Contacts of the helix formed by residues 75 - 83 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE 3.5 11.9 + - - +
72A TYR* 3.0 12.0 + + + +
74A ALA* 1.3 78.5 - - - +
76A ILE* 1.3 74.2 + - + +
77A CYS 3.2 4.6 + - - -
78A PRO* 3.6 1.6 - - - +
79A PHE* 3.3 49.8 - + - +
210A HIS* 3.0 38.9 + + - -
247A TYR* 3.5 22.7 - + - -
701A 3PE 3.5 43.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 3.3 60.1 + - + +
73A SER* 4.4 2.2 - - - -
75A TRP* 1.3 95.1 - - + +
77A CYS* 1.3 64.6 + - - +
78A PRO 3.5 0.4 - - - -
79A PHE* 3.7 13.0 - - + -
80A GLN* 3.3 42.2 + - + +
91A ILE* 5.2 8.5 - - + -
95A ASP* 4.7 9.2 - - + -
171A ARG* 3.6 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER 3.3 18.6 - - - +
74A ALA* 4.3 0.2 - - - -
75A TRP 3.2 2.0 - - - +
76A ILE* 1.3 83.2 - - - +
78A PRO* 1.4 64.0 - - + +
80A GLN* 4.8 2.1 - - - +
81A PHE* 3.5 9.9 + - - +
168A SER* 3.3 28.1 + - - +
169A MET* 3.3 27.1 - - - +
171A ARG* 3.6 37.5 + - - +
172A LEU* 4.0 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 3.8 11.7 - - - +
75A TRP 3.6 7.0 - - - +
77A CYS* 1.4 92.2 - - + +
79A PHE* 1.3 61.8 + - - +
80A GLN 3.6 0.4 - - - -
81A PHE* 3.6 5.1 - - + +
82A ALA* 3.6 12.8 + - - +
169A MET* 3.7 11.0 - - + -
172A LEU* 4.9 5.4 - - + -
207A PHE* 5.0 1.6 - - + -
210A HIS* 3.5 25.6 - - + -
211A CYS* 4.4 15.5 - - + -
214A CYS* 3.4 22.1 - - + +
215A PHE* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 3.3 47.7 + + + +
76A ILE* 3.9 9.0 - - + -
77A CYS 3.5 0.8 - - - -
78A PRO* 1.3 80.7 - - - +
80A GLN* 1.3 65.6 + - + +
81A PHE 3.2 0.2 - - - -
83A PHE* 3.0 62.3 + + + +
84A ILE* 3.7 13.5 + - + -
210A HIS* 4.1 6.1 - + - +
214A CYS* 4.4 4.5 - - - -
244A TRP 5.4 6.5 - - - -
245A ASN* 5.1 10.8 - - - -
247A TYR* 4.2 30.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 3.3 28.4 + - + +
77A CYS 4.8 2.6 + - - +
79A PHE* 1.3 79.1 - - + +
81A PHE* 1.3 64.8 + - - +
82A ALA 3.2 1.1 + - - -
84A ILE* 2.9 37.6 - - + +
87A LYS* 4.9 12.1 - - + +
91A ILE* 4.0 22.5 - - + +
95A ASP* 5.3 6.0 - - - +
165A ARG* 3.3 13.5 + - - +
168A SER* 4.4 5.3 + - - -
171A ARG* 3.4 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A CYS 3.5 17.9 - - - +
78A PRO 3.6 8.2 + - - +
79A PHE 3.2 0.8 - - - -
80A GLN* 1.3 83.2 - - + +
82A ALA* 1.3 58.5 + - + +
162A LEU* 5.5 2.5 - - + -
165A ARG* 3.4 63.9 + - + +
166A ILE* 4.0 26.7 - - + -
169A MET* 3.6 19.3 - - + -
214A CYS 5.0 0.2 - - - -
215A PHE* 3.8 26.2 - + - -
218A LEU* 3.5 41.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PRO 3.6 8.4 + - - +
79A PHE 3.5 1.8 + - - -
80A GLN 4.7 0.7 - - - -
81A PHE* 1.3 80.8 - - + +
83A PHE* 1.3 79.7 + - + +
84A ILE 3.8 0.2 - - - -
85A THR* 4.1 12.0 - - - -
214A CYS* 3.3 27.1 - - - +
217A TYR* 4.6 6.9 - - + -
218A LEU* 4.0 22.6 - - + +
221A ASP* 4.5 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.0 39.7 + + + +
82A ALA* 1.3 80.8 - - + +
84A ILE* 1.3 61.2 + - - +
85A THR* 3.0 9.0 + - - -
213A GLY 4.3 0.2 - - - -
214A CYS* 3.6 30.7 - - + -
217A TYR* 3.6 52.0 - + + -
221A ASP* 5.6 0.9 - - - +
244A TRP* 4.8 30.1 + + + +
247A TYR* 3.5 38.1 - + + -
250A ALA* 4.1 9.4 - - + -
----------------------------------------------------------
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