Contacts of the helix formed by residues 92 - 111 (chain D) in PDB entry 1EGE
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 92 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ALA* 3.8 15.9 + - + +
91D CYS* 1.3 71.1 - - - +
93D GLY* 1.3 56.6 + - - +
95D GLN* 3.8 7.4 - - - -
96D THR* 2.8 36.7 + - - -
217D GLN* 3.6 9.1 + - - -
262D GLY 4.1 4.0 - - - +
266D LEU* 3.9 31.3 - - + +
364D LYS* 4.6 1.6 - - - +
368D ASP* 2.7 36.6 + - - +
372D TYR* 3.4 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D CYS* 3.1 12.9 - - - -
92D THR* 1.3 82.1 + - - +
94D VAL* 1.3 57.1 + - - +
97D ALA* 2.9 26.3 + - - +
217D GLN* 3.9 23.9 - - - +
219D CYS* 3.7 15.5 - - - -
220D SER* 3.7 9.8 + - - -
368D ASP* 4.1 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D PHE* 5.5 1.6 - - + -
35D ILE* 3.7 31.4 - - + -
49D PRO* 3.9 19.5 - - + -
52D LEU* 4.4 24.2 - - + +
53D ILE* 4.6 9.0 - - + -
87D LEU* 6.1 1.3 - - + -
91D CYS* 3.5 30.2 - - + +
93D GLY* 1.3 69.6 - - - +
95D GLN* 1.3 68.3 + - - +
97D ALA* 3.0 9.3 + - - +
98D ILE* 3.0 29.5 + - + +
219D CYS* 3.6 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D SER* 3.4 34.5 - - - +
87D LEU* 3.7 13.8 - - + +
88D ALA* 3.5 13.0 - - - +
91D CYS 3.1 21.9 + - - +
92D THR* 3.8 6.7 - - - +
94D VAL* 1.3 82.3 - - - +
96D THR* 1.3 71.6 + - - +
98D ILE* 3.3 9.9 + - - +
99D GLU* 2.8 57.4 + - - +
258D VAL 5.6 0.8 + - - -
259D VAL* 6.4 0.2 - - - +
262D GLY* 4.5 6.8 - - - -
372D TYR* 4.4 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D THR 2.8 23.5 + - - -
93D GLY 3.8 1.8 - - - -
95D GLN* 1.3 84.1 + - - +
97D ALA* 1.3 64.6 + - - +
99D GLU* 2.9 6.3 + - + +
100D GLY* 2.8 22.0 + - - -
168D THR* 4.1 13.6 - - + +
217D GLN* 3.7 15.3 + - - +
220D SER* 3.6 15.9 - - - +
372D TYR* 4.2 2.9 + - - -
375D TYR* 3.0 32.8 + - + +
399D FAD 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR* 4.6 8.5 - - + -
49D PRO* 4.6 3.1 - - + -
53D ILE* 4.2 15.3 - - + -
93D GLY 2.9 15.4 + - - +
94D VAL* 3.1 15.5 - - - +
96D THR* 1.3 78.9 - - - +
98D ILE* 1.3 61.9 + - - +
100D GLY* 3.1 8.1 + - - -
101D ASN* 4.1 3.6 + - - -
130D MET* 4.9 0.6 - - - +
169D ASN* 3.2 41.0 - - - +
220D SER* 4.2 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ILE* 3.9 19.1 - - + -
56D ALA* 4.6 8.5 - - + -
61D LEU 3.3 26.7 - - - +
62D MET* 3.2 38.1 - - + +
87D LEU* 3.4 26.7 - - + -
94D VAL* 3.0 19.1 + - + +
95D GLN* 3.3 13.9 - - - +
97D ALA* 1.3 70.6 - - - +
99D GLU* 1.3 67.8 + - - +
100D GLY 3.0 5.9 + - - -
101D ASN* 3.4 25.2 + - - +
102D SER* 3.9 6.2 + - - -
130D MET* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D HIS* 5.9 0.3 - - - -
80D ALA* 4.7 4.4 - - - +
84D SER* 3.4 7.4 - - - -
95D GLN* 2.8 43.7 + - - +
96D THR* 2.9 6.7 + - - +
98D ILE* 1.3 80.7 - - - +
100D GLY* 1.3 65.4 + - - +
101D ASN 3.3 0.2 - - - -
102D SER* 3.1 30.2 + - - -
103D LEU* 3.1 27.4 + - + +
255D THR* 6.1 3.6 - - + -
258D VAL* 3.3 37.3 - - + +
259D VAL* 5.7 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D THR* 2.8 11.9 + - - -
97D ALA 3.1 7.8 + - - -
98D ILE 3.0 1.6 - - - -
99D GLU* 1.3 77.2 - - - +
101D ASN* 1.3 66.4 + - - +
103D LEU* 3.1 13.5 + - - +
104D GLY 3.0 15.4 + - - -
131D CYS 3.9 9.8 - - - +
132D ALA* 5.0 1.9 - - - -
133D TYR* 5.0 1.2 + - - +
168D THR* 4.8 18.4 - - - -
169D ASN* 5.2 1.3 - - - -
399D FAD 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D MET* 3.7 17.8 - - - -
63D ASN* 3.5 19.5 - - - +
97D ALA 4.1 1.2 + - - -
98D ILE* 3.4 13.7 + - - +
99D GLU 3.3 0.4 - - - -
100D GLY* 1.3 72.8 - - - +
102D SER* 1.3 53.1 + - - +
104D GLY 2.7 24.6 + - - -
105D GLN* 2.7 22.8 + - - +
124D MET* 3.2 6.2 - - - +
129D LEU 4.3 1.7 + - - -
130D MET* 3.0 37.4 - - - +
131D CYS* 2.7 45.4 + - - -
169D ASN* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ASN* 4.6 13.4 + - - -
64D THR* 5.3 1.2 + - - -
65D HIS* 4.8 20.1 - - - -
98D ILE 3.9 6.8 + - - -
99D GLU* 3.1 26.6 + - - -
100D GLY 3.5 0.4 - - - -
101D ASN* 1.3 75.9 - - - +
103D LEU* 1.3 57.3 + - - +
105D GLN* 2.9 16.1 + - - +
106D MET* 2.9 37.6 + - - +
109D ILE* 5.5 0.8 - - - +
255D THR* 5.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D GLU* 3.1 16.1 + - + +
100D GLY* 3.1 16.1 + - - +
101D ASN 2.9 0.6 + - - -
102D SER* 1.3 80.2 - - - +
104D GLY* 1.3 61.1 + - - +
106D MET* 3.8 3.3 - - - +
107D PRO* 3.3 14.9 - - - +
133D TYR* 3.5 41.5 - - + -
168D THR* 6.4 0.4 - - - -
251D ALA* 5.3 1.2 - - - +
252D PHE* 5.6 5.4 - - + -
255D THR* 3.8 29.2 + - + +
259D VAL* 5.6 3.8 - - + -
376D GLU* 3.7 35.4 - - + +
399D FAD 4.9 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D GLY 3.0 8.1 + - - -
101D ASN 2.7 12.2 + - - -
103D LEU* 1.3 72.7 - - - +
105D GLN* 1.3 57.5 + - - -
106D MET 3.5 0.2 - - - -
107D PRO* 3.3 11.3 - - - +
108D ILE* 3.8 2.6 - - - +
131D CYS* 4.6 1.1 - - - -
132D ALA 4.2 4.7 - - - -
133D TYR* 3.7 29.8 - - - +
175D TRP* 3.5 17.3 - - - -
177D PHE* 3.7 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ASN* 3.2 31.9 + - - +
66D ILE* 3.7 19.8 - - - +
101D ASN 2.7 18.3 + - - +
102D SER* 2.9 27.0 + - - +
104D GLY* 1.3 72.3 - - - +
106D MET* 1.3 66.8 + - - +
107D PRO* 3.2 2.7 - - - -
108D ILE* 2.9 15.9 + - - +
109D ILE* 2.9 27.0 + - + +
121D LEU* 5.1 4.6 - - + +
124D MET* 3.3 24.2 - - - +
131D CYS* 3.3 13.9 - - - -
175D TRP* 3.4 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D HIS* 4.2 26.9 - - + +
102D SER* 2.9 19.5 + - - +
103D LEU 3.8 4.0 - - - +
105D GLN* 1.3 75.0 - - - +
107D PRO* 1.3 68.3 - - + +
108D ILE 3.1 0.3 + - - -
109D ILE* 3.2 32.9 + - + +
110D ILE* 3.0 37.6 + - + +
251D ALA* 3.1 33.4 - - + +
254D LYS* 3.4 36.1 - - + +
255D THR* 3.8 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LEU 3.3 15.0 - - - +
104D GLY 3.3 5.6 - - - +
105D GLN 3.3 4.3 - - - -
106D MET* 1.3 92.7 - - + +
108D ILE* 1.3 56.3 + - - +
110D ILE* 3.5 7.9 - - + +
111D ALA* 3.1 32.4 + - - +
133D TYR* 4.0 8.1 - - + -
177D PHE* 3.6 53.6 - - + -
238D LEU* 3.5 3.8 - - - +
247D VAL* 3.7 8.0 - - + +
248D ALA* 5.2 0.2 - - - -
251D ALA* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D GLY 3.8 10.1 - - - +
105D GLN 2.9 5.4 + - - +
107D PRO* 1.3 73.8 - - + +
109D ILE* 1.3 64.6 + - - +
110D ILE 2.9 2.3 + - - -
111D ALA 2.9 0.2 + - - -
112D GLY* 2.7 34.1 + - - -
116D GLN* 4.6 7.2 - - + +
117D LYS* 3.9 21.8 - - + +
120D TYR* 5.3 1.8 - - + -
121D LEU* 3.5 24.0 - - + -
175D TRP* 3.1 44.6 - - + -
177D PHE* 5.2 6.1 - - + -
198D ILE* 3.3 22.7 - - + -
238D LEU* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D HIS* 3.9 29.2 - - + +
66D ILE* 4.1 15.9 - - + +
67D PRO* 4.1 18.5 - - + +
102D SER* 5.5 0.9 - - - +
105D GLN* 2.9 34.6 + - + +
106D MET* 3.6 27.6 - - + +
108D ILE* 1.3 75.5 - - - +
110D ILE* 1.3 59.0 + - + +
117D LYS* 4.3 22.1 + - - +
121D LEU* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D MET* 3.0 37.3 + - + +
107D PRO* 3.5 5.4 - - + +
109D ILE* 1.3 82.2 - - + +
111D ALA* 1.3 60.6 + - + +
112D GLY 3.5 1.7 - - - +
239D ILE* 5.4 1.2 - - - +
246D LYS 5.4 0.2 - - - +
247D VAL* 3.7 36.1 - - + +
250D GLY* 4.1 6.7 - - - -
251D ALA* 4.0 12.6 - - + +
254D LYS* 4.4 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D PRO 3.1 16.4 + - - +
108D ILE 2.9 2.4 + - - -
110D ILE* 1.3 79.7 - - + +
112D GLY* 1.3 61.0 + - - +
113D ASN 4.0 0.2 + - - -
238D LEU* 3.3 32.9 - - + +
239D ILE* 3.6 31.3 - - + +
247D VAL* 3.7 19.1 - - + -
----------------------------------------------------------
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