Contacts of the helix formed by residues 75 - 83 (chain C) in PDB entry 7CAL
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 TRP 75 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ILE 3.5 12.4 + - - +
72C TYR* 3.0 11.7 + + + +
74C ALA* 1.3 78.5 - - - +
76C ILE* 1.3 72.9 + - + +
77C CYS 3.2 4.8 + - - -
78C PRO* 3.6 1.6 - - - +
79C PHE* 3.3 49.9 - + - +
210C HIS* 3.0 38.4 + + - -
247C TYR* 3.5 23.8 - + - -
701C 3PE 3.6 42.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TYR* 3.3 60.1 + - + +
73C SER* 4.4 1.8 - - - -
75C TRP* 1.3 95.4 - - + +
77C CYS* 1.3 63.5 + - - +
78C PRO 3.5 0.4 - - - -
79C PHE* 3.7 14.6 - - + -
80C GLN* 3.3 43.3 + - + +
91C ILE* 5.2 8.5 - - + -
95C ASP* 4.7 8.5 - - + -
171C ARG* 3.6 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C SER 3.3 18.6 - - - +
75C TRP 3.2 2.0 - - - +
76C ILE* 1.3 82.9 - - - +
78C PRO* 1.4 63.4 - - + +
80C GLN* 4.8 2.1 - - - +
81C PHE* 3.5 10.0 + - - +
168C SER* 3.3 26.8 + - - +
169C MET* 3.3 27.3 - - - +
171C ARG* 3.6 40.0 + - - +
172C LEU* 4.0 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA 3.8 11.9 - - - +
75C TRP 3.6 6.7 - - - +
77C CYS* 1.4 92.6 - - + +
79C PHE* 1.3 60.6 + - - +
80C GLN 3.6 0.7 - - - -
81C PHE* 3.6 5.4 - - + +
82C ALA* 3.6 12.5 + - - +
169C MET* 3.7 11.0 - - + -
172C LEU* 4.9 5.6 - - + -
207C PHE* 5.0 1.3 - - + -
210C HIS* 3.5 26.0 - - + -
211C CYS* 4.4 15.0 - - + -
214C CYS* 3.4 22.6 - - + +
215C PHE* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TRP* 3.3 47.8 - + + +
76C ILE* 3.7 10.3 + - + -
77C CYS 3.5 1.0 - - - -
78C PRO* 1.3 79.5 - - - +
80C GLN* 1.3 66.1 + - + +
81C PHE 3.2 0.2 - - - -
82C ALA 3.5 0.2 + - - -
83C PHE* 3.0 63.4 + + + +
84C ILE* 3.7 13.3 + - + -
210C HIS* 4.1 6.1 - + - +
214C CYS* 4.4 4.5 - - - -
244C TRP 5.4 5.4 - - - -
245C ASN* 5.1 11.4 - - - -
247C TYR* 4.2 30.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE* 3.3 27.3 + - + +
77C CYS 4.8 2.9 + - - +
79C PHE* 1.3 79.9 - - + +
81C PHE* 1.3 65.0 + - - +
82C ALA 3.2 1.5 + - - -
84C ILE* 2.9 37.9 - - + +
87C LYS* 4.9 11.4 - - + +
91C ILE* 4.0 23.5 - - + +
95C ASP* 5.3 6.4 - - - +
165C ARG* 3.3 13.6 + - - +
168C SER* 4.4 5.5 + - - -
171C ARG* 3.4 32.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C CYS 3.5 18.1 + - - +
78C PRO 3.6 7.5 - - - +
79C PHE 3.2 0.6 - - - -
80C GLN* 1.3 83.6 - - - +
82C ALA* 1.3 59.0 + - + +
162C LEU* 5.4 2.9 - - + -
165C ARG* 3.4 64.0 + - + +
166C ILE* 4.0 27.8 - - + -
169C MET* 3.6 20.6 - - + -
214C CYS 5.0 0.4 - - - -
215C PHE* 3.8 27.4 - + - -
218C LEU* 3.5 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PRO 3.6 9.1 + - - +
79C PHE 3.5 1.4 + - - -
80C GLN 4.7 0.7 - - - -
81C PHE* 1.3 81.9 - - + +
83C PHE* 1.3 78.3 + - + +
84C ILE 3.8 0.2 - - - -
85C THR* 4.1 11.1 - - - -
214C CYS 3.3 26.9 - - - +
217C TYR* 4.6 7.6 - - + -
218C LEU* 4.0 22.1 - - + +
221C ASP* 4.5 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PHE* 3.0 40.4 + + + +
82C ALA* 1.3 82.2 - - + +
84C ILE* 1.3 63.1 + - - +
85C THR* 3.0 8.7 + - - -
213C GLY 4.3 0.7 - - - -
214C CYS* 3.6 30.5 - - + -
217C TYR* 3.6 51.8 - + + -
221C ASP* 5.6 0.9 - - - +
244C TRP* 4.8 28.8 - + + +
247C TYR* 3.5 39.7 - + + -
250C ALA* 4.1 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