Contacts of the helix formed by residues 828 - 839 (chain C) in PDB entry 1F66
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 PRO 828 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820C SER* 3.5 6.7 - - - +
826C GLN 3.7 1.8 - - - -
827C PHE* 1.3 95.4 - - + +
829C VAL* 1.3 65.1 + - - +
830C GLY 3.4 1.6 - - - +
831C ARG* 4.0 21.1 - - + +
832C ILE* 3.2 29.3 + - + +
855C ALA* 4.8 0.7 - - - -
1234D TYR* 4.4 13.7 - - + -
1237D TYR* 3.2 48.9 - - + +
30I A 5.0 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 829 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819C ARG* 4.1 24.2 - - + +
820C SER* 2.9 37.4 + - - +
825C LEU* 4.2 10.8 - - + -
827C PHE 3.9 6.5 - - - +
828C PRO* 1.3 71.9 - - - +
830C GLY* 1.3 59.2 + - - +
832C ILE* 3.1 6.6 + - - +
833C HIS* 2.7 28.1 + - - +
851C ALA* 3.9 17.9 - - + -
852C VAL* 4.0 24.5 - - + +
855C ALA* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 830 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819C ARG* 4.5 6.0 - - - +
820C SER* 4.6 0.8 + - - -
828C PRO* 3.4 0.6 - - - +
829C VAL* 1.3 78.4 - - - +
831C ARG* 1.3 57.4 + - - +
833C HIS* 3.3 7.8 + - - +
834C ARG* 3.0 26.9 + - - +
30I A 3.6 18.8 + - - -
31I G 4.5 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 831 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828C PRO* 3.6 19.6 + - + +
829C VAL 3.2 0.4 - - - -
830C GLY* 1.3 74.2 - - - +
832C ILE* 1.3 61.5 + - - +
834C ARG* 3.2 8.3 + - - +
835C HIS* 2.9 45.1 + - + +
1232D GLU* 2.7 40.6 + - - +
1233D SER 2.7 32.9 + - - +
1234D TYR* 4.5 16.5 - - - -
1237D TYR* 3.9 23.8 + - - -
30I A 3.3 25.9 + - - +
267J G 3.4 14.5 + - - -
268J G 2.9 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 832 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827C PHE* 5.8 0.2 - - + -
828C PRO* 3.2 22.4 + - + +
829C VAL* 3.1 5.0 + - - +
831C ARG* 1.3 81.9 - - + +
833C HIS* 1.3 63.4 + - - +
835C HIS* 3.4 7.6 + - - +
836C LEU* 3.0 23.6 + - + +
851C ALA* 3.8 25.6 - - - +
854C SER* 3.8 17.0 - - - -
855C ALA* 4.5 11.9 - - + -
858C LEU* 4.2 18.2 - - + -
1234D TYR* 3.1 38.8 - - + +
1267D PHE* 4.0 16.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 833 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819C ARG* 3.6 30.6 + - - +
829C VAL 2.7 16.3 + - - +
830C GLY 3.5 5.4 - - - +
832C ILE* 1.3 78.3 - - - +
834C ARG* 1.3 62.5 + - - +
836C LEU* 3.2 5.0 + - - +
837C LYS* 3.1 49.9 + - + +
846C VAL* 3.5 34.2 + - + +
847C GLY 3.8 8.4 + - - -
848C ALA* 5.0 1.6 - - - -
851C ALA* 3.5 21.5 - - + -
258J T 4.9 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 834 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830C GLY 3.0 9.9 + - - +
831C ARG* 3.2 14.3 - - - +
833C HIS* 1.3 78.6 + - - +
835C HIS* 1.3 78.0 + - - +
837C LYS* 3.1 18.2 + - - +
838C SER* 3.1 14.7 + - - -
1232D GLU* 2.7 39.4 + - - +
29I A 3.6 43.4 + - - -
30I A 2.9 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 835 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831C ARG* 2.9 38.4 + - + +
832C ILE* 3.4 5.8 + - - +
834C ARG* 1.3 91.8 + - - +
836C LEU* 1.3 61.6 + - - +
838C SER* 3.4 11.5 + - - -
839C ARG* 3.3 26.8 + - - +
1232D GLU* 3.7 24.3 + - + +
1234D TYR* 4.0 19.1 + + - -
1264D ASN* 5.9 2.0 + - - -
1267D PHE* 3.8 22.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 836 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832C ILE* 3.0 17.8 + - + +
833C HIS 3.7 5.8 - - - +
834C ARG 3.2 0.2 - - - -
835C HIS* 1.3 76.6 - - - +
837C LYS* 1.3 63.8 + - - +
839C ARG* 3.2 5.3 + - - +
840C THR* 3.2 21.1 + - - -
846C VAL* 3.7 31.9 - - + +
850C ALA* 4.0 18.2 - - + -
851C ALA* 4.0 17.3 - - + +
854C SER* 4.3 8.1 - - - +
1267D PHE* 3.3 29.6 - - + -
1270D ILE* 6.3 0.2 - - + -
1271D ALA* 3.9 20.9 - - + -
1286D ILE* 5.0 13.4 - - + +
1291D ILE* 4.7 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 837 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833C HIS* 3.1 35.6 + - + +
834C ARG* 3.1 12.2 + - - +
836C LEU* 1.3 76.0 - - - +
838C SER* 1.3 58.2 + - - +
840C THR* 2.9 28.0 + - - -
844C GLY 4.0 12.9 + - - -
846C VAL* 3.7 16.4 - - + +
1042G SER* 3.2 11.0 + - - -
258J T 2.4 45.3 + - - +
259J A 5.3 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 838 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834C ARG 3.1 11.9 + - - -
835C HIS* 3.4 16.3 + - - -
836C LEU 3.1 0.2 - - - -
837C LYS* 1.3 75.9 - - - +
839C ARG* 1.3 55.0 + - - +
840C THR 3.1 6.4 + - - -
1041G THR* 3.7 22.8 + - - -
1042G SER* 3.7 14.3 + - - -
1479H HIS* 5.9 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 839 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835C HIS* 3.3 17.6 + - - +
836C LEU* 3.2 9.2 + - + +
838C SER* 1.3 76.9 + - - +
840C THR* 1.3 66.2 + - - +
841C THR* 3.7 2.5 - - - -
1267D PHE* 4.3 15.7 - - - -
1268D GLU* 4.1 27.9 + - - +
1271D ALA* 3.4 31.7 - - + +
1272D GLY* 4.3 9.1 - - - +
1275D SER* 4.2 11.7 + - - +
1286D ILE* 5.4 1.7 - - - +
1040G THR 5.2 1.7 - - - +
1041G THR* 5.4 2.0 - - - +
1042G SER 4.7 1.6 - - - +
1479H HIS* 5.8 8.2 + - - -
----------------------------------------------------------
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