Contacts of the helix formed by residues 159 - 169 (chain C) in PDB entry 1IES
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 ALA 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C VAL* 3.6 29.3 + - + +
158C GLN* 1.3 75.6 - - - +
160C GLY* 1.3 58.1 + - - +
162C GLY* 3.7 0.3 - - - -
163C GLU* 3.0 32.1 + - - +
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Residues in contact with GLY 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLN* 5.3 1.0 - - - +
159C ALA* 1.3 77.1 - - - +
161C LEU* 1.3 57.6 - - - +
163C GLU* 3.5 7.8 + - - +
164C TYR* 3.0 29.6 + - - +
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Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLN* 4.1 22.8 - - + +
160C GLY* 1.3 73.8 - - - +
162C GLY* 1.3 57.6 + - - +
164C TYR* 3.2 9.6 + - + +
165C LEU* 2.8 47.5 + - + +
161E LEU* 4.0 33.4 - - + -
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Residues in contact with GLY 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ILE* 6.0 0.7 - - - -
154C LEU* 3.6 35.9 - - - +
155C VAL* 4.4 2.5 - - - -
158C GLN 2.8 23.9 + - - -
159C ALA 3.7 0.7 - - - -
161C LEU* 1.3 72.1 - - - +
163C GLU* 1.3 62.2 + - - +
165C LEU 4.5 0.2 - - - -
166C PHE* 3.0 26.7 + - - +
161E LEU* 4.6 3.3 - - - +
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Residues in contact with GLU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 3.6 22.6 - - + +
91C THR* 3.8 19.7 - - - +
92C THR* 2.7 48.3 + - - +
93C LEU 5.7 0.7 - - - +
151C ILE* 5.4 2.7 - - + -
155C VAL* 4.2 14.6 - - + +
159C ALA 3.0 15.3 + - - +
160C GLY* 3.8 9.8 - - - +
162C GLY* 1.3 74.6 - - - +
164C TYR* 1.3 64.1 + - - +
166C PHE* 4.0 4.9 - - - +
167C GLU* 3.2 24.8 + - - +
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Residues in contact with TYR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 4.8 9.6 - - + +
160C GLY 3.0 17.2 + - - +
161C LEU* 3.2 10.5 + - + +
163C GLU* 1.3 77.7 - - - +
165C LEU* 1.3 71.7 + - + +
167C GLU* 3.4 8.1 + - - +
168C ARG* 2.9 66.8 + - + +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C LEU* 4.8 1.8 - - + -
161C LEU* 2.8 39.1 + - + +
162C GLY* 4.0 3.4 - - - +
164C TYR* 1.3 83.9 - - + +
166C PHE* 1.3 56.5 + - - +
168C ARG* 4.0 3.6 - - + -
169C LEU* 2.6 56.3 + - + +
161E LEU* 3.9 26.7 - - + -
164E TYR* 3.4 16.5 + - + -
165E LEU* 4.4 19.1 - - + -
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Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C THR* 4.3 11.0 - - + -
96C MET* 4.8 2.0 - - + -
147C HIS* 3.7 30.7 - + + -
150C ASN* 3.9 21.5 - - + -
151C ILE* 3.7 36.8 - - + -
154C LEU* 3.6 18.9 - - + +
162C GLY 3.0 17.0 + - - +
163C GLU* 4.0 5.4 - - - +
165C LEU* 1.3 71.8 - - - +
167C GLU* 1.3 67.9 + - + +
170C THR* 2.9 49.9 + - + -
171C LEU* 2.9 37.3 + - + -
164E TYR* 3.5 7.2 + - - -
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Residues in contact with GLU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA 5.3 0.6 - - - +
44C LEU* 4.1 25.3 - - + +
45C GLU* 3.5 10.3 + - - +
46C GLY* 2.8 36.3 + - - +
47C VAL* 4.1 13.9 - - + +
163C GLU 3.2 15.8 + - - +
164C TYR* 3.7 5.6 - - - +
166C PHE* 1.3 80.3 - - + +
168C ARG* 1.3 96.4 + - - +
171C LEU* 3.3 11.0 - - - -
172C LYS* 2.6 35.0 + - - +
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Residues in contact with ARG 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C GLU* 4.2 7.5 + - - +
164C TYR* 2.9 54.9 + - + +
165C LEU* 3.5 9.0 - - + +
167C GLU* 1.3 122.6 + - - +
169C LEU* 1.3 61.1 + - + +
172C LYS* 3.0 54.0 + - - +
173C HIS* 2.6 35.6 + - + +
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C LEU* 2.6 34.3 + - + +
168C ARG* 1.3 84.6 - - + +
170C THR* 1.3 59.6 + - - +
173C HIS* 3.3 30.7 - - + +
164E TYR* 3.5 14.4 - - + +
165E LEU* 3.7 30.3 - - + -
168E ARG* 3.3 34.1 + - + +
169E LEU* 4.5 19.5 - - + -
173E HIS* 5.9 5.3 - - + -
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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