Contacts of the helix formed by residues 123 - 145 (chain E) in PDB entry 2EHO
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 SER 123 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E SER* 3.4 17.9 + - - -
48E PRO* 5.6 7.6 - - - -
122E LEU* 1.3 73.6 - - - +
124E PRO* 1.3 73.4 - - - +
125E GLU* 3.3 17.2 - - - +
126E GLU* 2.9 46.3 + - - +
127E LEU* 3.0 10.2 + - - +
124F TYR* 4.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E PRO* 5.9 5.2 - - + -
122E LEU 3.7 2.7 - - - +
123E SER* 1.3 82.9 - - - +
125E GLU* 1.3 81.0 + - - +
127E LEU* 3.6 11.9 + - + +
128E ALA* 3.3 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E SER* 3.3 15.2 + - - +
124E PRO* 1.3 106.1 - - - +
126E GLU* 1.3 61.8 + - - +
128E ALA* 3.6 7.9 - - - +
129E PHE* 3.3 14.0 + - - +
124F TYR* 3.4 27.0 - - + +
127F SER* 3.9 36.0 + - - +
128F LEU* 5.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LEU* 5.0 3.5 - - - +
96E ARG* 2.6 49.3 + - - +
97E LEU* 5.2 3.6 + - + +
100E ILE* 3.7 25.4 - - + +
121E SER 3.9 0.5 - - - +
122E LEU* 3.7 8.0 - - + -
123E SER* 2.9 33.0 + - - +
125E GLU* 1.3 74.6 - - - +
127E LEU* 1.3 52.5 + - - +
128E ALA 3.0 1.6 - - - -
129E PHE* 2.6 12.4 + - - +
130E ALA* 2.6 36.4 + - - +
124F TYR* 3.5 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E LEU* 3.6 26.2 - - + -
111E GLU* 4.5 22.2 - - + +
122E LEU* 3.8 20.9 - - + +
123E SER 3.0 11.0 + - - +
124E PRO* 3.7 15.5 - - + +
126E GLU* 1.3 76.6 - - - +
128E ALA* 1.3 56.7 + - - +
130E ALA* 4.1 4.0 - - - -
131E ARG* 2.8 78.7 + - + +
1012E SO4 4.0 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E PRO 3.3 10.2 + - - +
125E GLU* 3.6 12.1 - - - +
126E GLU 3.0 1.0 - - - -
127E LEU* 1.3 78.6 - - - +
129E PHE* 1.3 58.2 + - - +
131E ARG* 3.3 8.7 + - - +
132E GLU* 2.8 46.3 + - + +
123F THR* 6.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E LEU* 3.6 28.9 - - + -
100E ILE* 3.8 16.6 - - + -
101E GLU* 3.6 38.1 - - + -
125E GLU 3.3 10.7 + - - +
126E GLU* 2.6 18.8 + - - +
128E ALA* 1.3 75.3 - - - +
130E ALA* 1.3 56.2 + - - -
132E GLU* 3.2 11.9 + - - +
133E PHE* 2.8 38.2 + + - +
117F TYR* 4.1 14.6 - + - -
120F SER* 4.0 23.7 - - - -
121F LEU* 4.0 28.9 - - + -
124F TYR* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ILE* 4.1 23.3 - - + -
104E PHE* 4.8 6.0 - - + +
107E VAL* 4.4 9.6 - - + -
108E LEU* 3.5 28.1 - - + +
122E LEU* 4.8 1.1 - - + -
126E GLU 2.6 17.5 + - - +
127E LEU* 3.6 5.8 - - - +
129E PHE* 1.3 73.9 - - - +
131E ARG* 1.3 61.7 + - - +
133E PHE* 3.3 6.9 + - - +
134E MSE 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E LEU* 3.8 15.5 - - + -
112E LYS* 6.2 2.2 - - - +
127E LEU* 2.8 68.9 + - + +
128E ALA* 3.8 6.8 - - - +
130E ALA* 1.3 72.5 - - - +
132E GLU* 1.3 63.6 + - + +
134E MSE 3.5 3.7 + - - +
135E ALA* 3.2 21.8 + - - +
1012E SO4 2.8 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E ALA* 2.8 39.5 + - + +
129E PHE* 3.6 7.3 + - - +
131E ARG* 1.3 75.0 - - + +
133E PHE* 1.3 55.7 + - - +
135E ALA* 3.1 7.2 + - - +
136E ASN* 2.8 36.1 + - - +
120F SER* 2.8 45.3 + - - +
123F THR* 4.4 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ILE* 6.0 0.2 - - + -
101E GLU* 3.5 45.8 - - + -
104E PHE* 3.4 45.5 - + + -
129E PHE* 2.8 24.4 + + + +
130E ALA* 3.4 9.9 - - - +
132E GLU* 1.3 76.9 - - - +
134E MSE 1.3 55.6 + - - +
136E ASN* 3.3 6.7 + - - +
137E THR* 3.0 39.1 + - + +
81F TYR* 5.3 2.0 - + - -
85F LEU* 6.3 3.1 - - + -
88F ARG* 5.1 1.8 - - + -
113F TRP* 3.9 22.4 - + - -
117F TYR* 3.5 26.5 - + - -
120F SER* 5.7 1.5 - - - -
6H PHE* 6.2 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E PHE* 3.9 22.6 - - + -
105E PRO* 5.0 6.1 - - - -
108E LEU* 4.1 19.7 - - + -
130E ALA 3.1 13.4 + - - +
131E ARG* 3.7 5.4 - - - +
133E PHE* 1.3 81.7 - - - +
135E ALA* 1.3 57.6 + - + +
137E THR* 3.4 5.6 + - - -
138E GLU* 2.8 74.8 + - + +
158E LEU* 3.1 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E ARG 3.2 10.6 + - - +
132E GLU* 3.1 9.7 + - - +
134E MSE 1.3 81.5 - - + +
136E ASN* 1.3 57.7 + - - +
138E GLU* 4.0 8.9 - - - +
139E SER* 2.9 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E GLU 2.8 17.9 + - - +
133E PHE* 3.6 8.4 - - - +
134E MSE 3.2 0.2 - - - -
135E ALA* 1.3 76.0 - - - +
137E THR* 1.3 65.2 + - - +
139E SER* 3.6 4.0 - - - -
140E TYR* 3.0 17.7 + - - +
113F TRP* 2.8 57.5 + - - +
116F ASN* 2.8 40.5 + - + +
117F TYR* 3.9 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E PHE* 3.8 22.3 - - + -
133E PHE* 3.0 32.1 + - + +
134E MSE 3.4 4.0 + - - -
136E ASN* 1.3 75.8 - - - +
138E GLU* 1.3 64.8 + - - +
140E TYR* 3.1 4.1 + - - +
141E LEU* 3.0 32.1 + - - +
158E LEU* 4.2 3.8 - - - +
81F TYR* 5.3 7.2 - - + -
84F LEU* 3.9 13.2 - - + -
113F TRP* 2.8 43.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E MSE 2.8 58.3 + - + +
135E ALA* 4.0 6.2 - - - +
137E THR* 1.3 79.2 + - - +
139E SER* 1.3 62.4 + - - +
141E LEU* 3.4 7.0 + - - +
142E LYS* 3.2 21.0 + - - +
156E VAL 5.4 4.5 - - - +
158E LEU* 4.4 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E ALA 2.9 21.2 + - - -
136E ASN* 3.6 5.8 - - - -
138E GLU* 1.3 77.7 - - - +
140E TYR* 1.3 61.0 + - - +
142E LYS* 3.3 3.0 + - - +
143E ASN* 2.9 35.0 + - - -
1013E SO4 3.5 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E ASN 3.0 14.4 + - - +
137E THR 3.3 7.4 - - - +
139E SER* 1.3 73.4 + - - +
141E LEU* 1.3 86.2 + - + +
142E LYS 3.1 0.3 + - - -
143E ASN* 3.2 3.9 + - - +
144E VAL* 2.9 56.8 + - + +
24F PHE* 3.9 4.9 - - - -
80F LEU* 3.7 25.6 + - + +
84F LEU* 3.7 23.6 - - + -
107F ALA* 4.8 0.3 - - - +
109F GLU* 3.5 37.5 - - + -
110F GLU* 3.0 33.8 + - + +
113F TRP* 3.7 17.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E THR* 3.0 17.9 + - - +
138E GLU* 3.7 6.1 - - - +
140E TYR* 1.3 98.2 - - + +
142E LYS* 1.3 59.8 + - - +
144E VAL* 4.9 1.3 - - - +
145E ALA* 3.3 7.1 + - - +
146E LEU* 3.1 47.8 + - + +
156E VAL* 5.5 1.6 - - + -
158E LEU* 3.9 29.6 - - + -
77F VAL* 4.8 15.3 - - + +
80F LEU* 4.0 25.1 - - + -
81F TYR* 4.7 13.5 - - + +
84F LEU* 4.5 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138E GLU 3.2 10.5 + - - +
139E SER* 3.5 7.6 - - - +
140E TYR 3.1 1.0 - - - -
141E LEU* 1.3 81.4 - - - +
143E ASN* 1.3 63.0 + - - +
144E VAL 3.4 0.2 + - - -
145E ALA 3.5 1.2 + - - -
146E LEU* 4.1 12.5 - - + +
147E LYS* 3.0 50.5 + - + +
154E GLN* 6.0 1.8 - - - +
155E LYS* 6.0 7.7 - - - +
1013E SO4 3.4 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E SER* 2.9 31.1 + - - +
140E TYR* 3.2 3.8 + - - +
142E LYS* 1.3 82.0 - - - +
144E VAL* 1.3 64.2 + - + +
147E LYS* 3.1 41.7 + - - +
148E HIS* 3.9 9.0 - - - -
1013E SO4 3.5 29.1 + - - -
109F GLU* 4.6 12.2 - - + +
1014F SO4 5.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E TYR* 2.9 56.6 + - + +
141E LEU 4.6 0.9 - - - +
143E ASN* 1.3 79.8 - - + +
145E ALA* 1.3 62.4 + - + +
148E HIS* 4.3 9.0 + - - -
24F PHE* 4.0 20.4 - - + -
29F LEU* 3.7 12.2 - - + +
33F LEU* 4.7 0.9 - - - +
80F LEU* 4.2 10.1 - - + -
109F GLU* 3.2 19.7 - - + -
1014F SO4 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E LEU 3.3 3.8 + - - -
142E LYS 3.5 0.2 + - - -
143E ASN 3.5 2.6 + - - -
144E VAL* 1.3 82.4 - - - +
146E LEU* 1.3 73.5 + - + +
147E LYS 3.2 2.5 - - - -
148E HIS* 2.9 19.9 + - - +
149E MSE 3.3 14.4 + - + +
29F LEU* 4.3 9.9 - - + -
33F LEU* 4.1 11.8 - - + +
76F THR* 4.2 11.7 - - + +
80F LEU* 3.7 26.5 - - + -
----------------------------------------------------------
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