Contacts of the helix formed by residues 78 - 92 (chain 2) in PDB entry 1O1F
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 ASN 78 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682 LYS* 5.5 0.6 - - - +
702 PRO* 3.2 17.2 + - + +
762 ILE* 4.0 2.6 - - - +
772 THR* 1.3 81.1 - - + +
792 TRP* 1.3 63.8 + - - +
802 ASP* 3.3 17.8 + - - +
812 ASP* 3.0 45.4 + - + +
822 MET* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 79 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762 ILE* 3.8 48.5 + - + -
772 THR 4.6 7.5 + - - -
782 ASN* 1.3 73.5 + - - +
802 ASP* 1.3 63.0 + - - +
822 MET* 3.8 4.5 - - + +
832 GLU* 3.3 25.5 + - - +
862 TRP* 4.6 5.8 - + - -
1152 ASN* 3.6 53.6 + - + -
1182 LYS* 3.8 31.5 - - + +
1192 MET* 3.8 23.6 - - + -
1222 ILE* 3.6 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372 ARG* 3.3 13.5 + - - -
782 ASN* 3.3 15.1 + - - +
792 TRP* 1.3 76.3 - - - +
812 ASP* 1.3 86.7 + - - +
832 GLU* 3.6 7.3 + - - +
842 LYS* 3.3 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352 VAL* 3.4 20.0 - - + +
372 ARG* 2.9 25.8 + - - -
682 LYS* 3.1 32.0 - - - +
702 PRO* 3.4 19.0 - - + +
782 ASN* 3.0 27.7 + - + +
802 ASP* 1.3 90.0 + - - +
822 MET* 1.3 61.0 + - - +
842 LYS* 3.5 9.8 - - - +
852 ILE* 3.3 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122 ASN* 3.5 26.5 - - + +
172 VAL* 5.8 0.7 - - + -
332 SER* 5.3 1.6 - - - +
702 PRO* 3.9 10.8 - - - -
712 ILE* 3.7 36.1 - - + -
762 ILE* 3.8 20.0 - - + -
782 ASN 3.1 17.4 + - - +
792 TRP* 4.0 6.5 - - + +
802 ASP 3.3 0.6 - - - -
812 ASP* 1.3 71.1 - - - +
832 GLU* 1.3 58.6 + - - +
842 LYS 3.0 1.3 - - - -
852 ILE* 2.7 45.4 + - + +
862 TRP* 2.9 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792 TRP 3.3 16.4 + - - +
802 ASP* 3.8 6.8 - - - +
822 MET* 1.3 77.0 - - - +
842 LYS* 1.3 57.0 + - - +
862 TRP* 3.5 14.3 + - + -
872 HIS* 2.9 31.7 + - + +
1222 ILE* 4.1 20.5 - - + +
1262 THR* 4.2 27.5 + - - +
1272 PHE* 3.7 17.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352 VAL* 4.0 9.2 - - + -
372 ARG* 3.4 34.9 - - - +
512 ASP* 5.2 5.1 + - - +
522 SER* 3.5 26.7 - - - +
542 VAL* 4.4 10.9 - - + +
802 ASP* 3.3 26.7 + - - +
812 ASP* 3.5 25.8 - - - +
822 MET 3.0 0.2 - - - -
832 GLU* 1.3 77.1 - - - +
852 ILE* 1.4 61.7 + - - +
872 HIS* 3.2 7.3 + - + +
882 HIS* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122 ASN* 5.6 0.2 - - - +
172 VAL* 3.7 29.4 - - + -
312 PHE* 4.2 10.7 - - + -
332 SER* 3.9 26.7 - - - +
342 ILE 4.1 1.1 - - - +
352 VAL* 3.8 12.1 - - + -
542 VAL* 4.0 13.2 - - + -
702 PRO* 3.6 36.3 - - + -
812 ASP 3.3 7.4 + - - +
822 MET* 2.7 27.3 + - + +
842 LYS* 1.4 70.8 - - - +
862 TRP* 1.3 55.4 + - + +
882 HIS* 3.3 3.5 + - - +
892 THR* 2.7 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 86 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102 CYS* 4.0 16.9 - - - -
122 ASN* 2.9 36.7 + - - +
172 VAL* 6.1 0.4 - - + -
762 ILE* 4.2 10.3 - - + -
792 TRP* 4.6 2.0 - + - -
822 MET* 2.9 37.8 + - + +
832 GLU* 3.8 18.2 - - - +
852 ILE* 1.3 74.6 - - + +
872 HIS* 1.3 59.4 + - - +
892 THR* 2.8 23.9 + - - -
902 PHE* 3.0 27.7 + + + -
1052 LEU* 4.4 4.9 - - + +
1192 MET* 3.9 31.2 - - + -
1222 ILE* 4.1 24.5 - - + -
1232 MET* 3.3 30.0 - - + +
1272 PHE* 3.6 19.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832 GLU* 2.9 19.9 + - + +
842 LYS* 3.4 7.9 - - - +
862 TRP* 1.3 75.9 - - - +
882 HIS* 1.3 60.1 + - - +
902 PHE* 4.5 0.7 - - - -
912 TYR* 2.9 63.9 + + + +
922 ASN* 4.6 6.0 + - - -
1272 PHE* 3.9 17.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312 PHE* 3.6 20.9 - + - -
542 VAL* 3.9 37.7 + - + +
552 GLY* 5.2 0.6 - - - -
842 LYS 3.1 9.7 + - - +
852 ILE 3.4 8.5 - - - +
872 HIS* 1.3 79.3 - - - +
892 THR* 1.3 62.1 + - - +
922 ASN* 2.8 55.1 + - + +
932 GLU* 2.9 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102 CYS* 4.7 9.0 - - + -
172 VAL* 4.5 7.5 - - + +
192 ALA* 3.6 31.0 - - + -
312 PHE* 3.7 20.4 - - + -
852 ILE* 2.7 26.2 + - - +
862 TRP* 2.8 14.7 + - - -
882 HIS* 1.3 76.5 - - - +
902 PHE* 1.3 64.9 + - + -
932 GLU* 3.4 8.8 - - + +
942 LEU* 2.9 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82 LEU* 4.0 28.7 - - + -
102 CYS* 5.8 5.8 - - + -
862 TRP* 3.0 29.2 + + + +
872 HIS* 4.1 2.2 - - - +
892 THR* 1.3 83.2 - - + +
912 TYR* 1.3 62.7 + + + +
942 LEU* 3.5 4.5 - - + -
952 ARG 2.8 26.2 + - - -
962 VAL* 3.1 23.6 + - + +
982 PRO* 3.9 26.2 - - + -
1032 THR* 4.4 16.6 - - + -
1052 LEU* 6.1 0.7 - - + -
1232 MET* 4.1 23.6 - - + -
1272 PHE* 3.6 44.9 - + - -
1292 VAL* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872 HIS* 2.9 60.5 + + - +
902 PHE* 1.3 82.7 - - + +
922 ASN* 1.3 72.6 + - - +
952 ARG* 3.4 16.9 - - - +
962 VAL 3.8 11.9 - - - -
972 ALA* 4.6 4.7 - - + -
982 PRO* 3.7 35.6 - - + +
992 GLU* 4.2 11.3 + - - -
1272 PHE* 4.9 9.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872 HIS* 4.2 7.6 + - - +
882 HIS* 2.8 50.1 + - + +
912 TYR* 1.3 93.1 + - - +
932 GLU* 1.3 68.5 + - - +
952 ARG* 3.3 17.2 - - - +
----------------------------------------------------------
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