Contacts of the helix formed by residues 80 - 87 (chain C) in PDB entry 3Q37
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 SER 80 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ILE* 3.3 9.2 - - - -
71C ARG* 3.5 10.1 - - - -
72C SER* 2.6 44.5 + - - -
79C VAL* 1.3 76.7 - - - +
81C LEU* 1.3 64.4 + - - +
82C GLN 3.5 2.8 + - - -
83C ILE* 3.2 19.6 + - - +
84C LEU* 3.0 25.9 + - - +
15D CYS* 3.4 11.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ALA* 3.6 19.5 - - + +
69C ILE 2.9 18.3 + - - +
70C THR* 3.8 16.6 - - - +
80C SER* 1.3 70.5 - - - +
82C GLN* 1.3 58.8 + - + +
84C LEU* 3.3 3.3 + - + -
85C LYS* 2.9 31.2 + - - +
92C VAL* 4.2 12.1 - - + -
94C LEU* 5.1 2.2 - - + -
113C LYS* 3.7 13.0 - - + +
116C ALA* 3.8 14.6 - - + -
117C ALA* 3.5 43.1 - - + +
120C SER* 4.6 5.4 - - - +
122C PHE* 3.5 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C THR 4.5 6.5 + - - +
71C ARG* 3.5 21.7 - - - +
72C SER* 2.8 39.6 + - - +
80C SER* 3.2 6.3 + - - +
81C LEU* 1.3 77.6 - - + +
83C ILE* 1.3 57.3 + - - +
85C LYS* 3.4 8.1 + - - +
86C ASP* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C SER* 3.7 7.6 - - - +
79C VAL* 4.0 9.2 - - + -
80C SER* 3.2 24.7 + - - +
82C GLN* 1.3 72.1 - - + +
84C LEU* 1.3 65.4 + - - +
86C ASP* 3.4 9.6 + - - +
87C TYR* 3.2 21.0 + - - +
15D CYS* 3.8 10.5 - - - -
16D ASN 3.7 35.4 - - - +
17D GLY 3.4 16.6 - - - +
45D THR* 4.0 13.9 - - + +
47D LEU* 3.5 19.7 - - + -
48D HIS* 3.4 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C PHE* 4.5 3.1 - - + -
49C ILE* 4.2 16.2 - - + -
65C ALA* 3.7 32.3 - - + -
67C ASN 4.1 1.8 - - - +
68C ALA* 3.7 31.0 - - + -
79C VAL* 4.0 13.7 - - + -
80C SER 3.0 15.0 + - - +
81C LEU* 3.3 11.2 + - + +
83C ILE* 1.3 76.4 - - - +
85C LYS* 1.3 62.0 + - - +
87C TYR* 3.0 11.8 + - - -
89C ILE* 3.0 34.5 + - + +
92C VAL* 4.9 0.9 - - + -
122C PHE* 3.9 13.5 - - + -
47D LEU* 4.2 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU 2.9 17.3 + - - +
82C GLN* 3.6 8.1 - - - +
84C LEU* 1.3 75.4 - - - +
86C ASP* 1.3 63.4 + - - +
88C GLY* 3.0 14.0 + - - -
89C ILE 3.9 11.2 - - - +
120C SER* 3.1 45.9 + - - +
121C GLY* 5.2 0.2 - - - -
122C PHE* 4.0 8.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLN 3.1 13.4 + - - +
83C ILE* 3.6 11.6 - - - +
84C LEU 3.3 0.2 - - - -
85C LYS* 1.3 78.0 - - - +
87C TYR* 1.3 58.1 + - - +
88C GLY 3.2 3.0 + - - -
17D GLY 4.9 0.6 - - - +
18D SER* 3.5 25.5 - - - -
19D GLN* 2.9 50.9 + - - +
20D GLN* 5.3 0.7 + - - +
48D HIS* 5.0 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 4.9 6.7 - - + -
50C PRO* 3.6 39.2 - - + +
53C LYS* 3.4 23.4 - - + +
83C ILE 3.2 4.3 + - - +
84C LEU 3.0 9.8 + - - +
86C ASP* 1.3 76.2 - - - +
88C GLY* 1.3 61.6 + - - +
89C ILE* 3.3 7.7 + - + +
19D GLN* 3.7 27.3 + - + -
47D LEU* 3.7 44.1 + - + -
48D HIS* 4.3 6.1 - + - -
51D MET* 3.0 44.4 + - + +
----------------------------------------------------------
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