Contacts of the helix formed by residues 407 - 422 (chain 0) in PDB entry 5OA3
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 407 (chain 0).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3820 LYS* 5.1 14.9 - - + +
3830 PRO 4.5 7.4 - - - +
3840 LEU* 4.1 19.7 - - + -
3850 TYR* 4.0 1.6 - - - -
4060 LEU* 1.3 76.3 - - - +
4080 GLY* 1.3 65.2 + - - +
4090 SER* 3.3 17.2 + - - +
4100 GLU* 3.4 25.9 + - + +
4110 VAL* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 408 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3830 PRO 5.3 0.8 + - - -
3850 TYR* 3.6 26.9 - - - -
4070 GLU* 1.3 73.7 - - - +
4090 SER* 1.3 55.2 + - - +
4110 VAL* 3.2 3.5 + - - +
4120 ARG* 3.0 44.2 + - - +
4650 LEU* 4.2 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 409 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4070 GLU* 4.0 16.5 + - - +
4080 GLY* 1.3 74.9 - - - +
4100 GLU* 1.3 62.8 + - - +
4120 ARG* 3.4 9.8 + - - +
4130 THR* 2.9 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 410 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4000 HIS* 4.5 7.8 + - + -
4050 PHE 4.9 1.8 - - - +
4060 LEU* 3.9 25.2 - - + +
4070 GLU* 3.4 42.9 + - + +
4090 SER* 1.3 82.6 - - - +
4110 VAL* 1.3 59.6 + - - +
4130 THR* 3.8 6.0 - - - -
4140 ILE* 2.9 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 411 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3850 TYR* 4.4 4.5 - - + -
3950 PHE* 4.4 7.4 - - + -
4060 LEU* 4.0 21.5 - - + -
4070 GLU 3.5 13.0 - - - +
4080 GLY 3.2 7.5 + - - +
4100 GLU* 1.3 72.3 - - - +
4120 ARG* 1.3 61.4 + - + +
4140 ILE* 3.4 7.1 + - - +
4150 VAL* 2.9 48.3 + - + +
4610 LEU* 5.4 1.1 - - + +
4640 CYS* 4.6 7.6 - - + -
4650 LEU* 3.8 21.3 - - + -
4680 LEU* 3.6 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 412 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4080 GLY* 3.0 25.7 + - - +
4090 SER* 3.7 7.8 - - - +
4110 VAL* 1.3 75.1 - - + +
4130 THR* 1.3 60.8 + - - +
4150 VAL* 3.6 0.9 + - - +
4160 ILE* 3.0 41.6 + - + +
4610 LEU* 3.6 45.1 - - + +
4620 THR* 5.6 3.6 + - - +
4650 LEU* 3.6 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 413 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4090 SER* 2.9 21.7 + - - -
4100 GLU* 3.8 7.0 - - - -
4120 ARG* 1.3 75.2 - - - +
4140 ILE* 1.3 58.6 + - + +
4160 ILE* 3.8 6.7 - - - +
4170 ASN* 2.9 53.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 414 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3940 LEU* 4.5 13.0 - - + +
3950 PHE* 3.6 36.1 - - + -
3980 SER* 3.5 22.0 - - - +
4000 HIS* 3.4 35.7 - - + +
4060 LEU* 3.8 6.3 - - + -
4100 GLU* 2.9 28.2 + - + +
4110 VAL 3.8 3.1 - - - +
4130 THR* 1.3 75.9 - - + +
4150 VAL* 1.3 64.0 + - + +
4170 ASN* 3.8 6.4 - - - +
4180 TYR* 2.9 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 415 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3940 LEU* 4.6 11.2 - - + -
3950 PHE* 5.4 1.8 - - + -
4110 VAL* 2.9 27.3 + - + +
4140 ILE* 1.3 75.8 - - + +
4160 ILE* 1.3 61.5 + - - +
4180 TYR* 3.3 8.3 + - + +
4190 ALA* 2.9 27.4 + - - +
4390 LEU* 5.3 4.3 - - + -
4570 TRP* 5.2 1.1 - - + -
4600 LEU* 3.8 32.3 - - + -
4610 LEU* 3.8 20.9 - - + -
4640 CYS* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 416 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4120 ARG* 3.0 35.3 + - + +
4130 THR* 3.8 5.4 - - - +
4150 VAL* 1.3 71.7 - - - +
4170 ASN* 1.3 66.7 + - - +
4190 ALA* 3.2 2.9 + - - +
4200 LYS* 2.9 55.2 + - + +
4570 TRP* 4.1 29.1 - - + -
4610 LEU* 4.7 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 417 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4130 THR* 2.9 40.7 + - - +
4140 ILE* 3.8 7.2 - - - +
4160 ILE* 1.3 83.0 - - - +
4180 TYR* 1.3 57.3 - - - +
4200 LYS* 4.1 7.4 - - - +
4210 LYS* 3.0 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 418 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3930 LEU 4.9 2.2 - - - -
3940 LEU* 3.7 47.3 - - + +
3970 GLU* 5.2 15.7 - - + -
4140 ILE* 2.9 19.5 + - + +
4150 VAL* 3.6 9.2 - - + +
4160 ILE 3.2 0.4 - - - -
4170 ASN* 1.3 76.3 - - - +
4190 ALA* 1.3 62.7 + - - +
4210 LYS* 4.9 0.9 - - - -
4220 ASN* 3.1 53.4 + - - +
4240 LEU* 4.0 8.9 - - + +
4360 ASP* 2.9 35.6 + - - -
4380 ILE* 3.2 30.9 - - + +
4390 LEU* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 419 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4150 VAL 2.9 16.0 + - - +
4160 ILE 3.7 0.7 - - - +
4180 TYR* 1.3 78.8 - - + +
4200 LYS* 1.3 56.2 + - - +
4240 LEU* 3.0 36.6 + - + -
4250 VAL* 3.5 10.6 + - + +
4330 VAL* 3.9 20.9 - - + -
4390 LEU* 5.8 0.4 - - + -
4570 TRP* 3.4 33.9 - - + -
4600 LEU* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 420 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4160 ILE* 2.9 39.5 + - + +
4170 ASN* 4.1 8.1 - - - +
4190 ALA* 1.3 78.8 - - - +
4210 LYS* 1.3 63.9 + - - +
4220 ASN 3.4 0.4 - - - -
4230 ASP* 3.3 16.7 + - - +
4250 VAL* 4.5 18.9 - - + +
4300 LYS* 5.9 2.8 - - - +
4570 TRP* 5.0 6.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 421 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3970 GLU* 3.2 46.0 - - + +
4170 ASN 3.0 18.7 + - - +
4180 TYR* 4.9 0.9 - - - -
4190 ALA 3.7 0.2 - - - -
4200 LYS* 1.3 78.1 - - - +
4220 ASN* 1.3 70.9 + - - +
4230 ASP* 3.2 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 422 (chain 0).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3970 GLU* 5.9 1.8 - - - +
4180 TYR* 3.1 60.2 + - - +
4200 LYS 3.4 0.2 - - - -
4210 LYS* 1.3 85.8 - - - +
4230 ASP* 1.3 70.0 + - - +
4240 LEU* 3.4 23.0 + - + +
4340 ARG* 4.9 1.9 + - - -
4360 ASP* 4.7 3.3 - - - +
----------------------------------------------------------
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