Contacts of the helix formed by residues 217 - 225 (chain A) in PDB entry 1F6O
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 GLY 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ARG 2.7 13.4 + - - -
215A CYS 2.7 9.3 + - - -
216A SER* 1.3 75.8 - - - +
218A PRO* 1.3 75.6 - - - +
220A LYS* 3.9 2.0 - - - +
221A LEU* 2.9 25.5 + - - +
286A SER* 4.1 3.4 - - - -
9D T 3.1 16.8 - - - -
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Residues in contact with PRO 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE 3.5 9.0 - - - +
167A CYS* 4.6 10.2 - - - -
168A MET 4.8 0.5 + - - -
180A LEU* 4.5 13.9 - - + -
181A LEU 3.5 24.2 - - - +
182A ARG* 2.9 34.4 - - + +
217A GLY* 1.3 82.4 - - - +
219A SER* 1.3 59.2 + - - +
221A LEU* 3.3 17.2 - - + +
222A CYS* 3.5 9.7 - - - -
7D YRR 4.5 2.0 - - - +
8D T 3.7 32.5 - - - +
9D T 3.3 7.9 - - - +
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Residues in contact with SER 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A TYR* 3.0 34.3 - - - +
166A PHE 3.0 21.0 + - - -
167A CYS* 4.2 2.4 - - - -
218A PRO* 1.3 77.3 - - - +
220A LYS* 1.3 66.1 + - - +
221A LEU 3.4 0.4 - - - -
222A CYS* 3.4 3.1 + - - +
223A GLN* 3.1 27.4 + - - +
8D T 3.3 24.8 + - - -
9D T 2.9 12.6 + - - -
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Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ARG* 3.9 25.7 - - - +
212A ARG* 5.5 3.6 - - - +
213A GLU* 3.9 18.5 + - - +
214A LEU 3.4 18.1 - - - +
215A CYS 4.2 0.9 - - - -
216A SER* 2.9 43.5 + - - +
217A GLY 3.1 6.9 + - - +
219A SER* 1.3 76.8 - - - +
221A LEU* 1.3 58.7 + - - +
223A GLN* 3.0 6.1 + - - +
224A ALA 2.9 24.9 + - - -
9D T 3.0 33.3 + - - +
10D G 3.5 20.6 + - - -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 5.1 2.5 - - + -
168A MET* 4.7 10.8 - - + -
181A LEU* 3.7 30.1 - - + +
182A ARG 3.6 24.7 - - - -
183A ALA* 3.6 8.5 - - - +
184A LEU* 4.0 23.3 - - + -
215A CYS* 3.8 26.3 - - + +
217A GLY 2.9 21.2 + - - +
218A PRO 3.3 7.9 - - - +
220A LYS* 1.3 78.1 - - - +
222A CYS* 1.3 70.5 + - - +
224A ALA* 4.2 2.5 - - - -
225A LEU* 2.9 34.2 + - + +
227A ILE* 5.6 1.1 - - + -
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Residues in contact with CYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A VAL* 5.1 0.2 - - - -
166A PHE* 3.5 42.8 - - + +
167A CYS 4.1 0.4 - - - -
168A MET* 3.7 32.8 - - - -
218A PRO 3.5 10.5 + - - +
219A SER 3.4 9.1 + - - +
220A LYS 3.2 0.8 - - - -
221A LEU* 1.3 85.0 - - - +
223A GLN* 1.3 61.8 + - - +
225A LEU 3.6 0.2 + - - -
226A ALA* 3.1 2.9 + - - -
227A ILE* 2.7 50.5 + - - +
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Residues in contact with GLN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A MET 4.9 3.6 + - - -
165A TYR* 3.7 29.5 - - + -
166A PHE* 5.8 7.6 - - + +
196A LEU* 3.4 19.2 - - - +
197A ARG* 3.3 34.7 + - + +
200A LEU* 3.6 50.4 + - + +
219A SER 3.1 16.0 + - - +
220A LYS 3.0 6.3 + - - +
222A CYS* 1.3 77.5 - - + +
224A ALA* 1.3 62.1 + - - +
226A ALA* 3.2 11.4 + - - +
227A ILE 5.3 0.2 - - - -
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 3.5 2.1 - - - +
193A MET* 3.5 32.4 - - + +
196A LEU* 3.1 18.6 - - - +
197A ARG* 3.8 13.6 - - + +
214A LEU 3.4 25.1 - - - +
215A CYS* 3.8 19.7 - - - -
220A LYS 2.9 8.1 + - - +
221A LEU 3.8 1.6 - - - +
223A GLN* 1.3 77.4 - - - +
225A LEU* 1.3 58.2 + - - +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.6 42.4 - - + +
109A ARG* 2.9 38.1 + - + +
117A LEU* 3.7 18.4 - - + +
119A GLY 5.2 1.3 - - - +
184A LEU* 3.8 15.0 - - + -
193A MET* 3.4 33.7 - - + -
215A CYS* 4.8 2.9 - - - -
221A LEU* 2.9 19.4 + - + +
224A ALA* 1.3 83.6 - - + +
226A ALA* 1.3 69.4 + - - +
227A ILE* 3.3 13.8 + - + +
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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