Contacts of the helix formed by residues 155 - 162 (chain E) in PDB entry 5IXM
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 155 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111E PRO* 5.7 1.3 - - - -
127E GLY 5.3 1.2 + - - -
153E VAL* 3.1 7.1 + - - +
154E PHE* 1.3 84.6 + - - +
156E ALA* 1.3 61.6 + - + +
157E ALA* 3.5 10.8 - - + +
158E GLY* 4.0 13.5 - - - +
159E ASN* 2.7 35.9 + - - +
110F PRO* 6.0 1.2 - - - +
111F LEU* 5.0 8.2 - - + +
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Residues in contact with ALA 156 (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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111E PRO* 6.3 0.2 - - - +
155E THR* 1.3 76.6 - - + +
157E ALA* 1.3 59.2 + - - +
159E ASN* 3.8 3.8 - - - +
160E SER* 2.9 29.2 + - - -
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Residues in contact with ALA 157 (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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155E THR* 4.2 6.7 - - + +
156E ALA* 1.3 78.1 - - - +
158E GLY* 1.3 58.0 + - - +
160E SER* 3.1 6.8 + - - -
161E ASN* 2.9 45.1 + - - +
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Residues in contact with GLY 158 (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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153E VAL* 3.7 12.7 - - - +
155E THR* 3.4 10.7 + - - +
156E ALA 3.2 0.6 - - - -
157E ALA* 1.3 79.5 - - - +
159E ASN* 1.3 56.0 + - - +
161E ASN* 3.4 4.1 + - - +
162E ALA* 3.1 29.6 + - - +
110F PRO 5.1 0.9 - - - +
111F LEU* 3.7 32.1 - - - +
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Residues in contact with ASN 159 (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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151E PHE 3.6 12.1 - - - +
152E GLN* 4.1 6.8 - - - +
153E VAL* 3.4 37.5 + - - +
155E THR 2.7 21.3 + - - +
156E ALA* 3.9 4.3 - - - +
158E GLY* 1.3 72.3 - - - +
160E SER* 1.3 62.3 + - - +
161E ASN 3.5 0.2 + - - -
162E ALA* 3.6 11.8 + - - +
164E ARG* 5.1 7.2 + - - +
195E VAL* 4.6 14.6 - - - +
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Residues in contact with SER 160 (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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156E ALA 2.9 19.1 + - - -
157E ALA* 3.1 9.6 + - - -
159E ASN* 1.3 79.9 - - - +
161E ASN* 1.3 61.0 + - - +
162E ALA 3.8 0.2 + - - -
194E SER* 4.0 1.0 - - - -
195E VAL* 3.7 16.0 + - - +
196E ASN* 3.0 50.6 + - - +
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Residues in contact with ASN 161 (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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157E ALA* 2.9 31.6 + - - +
158E GLY* 3.8 3.4 - - - +
160E SER* 1.3 77.8 - - - +
162E ALA* 1.3 63.7 + - - +
163E TYR* 3.2 17.7 + - - -
194E SER* 4.3 1.6 - - - -
196E ASN* 2.9 30.9 + - - +
199E ASN* 2.9 19.2 + - - +
111F LEU 5.3 5.9 - - - +
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Residues in contact with ALA 162 (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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151E PHE* 4.9 13.9 - - + +
153E VAL* 3.7 21.8 - - + -
158E GLY 3.1 16.7 + - - +
159E ASN* 3.9 10.3 - - - +
160E SER 3.4 2.4 - - - -
161E ASN* 1.3 75.1 - - - +
163E TYR* 1.3 66.8 + - - +
164E ARG* 3.9 9.9 + - + +
193E THR 4.1 0.2 - - - +
194E SER* 3.6 13.7 - - - -
195E VAL* 4.8 1.4 + - - +
110F PRO 5.6 0.7 - - - +
111F LEU 5.4 7.2 - - - +
113F ALA* 5.8 4.5 - - + +
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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