Contacts of the helix formed by residues 1031 - 1039 (chain I) in PDB entry 3AOH
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 ASN1031 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030I GLY* 1.3 74.7 - - - +
1032I PRO* 1.3 65.8 - - - +
1033I GLN* 2.9 23.1 - - - +
1034I GLN* 2.6 77.4 + - - +
1035I ILE* 3.0 14.5 + - - +
32Y ILE* 2.8 38.9 - - + +
36Y LEU* 5.0 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1032 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004I THR* 4.7 9.9 - - + +
1008I PHE* 3.8 38.7 - - + -
1024I ALA* 5.4 5.3 - - + +
1030I GLY 4.5 2.7 - - - +
1031I ASN* 1.3 89.5 - - - +
1033I GLN* 1.3 61.4 + - - +
1035I ILE* 3.2 5.8 + - + +
1036I ARG* 3.0 23.3 + - - +
31Y LYS* 4.9 9.6 - - - +
32Y ILE* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1033 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004I THR* 5.9 1.9 - - - +
1031I ASN* 2.9 23.6 - - - +
1032I PRO* 1.3 77.8 - - - +
1034I GLN* 1.3 59.6 + - + +
1036I ARG* 2.4 56.5 + - - +
1037I GLN* 3.4 20.8 + - - +
29Y ALA* 5.7 3.4 - - - +
32Y ILE* 5.3 3.3 - - + +
50Y ALA* 5.5 9.4 - - + -
51Y ALA* 5.6 5.4 - - - +
54Y GLU* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1034 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877H PRO 4.8 6.5 - - - +
878H SER* 2.2 53.6 + - - +
880H MET* 4.3 21.5 - - + +
1030I GLY* 4.2 1.7 - - - -
1031I ASN* 2.6 59.1 + - - +
1033I GLN* 1.3 68.2 - - - +
1035I ILE* 1.3 57.4 + - + +
1036I ARG 2.9 1.8 - - - -
1037I GLN* 2.4 43.6 + - - +
1038I LEU* 3.2 9.2 + - + +
36Y LEU* 4.6 8.7 - - - +
46Y SER* 5.2 1.7 + - - +
47Y GLY* 5.5 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1035 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877H PRO* 5.3 3.4 - - + -
1007I VAL* 4.5 4.9 - - + -
1008I PHE* 4.4 15.5 - - + -
1011I PHE* 4.3 24.9 - - + -
1020I LEU* 3.8 43.7 - - + +
1021I TYR* 5.3 2.5 - - - -
1024I ALA* 4.1 20.6 - - + -
1030I GLY* 5.0 6.5 - - - -
1031I ASN 3.0 14.6 + - - +
1032I PRO* 3.7 8.1 - - + +
1034I GLN* 1.3 75.3 - - + +
1036I ARG* 1.3 57.0 + - - +
1038I LEU* 2.8 29.0 + - + +
1039I CYS* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1036 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000I THR* 4.0 18.5 + - - -
1003I VAL* 4.8 4.5 - - + -
1004I THR* 3.2 39.1 + - + +
1007I VAL* 5.3 5.2 - - + -
1008I PHE* 5.8 0.4 - - - -
1032I PRO 3.0 11.5 + - - +
1033I GLN* 2.4 51.1 + - - +
1034I GLN 2.8 0.4 + - - -
1035I ILE* 1.3 77.1 - - - +
1037I GLN* 1.3 83.0 + - - +
1038I LEU 3.0 0.4 - - - -
1040I GLY* 3.2 8.8 + - - +
1041I LEU 2.5 60.0 + - - +
1042I ARG* 3.7 11.8 - - - +
1043I GLY 4.6 2.7 - - - +
54Y GLU* 5.8 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1037 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880H MET* 3.2 39.6 - - - +
1033I GLN* 3.4 24.5 + - - +
1034I GLN* 2.4 27.3 + - - +
1036I ARG* 1.3 85.2 - - - +
1038I LEU* 1.3 56.8 + - + -
1042I ARG* 2.5 60.8 + - + +
1060I SER* 3.8 3.3 - - - -
1061I PHE* 2.9 33.1 + - + +
46Y SER* 5.1 0.4 + - - -
50Y ALA* 5.2 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1038 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876H VAL 5.9 1.1 - - - +
877H PRO* 4.6 17.7 - - + +
880H MET* 5.4 10.1 - - + -
882H LEU* 4.0 35.9 - - + -
954I ALA* 4.6 2.9 - - + -
1020I LEU* 3.9 28.9 - - + -
1034I GLN* 3.7 7.6 - - + +
1035I ILE* 2.8 43.1 + - + +
1037I GLN* 1.3 81.4 - - + +
1039I CYS* 1.3 61.6 + - - +
1060I SER* 3.2 21.7 - - - -
1061I PHE* 4.3 10.8 - - + +
1062I ARG* 3.3 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1039 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954I ALA* 3.5 14.8 - - - -
955I VAL 2.8 39.5 - - - +
956I ILE* 2.9 33.6 - - - +
957I PRO* 4.3 3.1 - - + -
1007I VAL* 3.6 17.7 - - + -
1011I PHE* 3.3 23.1 - - - -
1020I LEU* 4.2 9.2 - - - -
1035I ILE* 2.9 9.6 + - - +
1038I LEU* 1.3 77.3 - - - +
1040I GLY* 1.3 64.4 + - - +
1060I SER* 3.7 0.2 - - - -
----------------------------------------------------------
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