Contacts of the helix formed by residues 86 - 104 (chain D) in PDB entry 1EJI
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 THR 86 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LYS* 4.1 12.1 - - - -
73D TYR 4.2 0.9 - - - +
74D SER* 3.7 30.1 - - - -
81D ARG* 3.8 20.1 - - + +
83D TYR 4.2 17.3 + - - +
84D GLY* 4.3 1.1 - - - -
85D GLY* 1.3 78.5 + - - +
87D GLU* 1.3 55.9 + - - +
88D PHE 3.2 2.7 - - - -
89D ILE* 3.7 10.5 - - + -
90D ASP* 2.7 53.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 5.9 1.1 - - - -
85D GLY* 3.2 5.7 - - - -
86D THR* 1.3 79.6 + - - +
88D PHE* 1.3 107.6 + - + +
90D ASP* 3.5 9.1 - - - +
91D GLU* 3.3 24.7 + - + +
94D MSE 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.6 13.7 - - + +
39C LYS* 3.4 57.2 - - + -
40C GLU* 3.4 35.4 - - + +
43C ARG* 4.0 20.0 - - + -
69D LEU* 6.1 0.2 - - - -
85D GLY 4.5 0.8 + - - -
86D THR* 3.2 0.4 - - - +
87D GLU* 1.3 104.4 - - + +
89D ILE* 1.3 68.2 + - + +
90D ASP 2.9 1.6 - - - -
91D GLU* 2.9 31.5 + - - +
92D LEU* 2.9 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLU* 4.5 11.7 - - + +
69D LEU* 3.4 31.9 - - + -
72D LYS* 3.5 34.1 - - + -
74D SER* 3.4 17.9 - - - +
81D ARG* 4.1 9.0 - - - +
85D GLY 4.7 0.2 - - - +
86D THR* 3.3 15.8 + - - +
88D PHE* 1.3 76.6 - - - +
90D ASP* 1.3 57.2 + - - +
92D LEU* 3.6 6.0 - - + +
93D GLU* 2.9 29.4 + - + +
306D ASN* 3.0 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D PRO* 3.8 16.8 - - + +
81D ARG* 2.7 45.2 + - - +
86D THR* 2.7 33.2 + - - +
87D GLU* 3.5 8.4 + - - +
89D ILE* 1.3 75.7 - - - +
91D GLU* 1.3 64.7 + - - +
93D GLU* 4.0 0.4 - - - +
94D MSE 3.0 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.7 21.4 - - + +
39C LYS* 3.3 26.3 + - - -
87D GLU* 3.3 15.1 + - - +
88D PHE* 2.9 36.1 + - - +
90D ASP* 1.3 79.1 - - - +
92D LEU* 1.3 57.9 + - - +
94D MSE 3.3 11.6 + - + +
95D LEU* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 4.6 21.5 - - + -
36C ILE* 4.0 20.4 - - + +
37C ILE* 6.2 0.4 - - + -
69D LEU* 3.6 30.1 - - + -
88D PHE 2.9 8.6 + - - +
89D ILE* 3.6 10.5 - - + +
91D GLU* 1.3 79.5 - - - +
93D GLU* 1.3 61.9 + - - +
95D LEU* 3.2 5.1 + - + +
96D CYS* 3.0 22.0 + - - +
306D ASN* 3.5 31.0 - - + +
309D ILE* 4.5 8.1 - - + +
310D ALA* 3.9 22.4 - - + +
313D ALA* 4.6 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D TYR* 4.7 1.2 - - - -
78D PRO* 3.4 23.5 - - + +
81D ARG* 2.8 38.7 + - - +
89D ILE* 2.9 21.7 + - + +
90D ASP 4.0 2.0 - - - +
92D LEU* 1.3 73.4 - - - +
94D MSE 1.3 57.2 + - - +
96D CYS* 3.4 2.8 + - - +
97D GLN* 3.0 46.9 + - + +
115D VAL* 3.6 20.5 + - + +
116D GLN* 3.2 28.5 + - - +
304D PRO* 5.2 0.7 - - - +
306D ASN* 5.1 2.6 - - - +
309D ILE* 4.6 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D PRO* 3.9 27.1 - - + +
87D GLU 5.6 0.2 - - - +
90D ASP* 3.0 43.7 + - + +
91D GLU* 3.9 10.1 - - + +
93D GLU* 1.3 73.3 - - - +
95D LEU* 1.3 60.3 + - - +
97D GLN* 3.3 12.8 + - - +
98D LYS* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 3.7 31.9 - - + +
33C VAL* 3.9 18.2 - - + -
36C ILE* 4.2 10.8 - - + -
91D GLU 2.9 18.3 + - - +
92D LEU* 3.6 6.1 - - + +
94D MSE 1.3 76.6 - - - +
96D CYS* 1.3 57.9 + - - +
98D LYS* 3.2 27.3 + - - +
99D ARG* 2.9 69.8 + - - +
313D ALA* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU 3.0 15.9 + - - +
93D GLU 3.6 4.3 - - - +
95D LEU* 1.3 75.0 - - - +
97D GLN* 1.3 63.3 + - - +
99D ARG* 3.4 3.3 + - - +
100D ALA* 2.9 22.7 + - - +
115D VAL* 3.8 20.2 - - + -
309D ILE* 3.9 26.7 - - + -
312D VAL* 3.7 30.5 - - - -
313D ALA* 4.0 19.3 - - + +
316D LEU* 3.5 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D TYR* 5.3 6.5 - - - -
78D PRO* 4.5 11.9 - - - +
93D GLU* 3.0 47.7 + - - +
94D MSE 3.7 14.0 - - - +
96D CYS* 1.3 76.1 - - - +
98D LYS* 1.3 63.8 + - - +
100D ALA* 3.3 8.2 + - - +
101D LEU* 3.3 25.3 + - - +
113D VAL* 3.5 31.6 + - + +
114D ASN* 4.6 2.8 - - - +
115D VAL* 4.1 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLU* 5.1 4.6 + - - -
94D MSE 2.9 18.3 + - - +
95D LEU* 3.4 29.5 - - - +
97D GLN* 1.3 77.1 - - - +
99D ARG* 1.3 65.6 + - - +
100D ALA 3.2 0.5 + - - -
101D LEU* 3.3 7.8 + - - +
102D GLN* 3.1 55.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ASP* 2.5 40.0 + - - -
32C GLU* 3.1 25.3 + - - +
33C VAL* 3.9 3.4 - - - +
95D LEU* 2.9 50.3 + - + +
96D CYS* 3.9 0.9 - - - +
98D LYS* 1.3 75.5 - - - +
100D ALA* 1.3 56.9 + - - +
102D GLN* 3.7 14.9 - - - +
103D ALA* 2.9 32.2 + - - +
313D ALA* 2.9 35.0 + - - +
316D LEU* 3.5 14.7 - - + +
317D LYS* 3.6 17.7 - - - +
320D MSE 3.8 22.4 - - + +
----------------------------------------------------------
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 CYS 2.9 16.8 + - - +
97D GLN* 3.5 7.4 - - - +
98D LYS 3.1 0.2 - - - -
99D ARG* 1.3 79.8 - - - +
101D LEU* 1.3 62.2 + - - +
102D GLN 3.4 0.2 + - - -
104D TYR* 3.4 27.7 + - - +
113D VAL* 4.1 11.2 - - + -
115D VAL* 4.9 1.8 - - + -
266D MSE 4.2 11.2 - - - -
268D PHE* 3.8 21.2 - - + -
316D LEU* 3.2 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLN 3.3 6.0 + - - +
98D LYS* 3.3 9.0 + - - +
100D ALA* 1.3 76.2 - - - +
102D GLN* 1.3 65.0 + - + +
104D TYR 3.5 1.0 + - - -
105D HIS 3.3 2.1 + - - -
106D LEU* 2.8 64.2 + - + +
108D PRO* 3.7 28.0 - - + -
111D TRP* 3.5 31.4 - - + +
112D GLY* 4.3 4.5 - - - +
113D VAL* 3.4 28.7 - - + -
268D PHE* 3.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LYS* 3.1 47.6 + - + +
99D ARG* 3.7 15.6 - - - +
100D ALA 3.2 0.2 - - - -
101D LEU* 1.3 73.1 - - + +
103D ALA* 1.3 55.0 + - - +
104D TYR 2.6 4.9 + - - -
105D HIS* 2.5 36.6 + - - +
106D LEU 5.5 0.2 - - - -
320D MSE 3.8 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ARG 2.9 17.9 + - - +
100D ALA 3.9 3.4 - - - +
102D GLN* 1.3 74.7 - - - +
104D TYR* 1.3 67.3 + - + +
105D HIS* 3.8 7.8 + - - -
237D ALA* 3.7 28.4 - - + +
316D LEU* 3.8 24.9 - - + +
319D ALA* 5.1 2.7 - - + -
320D MSE 3.8 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ALA 3.4 15.0 + - - +
101D LEU 3.5 1.6 + - - -
102D GLN 2.6 4.8 + - - -
103D ALA* 1.3 86.4 - - + +
105D HIS* 1.3 70.3 + - - +
106D LEU* 3.2 30.6 + - + +
229D MSE 3.4 26.4 - - + +
233D SER 2.9 29.9 + - - -
236D VAL* 4.0 13.9 - - + -
237D ALA* 3.7 21.1 - - + +
245D PHE* 3.6 22.9 - + + +
259D LEU* 3.6 16.8 - - - +
266D MSE 4.9 3.1 - - + +
268D PHE* 3.8 19.3 - + - -
316D LEU* 4.6 10.1 - - + -
----------------------------------------------------------
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