Contacts of the strand formed by residues 75 - 82 (chain C) in PDB entry 3AP4
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 CYS 75 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PRO* 3.5 3.6 - - - +
69C ARG* 2.9 43.1 + - - +
74C GLY* 1.3 75.1 - - - +
76C ILE* 1.3 64.4 - - - +
77C VAL* 4.1 23.3 - - - -
91C ILE* 3.8 17.7 - - + -
92C THR 3.5 13.0 - - - +
93C TYR* 4.1 11.7 - - + +
95C THR* 3.8 13.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
66C PHE* 3.8 27.6 - - + -
67C ASN 3.7 17.0 - - - +
68C PRO* 4.2 2.9 - - + -
75C CYS* 1.3 76.2 - - - +
77C VAL* 1.3 63.7 + - - +
78C CYS* 4.0 5.1 - - - -
90C GLU 3.6 1.2 - - - +
91C ILE* 3.4 3.6 - - - +
92C THR* 2.9 40.2 + - + +
95C THR* 4.1 11.2 - - - +
96C PRO* 4.2 6.1 - - + -
97C PHE* 3.9 28.0 - - + -
123C THR* 3.5 32.1 - - + -
124C LEU* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C HIS* 3.5 1.6 - - + +
67C ASN* 2.9 39.2 + - + +
69C ARG* 3.6 46.0 - - - +
75C CYS* 4.1 12.8 - - - -
76C ILE* 1.3 75.5 - - - +
78C CYS* 1.3 63.9 + - - +
89C GLU* 3.7 37.9 - - + +
90C GLU 3.9 2.2 - - - -
91C ILE* 4.3 14.4 - - + +
2G GAL 3.9 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 3.8 17.5 - - + -
65C HIS* 3.0 12.3 - - - +
66C PHE* 4.1 5.6 - - - -
76C ILE* 4.0 6.5 - - - -
77C VAL* 1.3 79.7 - - - +
79C ASN* 1.3 64.7 + - - +
88C ARG 4.1 0.2 - - - +
89C GLU* 3.5 2.4 - - - -
90C GLU* 2.8 42.0 + - + +
124C LEU* 3.9 32.8 - - - -
126C TYR* 3.6 23.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PHE* 4.0 0.2 - - - -
65C HIS* 3.0 35.4 + - + +
78C CYS* 1.3 75.7 - - - +
80C THR* 1.3 74.8 + - - +
86C TRP* 3.7 16.5 - - + +
87C GLY 2.8 38.2 + - - +
88C ARG 3.7 5.4 - - - -
89C GLU* 3.5 9.6 - - - +
126C TYR* 3.0 17.5 + - - -
129C ARG* 3.0 18.5 + - - +
2G GAL 2.8 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL 3.0 18.2 - - - +
63C ALA 2.7 19.4 + - - +
79C ASN* 1.3 79.2 + - - +
81C LEU* 1.3 58.4 + - - +
82C ILE* 3.7 31.8 + - + +
85C LYS 3.6 1.7 - - - +
86C TRP* 3.6 5.8 - - - -
87C GLY* 3.1 24.4 + - - -
126C TYR* 2.8 21.8 + - - -
129C ARG* 3.6 21.2 - - + +
130C ILE* 3.9 11.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
59C ARG* 3.4 51.4 - - + +
60C ALA 3.7 11.9 - - - +
61C ASP* 3.2 9.5 - - - +
62C VAL* 2.9 41.1 + - + +
80C THR* 1.3 70.7 - - - +
82C ILE* 1.3 62.3 + - - +
83C ASN 4.2 0.2 - - - -
84C GLU* 3.6 17.7 - - - +
85C LYS 3.5 26.7 - - - +
86C TRP* 3.6 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASP* 3.7 8.7 - - - +
80C THR* 3.7 22.1 + - + +
81C LEU* 1.3 75.7 - - - +
83C ASN* 1.3 87.6 + - + +
84C GLU 3.2 1.1 - - - -
85C LYS* 3.0 25.1 + - - +
129C ARG* 4.6 12.6 - - + +
130C ILE* 4.0 20.4 - - + -
----------------------------------------------------------
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