Contacts of the helix formed by residues 80 - 97 (chain C) in PDB entry 4DHX
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 PRO 80 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.9 1.8 - - + -
40C CYS* 3.8 30.5 - - + -
78C LEU 3.1 11.4 - - - +
79C VAL* 1.3 92.9 - - + +
81C ASP* 1.3 66.2 + - - +
82C SER* 3.8 12.8 - - - +
83C VAL* 3.1 34.9 + - + +
84C LYS* 3.5 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL 3.7 2.0 + - - -
80C PRO* 1.3 72.6 - - - +
82C SER* 1.3 66.3 + - - -
84C LYS* 3.1 17.8 + - + +
85C LYS* 2.8 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PRO* 3.8 14.6 - - - +
81C ASP* 1.3 86.9 + - - +
83C VAL* 1.3 60.5 + - - +
85C LYS* 3.3 12.3 + - - +
86C GLU* 3.0 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.7 29.8 - - + -
36C LYS* 3.7 41.3 - - + +
37C LEU* 4.9 2.0 - - + -
40C CYS* 4.8 2.2 - - + -
79C VAL* 4.5 8.3 - - + -
80C PRO* 3.1 33.1 + - + +
82C SER* 1.3 84.9 + - - +
84C LYS* 1.3 62.2 + - - +
86C GLU* 3.3 8.3 + - - +
87C LEU* 3.1 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212A CYS* 3.8 11.1 - - - -
1216A VAL* 4.8 20.4 - - + -
76C ARG 4.6 8.5 + - - -
79C VAL* 3.9 35.7 + - + -
80C PRO 3.9 6.1 - - - +
81C ASP* 3.1 18.5 + - + +
83C VAL* 1.3 75.8 - - + +
85C LYS* 1.3 65.0 + - + +
87C LEU* 3.4 6.5 + - - -
88C LEU* 3.0 23.2 + - - +
----------------------------------------------------------
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 ASP* 2.8 43.0 + - + +
82C SER* 3.6 11.3 - - - +
84C LYS* 1.3 72.7 - - + +
86C GLU* 1.3 58.3 + - - +
88C LEU* 3.3 13.7 + - + +
89C GLN* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.8 6.1 - - + +
36C LYS* 3.0 40.1 + - - +
82C SER* 3.0 20.7 + - - +
83C VAL* 3.7 6.5 - - - +
84C LYS 3.2 0.4 - - - -
85C LYS* 1.3 74.9 - - - +
87C LEU* 1.3 63.8 + - + +
89C GLN* 3.4 7.0 + - + +
90C ARG* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212A CYS* 3.8 11.9 - - - -
1216A VAL* 3.7 26.2 - - + -
1219A PHE* 5.9 2.2 - - + -
29C LEU* 3.6 41.0 - - + +
32C LEU* 3.9 22.2 - - + -
33C LEU* 3.8 27.8 - - + +
36C LYS* 6.3 0.9 - - + -
83C VAL* 3.1 23.1 + - + +
84C LYS* 3.8 3.8 - - - +
86C GLU* 1.3 74.2 - - + +
88C LEU* 1.3 65.4 + - - +
90C ARG* 3.3 5.8 + - - +
91C ILE* 3.1 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208A CYS* 3.8 34.1 - - + +
1209A GLU* 3.9 25.8 - - + +
1212A CYS* 3.6 12.0 - - + -
84C LYS 3.0 14.3 + - - +
85C LYS* 3.4 15.5 - - + +
87C LEU* 1.3 78.7 - - - +
89C GLN* 1.3 63.2 + - - +
91C ILE* 3.2 4.0 + - + +
92C ARG* 3.0 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LYS 2.9 16.7 + - - +
86C GLU* 3.7 8.5 - - + +
87C LEU 3.2 0.2 - - - -
88C LEU* 1.3 77.0 - - - +
90C ARG* 1.3 57.0 + - - +
92C ARG* 3.3 26.7 + - - +
93C THR* 2.9 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLU* 3.0 23.6 + - - +
28C ARG* 3.6 46.2 + - - +
29C LEU* 3.9 15.3 - - + -
32C LEU* 4.0 24.0 - - + +
86C GLU 3.2 11.2 + - - +
87C LEU* 3.7 8.5 - - - +
88C LEU 3.3 0.2 - - - -
89C GLN* 1.3 79.9 - - - +
91C ILE* 1.3 56.8 + - - +
93C THR* 3.8 6.3 - - - -
94C PHE* 2.8 28.6 + - + +
1178D ARG* 3.5 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208A CYS* 3.9 27.8 - - + +
1211A VAL* 4.3 10.8 - - + -
1212A CYS* 3.8 39.3 - - + +
1215A LEU* 4.4 3.4 - - + -
16C ILE* 4.7 14.4 - - + -
20C LEU* 4.7 7.9 - - + -
25C GLU* 6.2 0.2 - - - -
29C LEU* 3.9 29.2 - - + -
87C LEU* 3.1 13.9 + - + +
88C LEU* 3.2 7.8 + - - +
90C ARG* 1.3 75.4 - - - +
92C ARG* 1.3 64.7 + - - +
94C PHE* 3.4 8.6 + - + +
95C LEU* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204A VAL* 6.5 1.3 - - + -
1205A ALA* 4.0 35.0 + - - +
1208A CYS* 4.5 11.9 - - + +
1209A GLU* 4.7 4.9 + - - +
88C LEU* 3.0 48.4 + - - +
89C GLN* 3.7 28.4 + - - +
91C ILE* 1.3 73.3 - - - +
93C THR* 1.3 67.3 + - - +
95C LEU* 3.2 8.1 + - + +
96C ALA* 3.1 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLN* 2.9 36.4 + - - +
90C ARG* 3.8 7.6 - - + -
92C ARG* 1.3 74.5 - - - +
94C PHE* 1.3 66.8 + - - +
96C ALA* 3.1 15.7 + - - +
97C GLN* 3.3 36.7 + - - +
1185D ARG* 3.9 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 5.2 0.9 - - + -
19C LYS* 3.6 36.1 - - + -
20C LEU* 3.6 22.0 - - + -
23C THR* 3.3 29.6 - - + -
25C GLU* 3.6 33.0 - - + +
28C ARG* 5.1 1.1 - - - -
90C ARG* 2.8 19.4 + - + +
91C ILE* 3.5 8.7 - - + +
93C THR* 1.3 77.3 - - - +
95C LEU* 1.3 72.8 + - + +
97C GLN* 3.2 11.5 + - - +
98C HIS* 2.8 61.6 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204A VAL* 3.6 23.8 - - + -
1208A CYS* 3.4 28.5 - - - -
16C ILE* 3.9 32.3 - - + -
19C LYS* 4.6 20.9 - - - -
91C ILE 3.0 15.7 + - - +
92C ARG* 3.5 7.2 - - + +
93C THR 3.1 0.4 - - - -
94C PHE* 1.3 88.5 - - + +
96C ALA* 1.3 63.1 + - - +
98C HIS* 3.3 21.1 + - - +
99C ALA 3.7 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ARG* 3.1 11.9 + - + +
93C THR* 3.1 11.5 + - - +
95C LEU* 1.3 76.9 - - - +
97C GLN* 1.3 57.3 + - - +
98C HIS 3.4 1.2 + - - -
99C ALA 4.8 5.0 + - - -
63E THR* 4.9 0.7 + - - -
65E ASP* 3.2 41.9 - - - +
66E ASP* 4.3 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C THR* 3.3 32.5 + - - +
94C PHE* 3.2 10.2 + - - +
96C ALA* 1.3 79.5 - - - +
98C HIS* 1.3 76.7 + - + +
99C ALA 3.9 1.7 + - - -
1181D MET* 5.5 8.3 - - - +
1185D ARG* 3.6 12.3 + - - -
65E ASP* 3.6 29.4 - - + +
66E ASP* 5.6 1.8 - - - +
68E VAL* 3.7 24.5 - - - +
69E ALA* 3.7 22.9 - - + +
----------------------------------------------------------
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