Contacts of the helix formed by residues 1035 - 1044 (chain K) in PDB entry 5ANC
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 GLY1035 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664K GLU* 3.8 15.8 + - - +
665K VAL* 5.9 0.9 - - - -
1006K ARG* 3.6 5.8 + - - -
1034K PHE* 1.3 73.3 - - - +
1036K PHE* 1.3 61.0 + - - +
1037K ALA 3.6 1.6 - - - -
1038K ASP* 3.7 23.6 + - - +
1039K GLU* 3.5 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1036 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K PHE* 6.3 0.9 - + + -
664K GLU* 4.1 3.6 - - + +
987K CYS* 5.1 9.2 - - + -
989K ILE* 4.5 6.7 - - + -
999K VAL* 5.4 2.2 - - + -
1002K VAL* 3.6 22.2 - - + -
1003K LEU* 4.3 15.5 - - + -
1006K ARG* 3.8 17.9 - - - +
1028K LEU* 3.3 35.2 - - + -
1032K GLU 4.4 2.7 - - - -
1033K SER* 3.2 24.3 + - - +
1034K PHE 3.3 0.2 - - - -
1035K GLY* 1.3 75.9 - - - +
1037K ALA* 1.3 63.3 + - - +
1038K ASP 3.2 0.2 - - - -
1039K GLU* 3.2 3.6 + - - +
1040K ILE* 2.9 63.8 + - + +
1050K PRO* 3.9 23.3 - - + -
1052K LEU* 5.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1037 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K ASP* 4.5 12.3 - - + -
99K PHE* 4.9 4.4 - - + -
125K PRO* 3.7 22.4 - - + +
664K GLU* 4.5 10.0 - - + +
1036K PHE* 1.3 78.7 - - - +
1038K ASP* 1.3 58.8 + - - +
1040K ILE* 3.2 5.6 + - - +
1041K ARG* 2.9 51.4 + - - +
1050K PRO* 4.0 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1038 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K VAL* 4.7 6.6 - - - +
98K ASP* 5.4 1.0 - - - +
664K GLU* 4.8 2.6 - - - +
665K VAL* 4.0 21.2 - - - +
1035K GLY* 3.7 23.1 - - - +
1036K PHE 3.2 0.2 - - - -
1037K ALA* 1.3 76.6 - - - +
1039K GLU* 1.3 58.2 + - - +
1041K ARG* 2.7 37.6 + - - +
1042K LYS* 2.9 29.2 + - - +
3363N A 4.9 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1039 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002K VAL* 4.4 22.0 - - + -
1005K LYS* 5.8 4.2 - - + -
1006K ARG* 4.1 17.9 + - - +
1035K GLY 3.5 13.0 + - - +
1036K PHE 3.2 10.0 + - - +
1038K ASP* 1.3 80.7 - - - +
1040K ILE* 1.3 56.9 + - - +
1042K LYS* 3.2 14.7 + - - +
1043K ARG* 2.9 53.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1040 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125K PRO* 5.2 0.9 - - + -
989K ILE* 4.2 5.4 - - + -
998K ARG 6.0 0.2 - - - -
999K VAL* 4.0 29.8 - - + -
1002K VAL* 4.6 12.1 - - + -
1036K PHE* 2.9 51.3 + - + +
1037K ALA* 3.2 11.2 + - - +
1039K GLU* 1.3 75.7 - - - +
1041K ARG* 1.3 65.5 + - - +
1043K ARG* 3.2 16.0 + - + +
1044K THR* 3.5 14.8 + - - +
1046K GLY* 4.1 4.2 + - - -
1047K LEU 5.2 0.2 - - - +
1048K ALA* 3.3 36.6 - - + +
1050K PRO* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1041 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K VAL* 3.2 43.5 + - - +
98K ASP* 4.3 4.4 - - - +
121K GLU* 5.5 0.4 - - - +
125K PRO* 3.6 19.5 - - + +
126K GLN* 3.4 31.3 - - - +
1037K ALA* 2.9 35.2 + - - +
1038K ASP* 2.7 35.1 + - - +
1040K ILE* 1.3 79.2 - - - +
1042K LYS* 1.3 63.5 + - - +
1044K THR 3.5 9.2 - - - +
1045K SER* 3.7 3.2 - - - -
1046K GLY* 3.5 34.3 + - - +
3363N A 4.0 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1042 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H LYS* 3.7 37.6 + - - +
1038K ASP 2.9 13.8 + - - +
1039K GLU* 3.4 19.3 - - - +
1041K ARG* 1.3 77.7 - - - +
1043K ARG* 1.3 65.3 + - - +
1044K THR 3.4 5.7 + - - +
3233N A 5.1 15.3 + - - +
3363N A 3.9 32.7 + - + +
3364N G 4.8 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1043 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H LYS* 5.5 5.4 - - - +
998K ARG* 4.6 23.3 + - + +
1001K ALA* 4.5 18.2 + - - +
1002K VAL* 3.8 29.5 - - + +
1005K LYS* 4.5 22.4 - - - +
1039K GLU* 2.9 36.5 + - - +
1040K ILE* 3.2 14.3 + - + +
1042K LYS* 1.3 78.7 - - - +
1044K THR* 1.3 65.0 + - + +
3175N C 4.8 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1044 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H LYS* 5.1 4.5 - - - -
995K VAL* 3.9 25.2 - - + +
998K ARG* 3.8 34.5 - - + +
1040K ILE* 3.5 7.7 + - - +
1041K ARG 3.5 6.4 - - - +
1042K LYS 3.8 4.3 - - - +
1043K ARG* 1.3 84.4 - - + +
1045K SER* 1.3 74.0 + - - -
1046K GLY 3.6 7.3 + - - -
1047K LEU* 3.7 13.5 + - - -
1048K ALA 5.0 1.0 + - - -
3363N A 4.4 9.9 + - - -
----------------------------------------------------------
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