Contacts of the helix formed by residues 95 - 107 (chain D) in PDB entry 1EN6
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 GLN 95 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D THR* 3.2 31.2 + - - +
94D LEU* 1.3 79.0 + - - +
96D GLY* 1.3 73.2 + - - +
98D LEU* 3.6 8.3 + - - +
99D LYS* 3.2 26.5 + - + -
195D ASP* 5.2 4.9 - - - +
198D ALA* 5.7 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLN* 1.3 84.3 - - - +
97D ASP* 1.3 64.6 + - - -
99D LYS* 3.6 2.6 - - - +
100D ALA* 3.1 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLN 3.7 0.2 + - - -
96D GLY* 1.3 70.8 - - - -
98D LEU* 1.3 57.3 + - - +
100D ALA* 3.2 9.0 + - - +
101D ALA* 2.9 29.6 + - - +
201D PHE* 3.7 18.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU* 3.6 20.9 - - + -
95D GLN 3.6 7.4 + - - +
96D GLY 3.3 1.0 + - - -
97D ASP* 1.3 77.1 - - - +
99D LYS* 1.3 64.8 + - - +
101D ALA* 3.1 3.6 + - - +
102D ILE* 2.9 38.8 + - + +
131D LEU* 5.0 2.5 - - + -
138D LEU* 4.4 8.5 - - + -
163D ILE* 4.6 11.2 - - + -
194D TRP* 3.8 12.3 - - + +
197D ALA* 3.8 28.7 - - + -
198D ALA* 3.8 21.5 - - + +
201D PHE* 3.8 36.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU* 3.7 32.6 + - + +
95D GLN* 3.2 35.7 + - + +
96D GLY 3.6 2.2 - - - +
98D LEU* 1.3 78.3 - - - +
100D ALA* 1.3 62.5 + - - +
102D ILE* 3.2 2.8 + - - +
103D GLU* 3.0 56.5 + - - +
109D VAL* 4.3 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLY 3.1 12.7 + - - +
97D ASP* 3.4 12.8 - - - +
98D LEU 3.2 0.2 - - - -
99D LYS* 1.3 78.4 - - - +
101D ALA* 1.3 56.8 + - - +
103D GLU* 3.4 11.8 + - - +
104D ARG* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ASP 2.9 11.1 + - - +
98D LEU 3.5 3.8 - - - +
100D ALA* 1.3 75.3 - - - +
102D ILE* 1.3 57.6 + - - +
104D ARG* 3.2 23.5 + - - +
105D ASP* 2.9 35.2 + - - +
138D LEU* 3.8 13.5 - - + -
201D PHE* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU* 3.8 31.6 - - + -
98D LEU* 2.9 26.4 + - + +
99D LYS* 3.5 6.7 - - - +
101D ALA* 1.3 77.1 - - - +
103D GLU* 1.3 55.1 + - - +
104D ARG 3.2 0.2 + - - -
106D PHE* 2.7 44.6 + - + +
108D SER 4.2 6.1 - - - +
109D VAL* 4.2 10.8 - - + -
112D PHE* 3.5 44.9 - - + -
131D LEU* 4.9 5.4 - - + -
138D LEU* 3.7 18.6 - - + -
194D TRP* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LYS* 3.0 47.8 + - - +
100D ALA* 3.9 9.7 - - - +
102D ILE* 1.3 75.0 - - - +
104D ARG* 1.3 57.3 + - - +
107D GLY* 2.8 36.8 + - - +
108D SER* 3.9 12.0 - - - +
109D VAL* 4.2 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ALA 2.9 19.1 + - - +
101D ALA* 3.4 20.3 + - - +
102D ILE 3.1 0.2 - - - -
103D GLU* 1.3 79.6 - - - +
105D ASP* 1.3 86.9 + - - +
107D GLY* 4.2 2.1 + - - -
136D ASP* 2.9 34.3 + - - +
138D LEU* 5.0 1.0 - - - +
201D PHE* 5.2 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ALA 2.9 16.6 + - - +
104D ARG* 1.3 107.7 + - - +
106D PHE* 1.3 73.0 + - + +
107D GLY 3.7 0.2 - - - -
137D LYS* 3.8 14.0 - - - +
138D LEU* 3.1 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ILE* 2.7 27.5 + - + +
105D ASP* 1.3 79.7 - - + +
107D GLY* 1.3 58.1 + - - +
108D SER 3.1 13.9 - - - +
111D ASN* 3.1 24.2 + - + +
112D PHE* 3.7 37.2 - + + +
115D GLU* 4.6 15.9 - - + -
131D LEU* 4.3 3.6 - - + -
138D LEU* 3.7 42.6 - - + -
139D ALA* 3.8 13.7 - - - -
140D VAL* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D GLU* 2.8 26.9 + - - +
104D ARG 4.2 2.5 + - - -
105D ASP 3.7 1.2 - - - -
106D PHE* 1.3 76.4 - - - +
108D SER* 1.3 61.5 + - - +
111D ASN* 3.6 5.8 - - - -
----------------------------------------------------------
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