Contacts of the helix formed by residues 131 - 146 (chain E) in PDB entry 3EBL
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 131 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ASP* 2.7 26.9 + - - -
51E ARG 3.4 8.7 - - - -
52E ARG* 3.9 1.8 - - - -
127E SER* 3.4 6.8 - - - -
128E SER* 2.7 32.9 + - - -
130E SER* 1.3 76.8 + - - +
132E THR* 1.3 67.7 + - - +
133E ILE* 3.2 6.1 - - - -
134E TYR* 2.8 20.3 + - - +
135E ASP 2.8 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ARG* 2.8 47.6 + - - +
52E ARG 3.4 18.7 - - - -
53E VAL* 3.6 6.5 - - + +
130E SER 3.2 3.2 + - - -
131E SER* 1.3 70.7 - - - +
133E ILE* 1.3 54.3 + - - +
135E ASP* 3.6 6.4 - - - +
136E SER* 2.8 33.6 + - - -
701E PO4 3.7 15.0 - - - +
48F TYR* 3.8 34.3 + - + +
49F LEU* 4.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU* 4.6 6.1 - - + -
27E PHE* 3.7 37.5 - - + -
51E ARG* 4.2 15.9 + - - +
127E SER* 4.8 2.0 - - - +
131E SER* 4.6 7.6 - - - -
132E THR* 1.3 76.2 - - - +
134E TYR* 1.3 79.3 - - + +
136E SER* 3.8 2.8 - - - -
137E LEU* 3.2 24.4 + - - +
330E LEU* 3.8 28.5 - - + +
401E GA4 3.5 32.5 - - + +
701E PO4 3.9 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E TYR* 4.7 0.4 - - - -
118E PHE* 3.6 25.8 - + + -
120E HIS* 3.4 21.3 - - + -
121E GLY* 3.3 17.0 + - - -
127E SER* 3.7 19.7 - - - -
128E SER 4.2 9.0 - - - +
129E ALA* 4.8 4.3 - - - +
131E SER* 2.8 11.0 + - - +
133E ILE* 1.3 98.9 - - + +
135E ASP* 1.3 58.8 + - - +
136E SER 3.3 0.2 - - - -
137E LEU* 3.7 8.6 - - + +
138E CYS* 2.9 35.1 + - - -
151E SER* 5.4 1.3 - - - +
197E ASP* 2.7 38.8 + - - -
330E LEU* 4.3 11.9 - - + -
401E GA4 2.7 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E VAL* 3.5 21.3 - - + +
54E PRO 4.9 0.9 - - - +
65E SER* 4.7 2.1 + - - -
79E ARG* 3.0 19.5 + - - +
81E TYR* 2.7 34.6 + - - +
129E ALA 4.3 4.5 + - - +
131E SER 2.8 11.5 + - - +
132E THR 3.6 5.2 - - - +
134E TYR* 1.3 75.5 - - - +
136E SER* 1.3 56.9 + - - +
138E CYS* 3.3 2.4 + - - +
139E ARG* 2.8 56.3 + - - +
48F TYR* 2.8 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E THR 2.8 21.0 + - - -
133E ILE 3.8 4.5 - - - -
135E ASP* 1.3 72.4 - - - +
137E LEU* 1.3 56.5 + - - +
139E ARG* 3.2 8.8 + - - +
140E ARG* 2.9 43.2 + - - +
330E LEU 5.2 1.4 + - - -
701E PO4 3.6 28.0 + - - -
48F TYR* 3.0 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E PHE* 3.7 34.5 - - + -
133E ILE 3.2 16.3 + - - +
134E TYR* 3.7 14.1 - - + +
135E ASP 3.3 0.2 - - - -
136E SER* 1.3 78.5 - - - +
138E CYS* 1.3 58.3 + - - +
140E ARG* 3.1 13.0 + - - +
141E PHE* 2.9 59.3 + - + -
224E LEU* 5.1 3.1 - - + -
329E TYR* 3.7 44.0 - - + +
330E LEU* 4.6 3.1 - - + -
341E MET* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E TYR* 3.4 36.8 - - + -
118E PHE* 3.6 30.5 - - - -
134E TYR 2.9 24.3 + - - +
135E ASP 3.7 0.2 - - - +
137E LEU* 1.3 72.7 - - - +
139E ARG* 1.3 61.1 + - - +
141E PHE* 3.3 11.8 + - - +
142E VAL* 2.9 33.4 + - - +
149E VAL* 3.7 19.0 - - + +
151E SER* 3.8 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ASN* 4.7 10.3 + - - +
58E ARG 5.6 0.6 + - - -
60E LEU* 3.6 34.6 + - - +
63E VAL* 2.9 43.7 + - + +
65E SER* 3.4 26.8 + - - +
81E TYR* 4.0 12.1 - - + -
135E ASP* 2.8 39.6 + - - +
136E SER* 3.2 9.6 + - - +
138E CYS* 1.3 76.8 - - - +
140E ARG* 1.3 60.4 + - + +
142E VAL* 3.3 9.2 + - - +
143E LYS* 3.3 28.9 + - + +
48F TYR* 3.7 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E SER* 2.9 30.7 + - - +
137E LEU* 3.1 14.3 + - + +
139E ARG* 1.3 75.5 - - + +
141E PHE* 1.3 62.6 + - + +
143E LYS* 3.2 12.4 + - + +
144E LEU* 2.9 32.3 + - + +
329E TYR 5.2 1.0 + - - -
330E LEU 4.9 8.7 + - - -
332E PRO* 4.9 9.7 - - - +
337E TYR* 2.9 40.2 + - - -
341E MET* 4.7 10.5 - - + -
701E PO4 5.7 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E ILE* 4.2 25.1 - - + -
118E PHE* 4.3 15.3 - + - -
137E LEU* 2.9 47.5 + - + -
138E CYS* 3.4 13.2 - - - +
140E ARG* 1.3 73.8 - - + +
142E VAL* 1.3 62.9 + - - +
144E LEU* 4.0 15.0 - - + +
145E SER* 2.7 32.3 + - - -
149E VAL* 3.7 15.3 - - + -
195E SER* 4.0 18.2 - - - -
222E ILE* 5.4 2.9 - - + -
224E LEU* 4.3 11.4 - - + -
341E MET* 4.3 9.4 - - + -
344E ILE* 3.9 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E VAL* 3.7 22.7 - - + -
81E TYR* 3.4 42.8 - - + +
83E ALA* 3.9 23.8 - - + +
138E CYS 2.9 14.6 + - - +
139E ARG 3.6 7.2 - - - +
140E ARG 3.3 0.2 - - - -
141E PHE* 1.3 74.2 - - - +
143E LYS* 1.3 65.5 + - - +
145E SER* 3.6 4.7 + - - -
146E LYS* 3.0 25.4 + - - -
147E GLY 3.8 15.0 - - - +
149E VAL* 3.7 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLU* 4.3 17.9 - - + +
63E VAL* 4.1 14.8 - - + -
139E ARG* 3.3 15.9 + - + +
140E ARG* 3.2 13.9 + - + +
142E VAL* 1.3 77.4 - - - +
144E LEU* 1.3 58.9 + - - +
146E LYS* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E ARG* 2.9 13.4 + - + +
141E PHE* 4.0 17.5 - - + +
142E VAL 3.3 0.2 - - - -
143E LYS* 1.3 80.1 - - - +
145E SER* 1.3 58.8 + - - +
146E LYS* 3.6 9.4 - - - +
341E MET* 3.2 43.7 - - + +
344E ILE* 3.9 21.1 - - + -
345E SER* 3.0 52.4 + - - +
348E LEU* 4.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 145 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E PRO* 3.4 24.9 - - - +
116E ILE* 3.9 10.2 - - - +
141E PHE 2.7 21.8 + - - -
142E VAL* 3.6 1.9 + - - -
144E LEU* 1.3 77.4 - - - +
146E LYS* 1.3 71.0 + - - +
147E GLY* 3.0 18.6 + - - -
148E VAL 4.6 0.3 + - - -
149E VAL* 5.1 0.7 - - - +
348E LEU* 3.6 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E PHE* 4.1 12.0 - - - +
114E PRO* 4.6 0.2 - - - -
142E VAL* 3.0 12.1 + - - -
143E LYS* 2.8 24.4 + - - +
144E LEU* 4.2 9.8 + - - +
145E SER* 1.3 78.4 - - - +
147E GLY* 1.3 58.7 + - - +
----------------------------------------------------------
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