Contacts of the helix formed by residues 93 - 104 (chain B) in PDB entry 4DTZ
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 GLU 93 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 2.7 46.2 + - - -
84B ASP* 4.5 7.2 - - - +
89B SER* 3.2 7.4 - - - -
90B TRP* 2.8 42.9 + - + +
91B THR 3.9 1.9 - - - +
92B HIS* 1.3 85.2 + - + +
94B LYS* 1.3 68.9 + - - +
95B ASN* 4.4 6.5 - - + +
96B TRP* 2.9 22.1 + - - +
97B LYS* 3.8 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B HIS 3.6 3.8 + - - -
93B GLU* 1.3 72.1 - - - +
95B ASN* 1.3 66.0 + - - +
96B TRP 3.4 0.3 + - - -
97B LYS* 3.5 3.4 + - - +
98B LYS* 3.2 29.8 + - + +
245B THR* 4.2 17.9 - - + -
247B GLU* 2.8 42.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP* 2.9 40.7 + - + +
86B LEU* 5.0 0.2 - - - +
93B GLU* 3.1 4.1 + - + +
94B LYS* 1.3 81.7 - - - +
96B TRP* 1.3 65.7 + - - +
98B LYS* 3.9 25.5 + - - +
99B ALA* 3.2 26.1 + - - +
249B LEU* 5.0 1.9 - - - +
250B ASP* 5.4 5.9 + - - -
253B ASN* 4.0 24.8 - - - +
257B GLN* 4.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP 5.6 0.2 - - - -
86B LEU* 3.5 18.5 - - + +
89B SER* 3.2 24.6 + - - +
90B TRP 3.3 26.5 - - - +
91B THR* 3.6 27.6 - - + -
93B GLU* 2.9 9.1 + - - +
95B ASN* 1.3 78.6 - - - +
97B LYS* 1.4 93.4 + - + +
100B HIS* 2.8 55.7 + + + +
397B GLN* 3.4 55.6 - - + -
398B ARG* 3.3 25.4 - - - +
500B HEM 2.8 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B THR 5.0 3.6 - - - +
93B GLU 3.8 2.5 + - - +
94B LYS* 3.5 7.2 + - - +
96B TRP* 1.4 104.9 - - + +
98B LYS* 1.3 56.6 + - - +
100B HIS* 4.0 12.6 - - + -
101B ASN* 2.9 62.7 + - - +
242B ASP* 5.2 0.2 - - - -
244B GLU* 5.5 6.6 - - + +
397B GLN* 5.1 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 3.2 29.2 + - + +
95B ASN* 3.9 20.7 + - - +
97B LYS* 1.3 78.7 - - - +
99B ALA* 1.3 61.6 + - - +
101B ASN* 3.3 2.3 + - - +
102B ILE* 3.1 31.5 + - + +
242B ASP* 3.8 29.4 + - + +
245B THR* 4.1 6.0 - - + +
247B GLU* 2.7 38.1 + - - +
248B PRO 2.9 33.1 + - - -
249B LEU* 4.3 11.3 - - + +
250B ASP* 5.0 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.9 11.9 - - + -
95B ASN 3.2 16.0 + - - +
98B LYS* 1.3 75.4 - - - +
100B HIS* 1.4 60.0 + - - +
102B ILE* 3.3 2.1 + - - -
103B LEU* 2.8 39.5 + - + +
249B LEU* 3.8 19.1 - - + -
257B GLN* 3.2 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.6 11.7 - - + +
96B TRP* 2.8 45.4 + + + +
97B LYS* 3.6 17.3 - - - +
99B ALA* 1.4 77.4 - - - +
101B ASN* 1.3 79.8 + - - +
103B LEU* 4.9 0.2 - - - -
104B LEU* 3.0 59.9 + - + +
397B GLN* 3.9 25.7 + - + +
401B ILE* 4.7 6.2 - - + +
500B HEM 4.6 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LYS* 2.9 50.8 + - - +
98B LYS 3.3 0.9 + - - +
100B HIS* 1.3 84.3 - - - +
102B ILE* 1.3 63.2 + - - +
104B LEU* 4.5 2.3 - - - +
105B PRO* 3.4 17.3 - - - +
242B ASP* 2.9 29.0 + - - +
243B PRO* 4.0 14.8 - - + +
244B GLU* 3.4 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LYS* 3.1 20.2 + - + +
99B ALA* 3.8 4.0 - - - +
101B ASN* 1.3 75.8 - - - +
103B LEU* 1.3 67.6 - - + +
105B PRO* 3.4 12.1 - - - +
106B SER* 4.6 4.7 + - - -
236B HIS* 4.8 8.6 - - + +
237B MET* 4.9 7.0 - - + +
240B GLY* 4.4 18.2 - - - +
241B LYS* 3.7 8.3 - - - -
242B ASP* 3.4 35.0 - - + +
243B PRO* 5.3 0.7 - - - -
247B GLU 3.7 11.2 - - - +
248B PRO* 4.3 1.6 - - + -
249B LEU* 3.8 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.8 15.9 - - + -
99B ALA* 2.8 22.1 + - + +
102B ILE* 1.3 81.0 - - + +
104B LEU* 1.3 66.1 + - - +
105B PRO 3.2 3.6 - - - -
106B SER* 2.7 35.6 + - - +
107B PHE* 3.4 9.8 + - + -
233B LEU* 4.1 15.0 - - + +
236B HIS* 5.6 1.3 - - + -
237B MET* 3.6 32.8 - - + +
249B LEU* 4.9 1.3 - - + -
257B GLN* 4.2 19.1 - - + -
261B PHE* 3.8 22.9 - - + -
401B ILE* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B HIS* 3.0 47.9 + - + +
101B ASN* 4.5 2.5 - - - +
103B LEU* 1.3 74.6 - - - +
105B PRO* 1.4 68.6 - - + +
107B PHE* 3.1 14.4 + - + +
108B SER* 3.4 11.6 + - - -
401B ILE* 4.0 23.9 - - + +
----------------------------------------------------------
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