Contacts of the helix formed by residues 403 - 430 (chain 0) in PDB entry 4BOG
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 403 (chain 0).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4040 ALA* 1.3 86.8 + - - +
4050 VAL* 3.3 9.0 - - + +
4060 GLU* 3.3 26.6 + - - +
4070 ALA* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 404 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4030 GLU* 1.3 89.3 + - + +
4050 VAL* 1.3 63.2 + - + +
4070 ALA* 2.6 36.3 + - + +
4080 ILE 3.2 3.5 + - - -
376Z ILE* 5.7 0.2 - - + -
377Z GLU* 3.1 42.6 - - + +
380Z LYS* 3.7 7.4 - - + +
381Z TYR* 5.7 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 405 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4030 GLU* 4.6 7.9 - - + +
4040 ALA* 1.3 74.9 - - + +
4060 GLU* 1.3 59.4 + - + +
4080 ILE* 2.6 34.7 - - - +
4090 LYS* 2.9 27.4 - - - +
4231 ILE* 3.8 14.4 - - + -
376Z ILE* 4.4 15.9 - - + -
380Z LYS* 3.5 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 406 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4030 GLU* 3.3 21.8 + - - +
4040 ALA 3.1 0.2 - - - -
4050 VAL* 1.3 79.3 - - + +
4070 ALA* 1.3 53.8 + - - +
4090 LYS* 2.9 27.9 - - + +
4100 TYR* 2.6 35.1 + - - +
4130 GLU* 4.3 3.8 - - - +
4221 GLY* 3.2 36.5 - - - +
4231 ILE* 4.4 3.4 - - + +
4251 SER* 4.7 3.8 - - - -
4261 THR* 3.6 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4030 GLU* 3.0 8.2 + - - +
4040 ALA* 2.6 32.4 + - + +
4060 GLU* 1.3 69.3 - - - +
4080 ILE* 1.3 51.4 + - - +
4100 TYR* 2.8 12.4 + - + +
4110 ILE* 2.5 50.6 + - + +
380Z LYS* 5.6 0.2 - - + -
381Z TYR* 5.7 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 408 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4040 ALA 3.2 2.2 + - - -
4050 VAL 2.6 27.5 + - - +
4070 ALA* 1.3 77.5 - - - +
4090 LYS* 1.3 70.7 + - + +
4110 ILE* 3.0 13.4 + - + +
4120 ALA* 2.6 35.6 + - + +
380Z LYS* 3.1 63.6 - - + +
381Z TYR* 6.2 0.2 - - - -
383Z ALA* 4.9 7.6 - - + -
384Z GLU* 3.5 17.2 - - + +
387Z LYS* 5.8 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 409 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4050 VAL* 2.9 42.4 + - - +
4060 GLU* 2.9 26.0 - - + +
4080 ILE* 1.3 86.9 - - + +
4100 TYR* 1.3 47.5 + - - +
4120 ALA* 2.6 12.6 + - - +
4130 GLU* 2.4 43.1 + - - +
4231 ILE* 3.1 30.8 - - - +
4261 THR* 2.6 48.2 - - + +
4271 ASN* 5.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 410 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4060 GLU 2.6 16.6 + - - +
4070 ALA* 3.0 17.3 - - + +
4090 LYS* 1.3 73.7 - - - +
4110 ILE* 1.3 60.4 + - + -
4130 GLU* 3.1 27.4 + - + +
4140 GLN* 2.9 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 411 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4070 ALA* 2.5 43.6 + - + +
4080 ILE* 3.3 14.8 - - + +
4100 TYR* 1.3 79.5 - - + +
4120 ALA* 1.3 55.4 + - - +
4140 GLN* 4.0 5.3 - - + +
4150 LEU* 3.2 24.4 + - - +
381Z TYR* 5.0 16.8 - - + +
384Z GLU* 3.0 43.2 - - + +
387Z LYS* 4.7 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 412 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4080 ILE* 2.6 18.2 + - + +
4090 LYS* 2.6 20.8 + - - +
4110 ILE* 1.3 70.9 - - - +
4130 GLU* 1.3 63.1 + - + +
4150 LEU* 3.2 15.0 + - - +
4160 GLU* 3.5 15.1 + - - +
4261 THR* 5.7 1.8 - - + -
4291 ILE* 6.0 3.6 - - + -
387Z LYS* 4.7 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 413 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4060 GLU* 4.3 3.3 - - - +
4090 LYS* 2.4 24.1 + - - +
4100 TYR* 3.1 42.5 + - + +
4120 ALA* 1.3 74.1 - - + +
4140 GLN* 1.3 55.6 + - + +
4160 GLU* 4.6 1.3 - - - +
4170 SER* 2.5 33.5 + - - -
4261 THR* 4.4 15.1 + - + +
4291 ILE* 4.5 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 414 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4100 TYR* 2.9 42.6 + - + +
4110 ILE* 4.3 5.6 - - - +
4130 GLU* 1.3 80.4 - - - +
4150 LEU* 1.3 66.7 + - - +
4170 SER* 3.5 8.6 + - - -
4180 ALA* 2.7 39.6 + - + +
4210 PHE* 5.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4110 ILE 3.2 19.0 + - - +
4120 ALA* 3.2 7.3 + - - +
4140 GLN* 1.3 83.0 - - - +
4160 GLU* 1.3 75.2 + - + +
4180 ALA* 3.6 2.2 - - - +
4190 SER* 3.3 20.9 + - - +
384Z GLU* 5.6 0.7 - - - +
387Z LYS* 4.1 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 416 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4120 ALA 3.5 11.6 + - - +
4130 GLU 4.6 1.6 - - - +
4150 LEU* 1.3 91.5 - - + +
4170 SER* 1.3 68.2 + - - +
4190 SER* 3.2 4.1 + - - -
4200 GLU* 3.0 34.2 + - + +
4291 ILE* 4.9 0.7 - - - +
4301 VAL* 5.4 2.6 - - - +
4331 ILE* 2.6 59.1 - - + +
4361 LYS* 5.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 417 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4130 GLU 2.5 25.4 + - - -
4140 GLN* 3.3 14.7 + - - -
4160 GLU* 1.3 81.1 - - - +
4180 ALA* 1.3 68.6 + - - +
4200 GLU* 3.1 15.2 + - - +
4210 PHE* 2.8 42.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 418 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4140 GLN* 2.7 38.9 + - + +
4150 LEU* 3.6 3.1 - - - +
4170 SER* 1.3 73.0 + - - +
4190 SER* 1.3 59.5 + - - +
4210 PHE* 3.0 26.7 - - + +
4220 ASP* 3.5 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 419 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4150 LEU* 3.3 13.8 + - - +
4160 GLU* 3.2 9.4 + - - -
4180 ALA* 1.3 75.2 - - - +
4200 GLU* 1.3 63.7 + - - +
4210 PHE 3.1 1.8 - - - -
4220 ASP* 2.9 13.6 + - - +
4230 ASP* 2.7 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 420 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4160 GLU* 3.0 31.4 + - + +
4170 SER* 3.1 6.5 + - - +
4190 SER* 1.3 77.3 + - - +
4210 PHE* 1.3 53.2 + - + +
4230 ASP* 3.0 9.8 + - + +
4240 LEU* 2.3 59.8 + - + +
4331 ILE* 5.9 0.2 - - - +
4361 LYS* 5.8 2.1 + - - -
4371 ASN* 4.6 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 421 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4140 GLN* 5.6 3.8 - - - -
4170 SER* 2.8 47.8 - - - -
4180 ALA* 3.0 18.6 - - + +
4190 SER 3.1 0.2 - - - -
4200 GLU* 1.3 76.2 - - + +
4220 ASP* 1.3 52.9 + - - +
4240 LEU* 3.0 24.6 - - + +
4250 LYS* 2.4 36.1 + - - +
4280 TRP* 4.1 3.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 422 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4180 ALA 3.5 3.4 + - - +
4190 SER* 2.9 26.1 + - - +
4210 PHE* 1.3 80.3 - - - +
4230 ASP* 1.3 58.8 + - - +
4250 LYS* 3.0 31.6 + - - +
4260 LYS* 3.3 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 423 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4190 SER* 2.7 27.6 + - - +
4200 GLU* 3.1 10.6 - - + +
4220 ASP* 1.3 73.4 - - - +
4240 LEU* 1.3 63.6 + - - +
4250 LYS 3.1 0.7 - - - -
4260 LYS* 3.4 44.1 + - + +
4270 ASP* 3.5 5.2 + - - +
4300 TYR* 4.1 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 424 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4200 GLU* 2.3 48.6 + - + +
4210 PHE* 3.0 40.2 - - + +
4230 ASP* 1.3 68.8 - - - +
4250 LYS* 1.3 58.9 + - - +
4260 LYS 3.2 0.2 - - - -
4270 ASP* 3.0 16.6 + - + +
4280 TRP* 2.8 61.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 425 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3100 ASN* 5.8 0.4 - - - -
4210 PHE 2.4 19.8 + - - +
4220 ASP* 3.0 23.3 - - - +
4240 LEU* 1.3 70.7 - - - +
4260 LYS* 1.3 63.8 + - - +
4280 TRP* 2.7 25.5 + - + +
4290 GLN* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 426 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3100 ASN* 3.6 42.8 + - + +
4220 ASP* 3.3 14.4 + - - +
4230 ASP* 3.4 34.4 + - - +
4240 LEU 3.2 0.2 - - - -
4250 LYS* 1.3 80.5 - - - +
4270 ASP* 1.3 56.3 + - - +
4290 GLN* 3.1 7.3 + - - +
4300 TYR* 2.8 66.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 427 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4230 ASP 3.5 3.3 + - - +
4240 LEU* 3.0 23.2 + - + +
4260 LYS* 1.3 75.3 - - - +
4280 TRP* 1.3 93.3 - - + +
4290 GLN 3.0 0.9 + - - -
4300 TYR* 3.1 22.9 + - + +
4310 VAL* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 428 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4210 PHE* 4.1 3.2 + - - +
4240 LEU* 2.8 51.2 + - + +
4250 LYS* 2.7 34.4 - - + +
4270 ASP* 1.3 102.2 - - - +
4290 GLN* 1.3 64.0 + - - +
4310 VAL* 2.7 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 429 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3070 ARG* 3.4 15.8 + - - -
3080 SER* 4.6 4.8 + - - -
3090 PRO* 4.6 20.9 - - + +
3100 ASN* 4.2 20.7 + - + +
4250 LYS* 2.9 23.6 + - - +
4260 LYS* 3.3 12.8 - - - +
4270 ASP 3.0 0.2 - - - -
4280 TRP* 1.3 84.9 + - - +
4300 TYR* 1.3 60.8 + - + +
4310 VAL* 3.7 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 430 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3070 ARG* 4.1 7.0 - - - +
3080 SER* 4.2 3.8 - - - +
3100 ASN* 5.3 0.4 - - + -
3110 THR* 2.7 51.4 - - + +
4230 ASP* 4.1 6.6 + - - +
4260 LYS* 2.8 60.7 + - + +
4270 ASP* 3.4 18.0 - - + +
4290 GLN* 1.3 74.5 - - + +
4310 VAL* 1.3 59.5 + - - +
4320 ALA 3.7 2.0 + - - -
----------------------------------------------------------
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