Contacts of the helix formed by residues 159 - 169 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155F VAL* 3.4 30.8 + - + +
157F SER 4.0 0.8 + - - -
158F GLN* 1.3 69.8 - - - +
160F GLY* 1.3 57.8 + - - +
162F GLY* 3.9 0.2 - - - -
163F GLU* 3.1 32.5 + - - +
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Residues in contact with GLY 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F GLN* 3.6 1.2 - - - +
159F ALA* 1.3 74.5 - - - +
161F LEU* 1.3 66.1 + - - +
163F GLU* 3.5 7.7 + - - +
164F TYR* 3.1 24.3 + - - +
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Residues in contact with LEU 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 4.0 33.9 - - + -
158F GLN* 3.7 30.0 - - + +
160F GLY* 1.3 75.9 - - - +
162F GLY* 1.3 61.2 + - - +
164F TYR* 3.2 9.5 + - + +
165F LEU* 2.9 40.0 + - + +
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Residues in contact with GLY 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 4.7 2.7 - - - -
151F ILE* 6.1 0.4 - - - -
154F LEU* 3.7 38.8 - - - +
155F VAL* 4.5 2.0 - - - -
158F GLN* 2.6 22.2 + - - +
159F ALA 3.9 0.7 - - - -
161F LEU* 1.3 71.3 - - - +
163F GLU* 1.3 62.6 + - - +
165F LEU* 3.3 0.6 + - - -
166F PHE* 3.0 25.7 + - - +
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Residues in contact with GLU 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 3.5 24.1 - - + +
91F THR* 3.8 18.1 - - - +
92F THR* 2.7 49.1 + - - +
93F LEU 5.6 0.2 - - - +
151F ILE* 5.4 1.8 - - + -
155F VAL* 4.1 15.9 - - + +
159F ALA 3.1 20.1 + - - +
160F GLY* 3.9 6.6 - - - +
162F GLY* 1.3 75.5 - - - +
164F TYR* 1.3 60.6 + - - +
166F PHE* 3.5 6.1 + - - +
167F GLU* 3.3 24.1 + - - +
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Residues in contact with TYR 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F LEU* 4.9 10.5 - - + +
160F GLY 3.1 18.3 + - - +
161F LEU* 3.6 9.2 - - + +
163F GLU* 1.3 75.9 - - - +
165F LEU* 1.3 73.8 + - + +
167F GLU* 3.5 9.1 + - - +
168F ARG* 2.9 65.9 + - + +
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Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 3.9 29.2 - - + -
164B TYR* 3.4 15.8 + - + -
165B LEU* 4.2 20.9 - - + -
154F LEU* 4.8 2.7 - - + -
161F LEU* 2.9 34.0 + - + +
162F GLY* 3.9 3.4 - - - +
164F TYR* 1.3 88.1 - - + +
166F PHE* 1.3 53.2 + - - +
168F ARG* 4.0 3.8 - - + -
169F LEU* 2.6 55.9 + - + +
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Residues in contact with PHE 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B TYR* 3.5 6.5 - - - -
92F THR* 4.1 12.8 - - + -
96F MET* 4.6 2.9 - - + -
147F HIS* 3.8 35.7 - + + -
150F ASN* 4.0 11.4 - - + -
151F ILE* 3.7 42.0 - - + -
154F LEU* 3.8 18.9 - - + +
162F GLY 3.0 18.0 + - - +
163F GLU* 3.8 6.3 - - - +
165F LEU* 1.3 74.0 - - - +
167F GLU* 1.3 59.5 + - - +
170F THR* 2.8 53.6 + - + -
171F LEU* 2.9 36.7 + - + -
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Residues in contact with GLU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ALA 5.3 0.6 - - - +
44F LEU* 4.1 22.4 - - + +
45F GLU* 3.5 9.5 + - - +
46F GLY* 2.8 34.4 + - - +
47F VAL* 4.1 17.7 - - + +
163F GLU 3.3 14.8 + - - +
164F TYR* 3.7 6.2 - - - +
166F PHE* 1.3 79.5 - - + +
168F ARG* 1.3 96.6 + - - +
171F LEU* 3.4 10.8 - - - -
172F LYS* 2.6 37.2 + - - +
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Residues in contact with ARG 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F GLU* 4.4 9.5 + - - +
164F TYR* 2.9 54.5 + - + +
165F LEU* 3.6 9.0 - - + +
167F GLU* 1.3 121.4 + - - +
169F LEU* 1.3 60.7 + - + +
172F LYS* 2.9 52.5 - - - +
173F HIS* 2.6 36.6 + - + +
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Residues in contact with LEU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B TYR* 3.5 16.2 - - + +
165B LEU* 3.7 30.1 - - + -
168B ARG* 3.3 36.6 + - + +
169B LEU* 4.3 21.5 - - + -
173B HIS* 5.8 5.5 - - + -
165F LEU* 2.6 31.0 + - + +
168F ARG* 1.3 81.8 - - + +
170F THR* 1.3 58.9 + - - +
173F HIS* 3.3 30.4 - - + +
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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