Contacts of the helix formed by residues 95 - 106 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E PHE* 5.1 2.0 - - + -
91E SER 3.5 7.6 - - - +
92E VAL* 3.7 8.1 - - - +
93E LYS 3.5 8.1 - - - +
94E ASP* 1.4 86.7 - - - +
96E SER* 1.3 65.4 + - - +
97E PRO* 3.3 3.6 - - + -
98E LEU* 2.9 25.1 + - + +
99E TYR* 3.1 26.8 + - + -
26F LEU* 3.7 31.0 - - + -
27F PRO* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ASP* 3.1 11.8 + - - -
95E PRO* 1.3 77.1 - - - +
97E PRO* 1.3 66.6 - - - +
99E TYR* 3.2 8.6 + - - +
100E ASP* 2.9 40.2 + - - +
103E ARG* 5.0 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU* 3.6 12.4 - - + +
87E ARG* 3.6 49.4 - - - +
90E PHE* 4.5 11.7 - - + -
94E ASP* 3.3 14.8 - - - +
95E PRO* 3.3 6.3 - - + -
96E SER* 1.3 93.4 - - - +
98E LEU* 1.3 63.2 + - - +
100E ASP* 3.5 14.5 + - + +
101E MET* 3.2 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E MET* 4.2 13.7 - - + -
56E LEU* 3.5 24.7 - - + -
81E LEU* 5.0 3.1 - - + -
85E LEU* 3.8 10.9 - - + +
90E PHE* 4.1 29.6 - - + -
95E PRO* 2.9 12.4 + - + +
97E PRO* 1.3 79.9 - - - +
99E TYR* 1.3 64.0 + - + +
101E MET* 3.2 22.3 + - + +
102E LEU* 2.9 38.2 + - + +
23F TRP* 3.6 29.2 - - + -
26F LEU* 4.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E VAL* 6.0 5.2 - - + -
53E MET* 3.7 27.7 - - + +
95E PRO* 3.1 37.6 + - + -
96E SER* 3.7 8.5 - - - +
98E LEU* 1.3 81.6 - - + +
100E ASP* 1.3 65.3 + - - +
102E LEU* 3.8 14.9 - - + +
103E ARG* 3.0 58.6 + - + +
26F LEU* 3.9 6.6 - - + +
27F PRO* 3.4 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E SER* 2.9 28.0 + - - +
97E PRO* 3.5 15.9 - - + +
99E TYR* 1.3 76.7 - - - +
101E MET* 1.3 61.6 + - - +
103E ARG* 3.6 22.1 + - - +
104E LYS* 3.5 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E LEU* 4.8 7.9 - - + -
56E LEU* 4.8 2.2 - - + -
81E LEU* 4.0 23.1 - - + -
84E LEU* 3.6 37.5 - - + +
85E LEU* 3.6 17.9 - - + -
97E PRO 3.2 3.2 + - - +
98E LEU* 3.2 32.3 + - + +
100E ASP* 1.3 77.5 - - - +
102E LEU* 1.3 76.6 + - + +
104E LYS* 3.1 7.6 + - - +
105E ASN* 2.8 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E LEU* 3.9 25.6 - - + -
49E VAL* 6.4 0.7 - - + -
52E VAL* 4.2 14.6 - - + -
53E MET* 3.6 30.3 - - + -
56E LEU* 4.4 8.5 - - + -
98E LEU* 2.9 34.5 + - + +
99E TYR* 3.2 18.8 + - + +
101E MET* 1.3 91.5 - - + +
103E ARG* 1.3 58.1 + - + +
105E ASN* 3.1 1.2 + - - +
106E LEU* 2.9 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E SER* 5.0 0.6 + - - +
99E TYR* 3.0 44.3 + - + +
100E ASP* 3.6 30.5 + - - +
101E MET 3.3 0.2 - - - -
102E LEU* 1.3 77.8 - - + +
104E LYS* 1.3 62.3 + - + +
105E ASN 3.6 0.2 + - - -
107E VAL* 3.4 26.2 + - - +
500E ILE* 4.2 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E LYS* 3.6 23.2 + - - +
100E ASP* 3.5 19.2 + - - +
101E MET* 3.1 12.3 + - - +
103E ARG* 1.3 78.9 - - + +
105E ASN* 1.3 66.0 + - - +
106E LEU 3.5 0.2 - - - -
107E VAL* 3.6 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E PRO* 3.3 4.3 - - - +
30E LYS* 2.8 46.4 + - - +
32E PRO* 3.9 22.5 - - - +
33E LEU* 3.9 24.3 - - + +
84E LEU* 4.2 11.8 + - - +
101E MET* 2.8 46.4 + - - +
102E LEU 3.1 1.7 + - - +
104E LYS* 1.3 85.6 - - - +
106E LEU* 1.3 58.3 + - - +
107E VAL 3.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E VAL* 3.9 37.8 - - + +
28E ARG* 4.2 17.8 + - - +
29E PRO* 3.8 21.3 - - + -
33E LEU* 3.5 26.2 - - + -
49E VAL* 4.8 11.7 - - + -
52E VAL* 4.2 11.9 - - + -
102E LEU* 2.9 39.5 + - + +
103E ARG 4.5 0.4 - - - -
105E ASN* 1.3 78.3 - - - +
107E VAL* 1.3 65.5 + - - +
500E ILE* 4.5 17.2 - - + +
----------------------------------------------------------
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