues 288 - 302 (chain B) in PDB entry 3V4K
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 CYS 288 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ZN 2.3 38.0 - - - -
257B HIS* 3.6 12.3 - - + -
259B GLU* 4.6 0.4 + - - -
286B SER 3.7 1.6 + - - -
287B PRO* 1.3 76.6 - - - +
289B PHE* 1.3 66.9 + - - +
290B SER* 3.4 24.5 - - - -
291B CYS 3.3 4.7 + - - -
292B ALA* 2.9 20.5 + - - +
315B TYR* 4.1 24.9 - - + -
321B CYS* 4.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B CYS* 1.3 75.0 - - - +
290B SER* 1.3 71.0 + - - +
292B ALA* 3.2 5.3 + - - +
293B GLN* 2.9 57.3 + - + +
317B ASP* 5.9 1.3 - - - +
320B ARG* 3.1 84.6 - - + +
321B CYS* 4.4 8.1 - - - +
323B GLU* 3.6 24.5 - - + -
324B GLY* 3.7 13.9 - - - -
327B THR* 5.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B HIS* 5.4 1.4 + - - -
260B LEU* 5.6 0.4 - - - -
288B CYS* 3.3 13.3 - - - -
289B PHE* 1.3 89.7 - - - +
291B CYS* 1.3 61.1 + - - +
293B GLN* 3.4 12.4 + - - +
294B GLU* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ZN 2.3 35.4 - - - -
257B HIS* 3.6 19.1 - - - -
259B GLU* 3.8 23.3 - - + -
260B LEU* 3.9 20.6 - - + -
263B LEU* 5.1 0.2 - - - +
287B PRO* 4.0 6.7 - - + -
288B CYS* 3.3 5.8 + - - +
289B PHE 3.2 0.4 - - - -
290B SER* 1.3 78.8 + - - +
292B ALA* 1.3 57.9 + - - +
294B GLU* 3.2 6.8 + - - +
295B MET* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B PRO* 3.9 13.7 - - + +
288B CYS 2.9 17.7 + - - +
289B PHE 3.5 4.5 - - - +
291B CYS* 1.3 75.0 - - - +
293B GLN* 1.3 57.3 + - - +
295B MET* 3.4 3.3 + - - +
296B ALA* 2.9 29.6 + - - +
324B GLY* 3.4 35.9 - - - +
325B LEU* 4.4 1.1 - - + +
327B THR* 5.6 0.4 - - - -
328B LEU* 3.9 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 2.9 47.9 + - + +
290B SER* 3.6 11.4 + - - +
292B ALA* 1.3 76.3 - - - +
294B GLU* 1.3 71.9 + - - +
296B ALA* 3.4 7.2 + - - +
297B LYS* 3.0 22.6 + - + +
320B ARG* 5.2 0.7 + - - -
324B GLY* 5.3 1.0 - - - -
327B THR* 5.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU* 4.0 26.2 - - + -
263B LEU* 3.9 9.8 - - + +
290B SER* 3.0 19.1 + - - +
291B CYS 3.6 6.1 - - - +
293B GLN* 1.3 88.2 + - - +
295B MET* 1.3 57.0 + - - +
297B LYS* 3.2 12.6 + - - +
298B PHE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 5.7 1.6 - - + -
259B GLU* 3.9 23.3 - - + -
262B PHE* 4.6 19.7 - - + -
263B LEU* 4.0 23.3 - - + -
281B CYS* 5.4 2.7 - - - -
287B PRO* 3.9 24.5 - - + -
291B CYS 2.8 21.7 + - - +
292B ALA 3.7 0.7 - - - +
294B GLU* 1.3 75.0 - - - +
296B ALA* 1.3 63.4 + - - +
298B PHE* 3.3 4.6 + - - +
299B ILE* 3.0 27.9 + - - +
307B LEU* 3.8 16.4 - - + -
309B ILE* 3.8 25.8 - - + -
328B LEU* 3.7 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA 2.9 17.0 + - - +
293B GLN 3.6 5.2 - - - +
294B GLU 3.2 0.2 - - - -
295B MET* 1.3 73.2 - - - +
297B LYS* 1.3 61.1 + - - +
299B ILE* 3.4 6.5 + - - +
300B SER* 2.6 34.5 + - - +
327B THR* 4.1 25.1 - - + +
328B LEU* 3.7 11.4 - - + +
331B ALA* 3.9 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLN* 3.0 14.7 + - + +
294B GLU* 3.4 19.3 - - - +
296B ALA* 1.3 76.3 - - - +
298B PHE* 1.3 63.1 + - - +
300B SER* 3.2 8.0 + - - -
301B LYS* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.9 42.0 - - + -
266B ILE* 3.7 41.3 - - + -
267B PRO* 4.9 10.3 - - + -
294B GLU 2.9 13.4 + - - +
295B MET 3.5 7.0 - - - +
297B LYS* 1.3 76.1 - - - +
299B ILE* 1.3 70.3 + - + +
301B LYS* 3.1 3.6 + - - -
302B ASN* 2.8 67.9 + - + +
304B HIS* 6.0 0.4 - + - -
305B VAL* 4.6 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 6.2 0.2 - - + -
295B MET 3.0 12.5 + - - +
296B ALA 3.6 9.9 - - - +
298B PHE* 1.3 87.9 - - + +
300B SER* 1.3 63.8 + - - +
301B LYS 3.4 0.2 + - - -
302B ASN 3.4 20.2 + - - +
303B LYS* 3.8 11.7 + - - -
305B VAL* 4.7 18.2 - - + +
307B LEU* 4.0 29.6 - - + +
328B LEU* 4.1 9.9 - - + -
331B ALA* 3.7 25.1 - - + +
332B GLY 4.3 1.1 - - - -
333B ALA* 3.6 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ALA* 2.6 24.2 + - - +
297B LYS* 3.5 7.9 - - - -
298B PHE 3.2 0.2 - - - -
299B ILE* 1.3 77.7 - - - +
301B LYS* 1.3 58.2 + - - +
303B LYS* 3.7 26.2 + - - +
331B ALA* 3.9 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LYS 3.2 10.7 + - - +
298B PHE* 3.1 9.2 + - - +
300B SER* 1.3 77.7 - - - +
302B ASN* 1.3 69.0 + - - +
303B LYS* 3.8 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 5.6 0.3 - - - +
298B PHE* 2.8 67.7 + - + +
299B ILE 3.4 8.4 + - - +
301B LYS* 1.3 89.3 - - - +
303B LYS* 1.3 56.6 + - - +
304B HIS* 3.1 33.4 + - + -
305B VAL* 3.0 28.1 + - + +
----------------------------------------------------------
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