Contacts of the helix formed by residues 95 - 106 (chain C) in PDB entry 3DAB
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 95 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C PHE* 5.0 2.2 - - + -
91C SER 3.6 7.9 - - - +
92C VAL* 3.7 8.1 - - - +
93C LYS 3.5 8.7 - - - +
94C ASP* 1.4 86.0 - - - +
96C SER* 1.3 63.2 + - - +
97C PRO* 3.4 3.6 - - + -
98C LEU* 3.0 28.5 + - + +
99C TYR* 3.3 24.5 + - + -
26D LEU* 3.7 31.0 - - + -
27D PRO* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASP* 3.1 14.2 + - - -
95C PRO* 1.3 76.0 - - - +
97C PRO* 1.3 65.9 - - - +
99C TYR* 3.1 8.4 + - - +
100C ASP* 2.9 36.7 + - - +
103C ARG* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU* 3.3 19.9 - - + +
87C ARG* 3.4 48.0 - - - +
90C PHE* 4.5 12.1 - - + -
94C ASP* 3.6 10.1 - - - +
95C PRO* 3.4 5.6 - - + -
96C SER* 1.3 93.9 - - - +
98C LEU* 1.3 60.6 + - - +
100C ASP* 3.6 13.9 + - - +
101C MET* 3.1 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C MET* 4.1 19.3 - - + -
56C LEU* 4.3 14.4 - - + -
60C ILE* 6.2 0.4 - - + -
81C LEU* 5.1 2.2 - - + -
85C LEU* 3.6 13.6 - - + +
90C PHE* 4.3 27.9 - - + -
95C PRO* 3.0 15.5 + - + +
97C PRO* 1.3 79.1 - - - +
99C TYR* 1.3 63.6 + - + +
101C MET* 3.2 25.0 + - + +
102C LEU* 2.9 38.6 + - + +
23D TRP* 3.7 30.3 - - + -
26D LEU* 4.5 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C VAL* 6.0 4.9 - - + -
53C MET* 3.8 20.8 - - + +
95C PRO* 3.4 38.4 - - + -
96C SER* 3.1 10.0 + - - +
98C LEU* 1.3 85.9 - - + +
100C ASP* 1.3 65.2 + - - +
102C LEU* 3.8 17.2 - - + +
103C ARG* 2.9 54.7 + - + +
26D LEU* 4.0 4.6 - - + +
27D PRO* 3.2 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C SER* 2.9 25.9 + - - +
97C PRO* 3.7 15.3 - - + +
99C TYR* 1.3 75.6 - - - +
101C MET* 1.3 61.7 + - - +
103C ARG* 3.6 22.6 + - - +
104C LYS* 3.4 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.3 16.8 - - + -
56C LEU* 4.5 1.8 - - + -
81C LEU* 4.3 18.8 - - + -
84C LEU* 3.6 35.0 - - + +
85C LEU* 3.8 9.4 - - + +
97C PRO 3.1 11.9 + - - +
98C LEU* 3.2 30.3 + - + +
100C ASP* 1.3 78.2 - - - +
102C LEU* 1.3 80.2 + - + +
104C LYS* 3.2 7.5 + - - +
105C ASN* 2.8 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.7 26.5 - - + -
49C VAL* 6.0 2.9 - - + -
52C VAL* 4.0 10.3 - - + -
53C MET* 3.6 30.7 - - + -
56C LEU* 3.8 19.1 - - + -
98C LEU* 2.9 30.5 + - + +
99C TYR* 3.8 19.1 - - + +
101C MET* 1.3 87.3 - - + +
103C ARG* 1.3 57.4 + - + +
105C ASN* 4.3 0.9 - - - +
106C LEU* 2.9 49.6 + - + +
500C ILE* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C SER 5.5 0.2 + - - -
99C TYR* 2.9 40.8 + - + +
100C ASP* 3.7 27.6 + - - +
102C LEU* 1.3 76.9 - - + +
104C LYS* 1.3 62.6 + - + +
105C ASN 3.6 0.2 + - - -
106C LEU 4.0 11.8 - - - +
107C VAL* 5.0 1.6 - - - +
500C ILE* 4.3 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LYS* 4.1 4.7 - - - +
100C ASP* 3.4 24.4 + - - +
101C MET* 3.2 10.9 + - - +
103C ARG* 1.3 80.3 - - + +
105C ASN* 1.3 66.3 + - - +
106C LEU 3.7 0.4 - - - -
107C VAL* 3.0 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PRO* 3.3 4.0 - - - +
30C LYS* 2.7 49.0 + - + +
32C PRO* 4.0 16.8 - - - +
33C LEU* 3.8 21.3 - - + +
84C LEU* 4.0 13.3 + - - +
101C MET* 2.8 46.1 + - - +
102C LEU 3.2 1.8 + - - +
104C LYS* 1.3 87.3 - - - +
106C LEU* 1.3 61.4 + - - +
107C VAL 3.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 4.0 38.6 - - + -
28C ARG 3.9 7.2 - - - -
29C PRO* 3.9 19.7 - - + -
33C LEU* 3.8 19.5 - - + -
49C VAL* 4.6 12.8 - - + -
52C VAL* 4.2 9.4 - - + -
102C LEU* 2.9 36.7 + - + +
103C ARG 4.0 8.7 + - - +
104C LYS 3.7 0.2 - - - -
105C ASN* 1.3 84.1 - - - +
107C VAL* 1.3 57.5 + - - +
500C ILE* 4.1 26.2 - - + +
----------------------------------------------------------
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