Contacts of the helix formed by residues 85 - 90 (chain 2) in PDB entry 6Q8W
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 85 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981 PRO* 3.5 36.6 - - + -
3431 ASN* 3.8 8.1 - - - +
3441 LEU* 5.5 2.5 - - + -
3471 PHE* 4.5 9.2 - - + -
832 CYS* 3.6 7.7 - - - -
842 ALA* 1.3 78.5 - - - +
862 LEU* 1.3 64.6 + - + +
872 SER* 3.4 3.8 - - - -
882 CYS 3.3 3.4 + - - -
892 LYS* 2.8 31.8 + - - +
1232 GLU* 3.0 16.5 + - - +
1242 CYS* 2.5 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981 PRO* 5.9 1.1 - - + -
2911 ILE* 4.2 11.4 - - + -
3291 ILE* 4.6 16.4 - - + -
3311 ILE* 4.0 25.4 - - + -
3351 VAL* 6.0 0.9 - - + -
3391 ASP* 5.9 0.2 - - - +
3401 ALA* 3.6 35.4 - - + +
3431 ASN* 3.4 10.0 + - + +
3441 LEU* 3.8 29.2 - - + -
852 THR* 1.3 79.2 - - + +
872 SER* 1.3 65.4 + - - +
892 LYS* 2.9 16.1 + - + +
902 LEU* 2.9 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981 PRO* 4.9 3.4 - - - +
991 GLY 4.0 7.7 + - - -
2551 SER* 3.9 10.6 + - - -
2561 GLY* 6.0 2.3 - - - -
3291 ILE* 3.3 36.8 - - - +
852 THR* 3.4 3.5 - - - +
862 LEU* 1.3 80.1 - - - +
882 CYS* 1.3 62.8 + - - +
902 LEU* 3.4 16.6 + - - +
912 ALA* 3.8 4.2 + - - +
1282 CYS* 4.0 27.1 - - - -
1312 ALA* 4.3 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 88 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832 CYS* 3.8 34.3 - - + +
852 THR* 3.3 7.6 + - - +
862 LEU 3.3 0.2 - - - -
872 SER* 1.3 77.1 - - - +
892 LYS* 1.3 64.8 + - - +
912 ALA* 3.1 15.3 + - - +
932 ALA* 3.4 16.0 + - + +
1272 SER 4.4 5.6 - - - -
1282 CYS* 4.7 5.2 - - - -
1312 ALA* 3.5 26.5 - - + -
1322 PRO* 4.0 9.3 - - + +
1332 VAL* 3.7 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3351 VAL* 6.0 1.1 - - + -
3391 ASP* 3.6 21.1 + - - +
3421 TRP* 5.2 6.7 - - - -
3431 ASN* 3.0 43.0 - - + +
3461 ARG* 5.4 0.8 - - - +
4331 ARG* 3.4 34.5 - - - +
4361 LEU* 4.2 5.2 - - - +
842 ALA 4.1 5.6 - - - +
852 THR 2.8 19.5 + - - +
862 LEU* 2.9 15.7 + - + +
882 CYS* 1.3 72.9 - - - +
902 LEU* 1.3 60.1 + - + +
912 ALA 3.0 5.4 - - - -
922 GLY* 2.8 21.5 + - - -
932 ALA* 3.6 13.4 + - + +
942 GLU* 3.7 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2561 GLY* 5.3 3.6 - - - -
2571 PRO* 4.5 9.2 - - + +
3291 ILE* 5.1 6.7 - - + -
3301 LEU 3.6 24.0 - - - +
3311 ILE* 4.3 12.1 - - + -
3321 PRO* 3.6 23.3 - - + -
3351 VAL* 4.9 19.7 - - + -
4361 LEU* 3.1 27.9 - - + +
862 LEU* 2.9 49.1 + - + +
872 SER* 3.6 11.4 - - - +
882 CYS 3.3 0.2 - - - -
892 LYS* 1.3 79.0 - - + +
912 ALA* 1.3 55.5 + - - +
922 GLY 3.3 0.9 - - - -
----------------------------------------------------------
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