Contacts of the helix formed by residues 139 - 148 (chain E) in PDB entry 1S9D
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 ASN 139 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ASP 4.2 0.4 + - - -
138E LEU* 1.3 77.0 - - - +
140E LEU* 1.3 65.4 + - - +
141E VAL* 3.0 10.4 + - - +
142E GLN* 2.9 52.8 + - - +
143E ALA* 3.1 17.7 + - - +
171E TYR* 3.6 4.7 - - - -
233E ASN* 5.8 7.0 - - - +
234E LEU* 4.7 9.6 - - + +
237E SER* 6.3 1.0 - - - -
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Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ASN* 1.3 76.5 - - - +
141E VAL* 1.3 59.3 + - + +
143E ALA* 3.4 1.9 + - - +
144E LEU* 2.9 37.4 + - + +
167E PHE* 3.8 13.9 - - + -
171E TYR* 3.7 21.1 + - + -
179E PHE* 4.1 11.4 - - + -
185E CYS* 3.7 22.2 - - - +
188E LEU* 3.5 39.3 - - + -
189E SER* 3.6 33.7 - - - +
192E VAL* 4.7 2.9 - - + -
230E LEU* 6.4 0.2 - - + -
234E LEU* 4.2 17.0 - - + +
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Residues in contact with VAL 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E ASN* 3.0 6.7 + - - +
140E LEU* 1.3 79.4 - - - +
142E GLN* 1.3 67.4 - - + +
144E LEU* 3.1 5.4 + - - +
145E ARG* 2.9 38.2 + - + +
192E VAL* 4.0 23.8 - - + -
234E LEU* 3.5 36.2 - - + +
237E SER* 3.5 26.0 - - - +
238E ILE* 3.8 20.6 - - + -
243E PHE* 4.6 2.0 - - + -
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Residues in contact with GLN 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ASP 4.5 2.3 - - - +
138E LEU* 3.7 27.8 - - + +
139E ASN* 2.9 51.0 + - - +
141E VAL* 1.3 78.1 - - + +
143E ALA* 1.3 60.3 + - - +
145E ARG* 3.3 13.7 + - - +
146E GLN* 3.3 19.9 + - - +
237E SER* 6.1 0.7 - - - +
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Residues in contact with ALA 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E PHE* 3.5 35.9 - - + -
138E LEU* 3.9 10.2 - - + +
139E ASN 3.1 17.2 + - - +
140E LEU 3.8 2.2 - - - +
142E GLN* 1.3 71.7 - - - +
144E LEU* 1.3 66.5 + - - +
146E GLN* 3.1 3.2 + - - +
147E PHE 2.9 19.1 + - - -
167E PHE* 3.9 6.3 - - + -
171E TYR* 3.7 24.0 - - + -
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Residues in contact with LEU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E LEU* 2.9 29.0 + - + +
141E VAL* 3.7 4.0 - - - +
143E ALA* 1.3 76.2 - - - +
145E ARG* 1.3 55.4 + - - +
147E PHE* 4.3 3.6 - - + -
148E LEU* 2.8 41.9 + - + +
164E MET* 3.7 27.8 - - + -
167E PHE* 3.6 32.3 - - + -
189E SER* 4.3 15.5 - - - +
192E VAL* 3.7 34.3 - - + -
193E ILE* 4.8 1.8 - - + -
243E PHE* 3.9 15.0 - - + -
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Residues in contact with ARG 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E VAL* 2.9 31.1 + - - +
142E GLN* 3.6 14.4 - - - +
143E ALA 3.2 0.2 - - - -
144E LEU* 1.3 75.7 - - - +
146E GLN* 1.3 62.2 + - - +
148E LEU* 3.9 1.9 - - - +
149E TRP* 3.2 22.9 + - - +
237E SER* 2.9 34.6 + - - -
238E ILE* 4.0 3.6 - - - +
241E GLU* 2.7 57.2 + - - +
242E PRO 3.3 17.8 + - - -
243E PHE* 3.9 22.2 - - + +
244E LYS 4.9 0.8 - - - +
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Residues in contact with GLN 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E TYR* 4.6 6.9 + - - -
133E HIS* 3.5 25.9 - - + +
134E GLU* 3.3 38.8 + - - +
135E PHE* 4.3 4.0 - - - -
138E LEU* 3.8 13.2 - - + +
142E GLN 3.3 8.5 + - - +
143E ALA* 3.1 9.0 + - - +
145E ARG* 1.3 76.6 - - - +
147E PHE* 1.3 64.2 + - - +
149E TRP* 3.2 15.2 + - - +
150E SER* 3.6 11.8 + - - +
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Residues in contact with PHE 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E LEU* 4.6 8.3 - - + -
129E PHE* 4.4 5.4 - + - -
130E VAL* 3.7 33.7 - - + -
133E HIS* 3.8 32.3 - + - -
135E PHE* 4.0 13.0 - + + -
143E ALA 2.9 16.1 + - - +
144E LEU* 3.7 4.5 - - + +
146E GLN* 1.3 76.5 - - - +
148E LEU* 1.3 70.0 + - + +
150E SER* 3.1 19.8 + - - -
151E PHE* 3.3 45.0 - + - -
163E MET* 3.9 12.6 - - + -
164E MET* 4.2 9.2 - - + -
167E PHE* 3.7 32.3 - + + -
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Residues in contact with LEU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 4.2 14.5 - - + +
144E LEU* 2.8 24.7 + - + +
145E ARG* 3.9 3.1 - - - +
147E PHE* 1.3 89.0 - - + +
149E TRP* 1.3 58.2 + - - +
151E PHE* 3.1 41.2 - - + +
153E LEU* 4.0 22.9 - - + -
164E MET* 4.6 4.0 - - + -
193E ILE* 3.8 26.9 - - + -
243E PHE* 3.9 32.8 - - + -
244E LYS 4.7 4.8 - - - +
246E PRO* 3.9 12.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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