Contacts of the helix formed by residues 209 - 219 (chain I) in PDB entry 6IY6
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 209 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194I LYS* 3.5 12.3 - - - +
195I THR 2.9 13.9 + - - -
208I GLU* 1.3 70.4 - - - +
210I GLU* 1.3 62.1 + - - -
211I GLY 3.1 3.8 - - - -
212I ASN* 2.9 21.5 + - - +
213I ILE* 3.1 13.9 + - - +
241I ILE* 6.2 0.2 - - - -
83K GLU* 3.4 24.7 - - - -
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Residues in contact with GLU 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I PRO* 3.7 20.5 - - + +
134I SER* 2.6 29.3 + - - +
135I LEU* 4.0 6.9 - - + +
194I LYS* 5.2 0.2 - - - +
195I THR* 3.9 32.3 + - + +
209I GLY* 1.3 69.2 - - - -
211I GLY* 1.3 59.5 + - - +
213I ILE* 4.0 8.3 - - - -
214I ALA* 3.0 29.5 + - - +
241I ILE* 3.4 27.1 - - + +
245I LYS* 3.0 32.9 + - - +
284I VAL* 5.2 2.2 - - - +
287I GLN* 4.7 7.8 + - - +
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Residues in contact with GLY 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209I GLY* 3.1 1.2 - - - -
210I GLU* 1.3 82.9 - - - +
212I ASN* 1.3 60.7 + - - +
214I ALA* 3.4 6.3 + - - +
215I ARG* 3.2 35.1 + - - +
237I VAL* 3.6 21.7 - - - +
241I ILE* 3.8 16.1 - - - +
280I VAL* 5.2 0.4 - - - -
83K GLU* 4.9 4.0 + - - -
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Residues in contact with ASN 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207I ILE* 3.8 18.2 - - + -
208I GLU 2.8 22.4 + - - -
209I GLY 2.9 7.1 + - - +
211I GLY* 1.3 71.7 - - - +
213I ILE* 1.3 64.4 + - - +
215I ARG* 2.7 34.4 + - - +
216I PHE* 3.4 19.8 + - - +
56K ARG* 4.9 0.7 + - - -
76K THR* 4.1 7.6 - - - +
79K ASP* 3.0 27.2 - - + +
80K HIS* 3.5 10.5 - - - +
83K GLU* 2.8 34.4 + - - +
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Residues in contact with ILE 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I ILE* 4.1 15.9 - - + -
135I LEU* 3.5 19.3 - - + -
195I THR* 3.3 40.2 - - + +
196I GLN* 3.6 5.2 - - - +
197I MET* 3.6 48.5 - - + +
207I ILE* 4.0 13.9 - - + +
209I GLY 3.1 11.3 + - - +
210I GLU* 4.0 4.7 - - - +
212I ASN* 1.3 72.0 - - - +
214I ALA* 1.3 64.6 + - - +
216I PHE* 3.2 9.2 + - - +
217I LEU* 3.0 24.9 + - + +
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Residues in contact with ALA 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I SER* 5.0 2.2 - - - -
135I LEU* 4.2 4.5 - - + -
138I LEU* 3.4 27.3 - - + +
210I GLU 3.0 21.2 + - - +
211I GLY 3.5 4.7 - - - +
213I ILE* 1.3 73.3 - - - +
215I ARG* 1.3 64.7 + - - +
217I LEU 3.4 0.7 + - - -
218I PHE 3.1 19.4 + - - -
276I VAL* 3.6 7.1 - - + +
280I VAL* 3.4 31.6 - - + -
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Residues in contact with ARG 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211I GLY* 3.2 8.9 + - - +
212I ASN* 2.7 51.2 + - - +
213I ILE 3.3 0.2 - - - -
214I ALA* 1.3 77.2 - - - +
216I PHE* 1.3 55.5 + - - +
218I PHE* 3.6 1.7 + - - +
219I SER* 2.8 39.0 + - - +
234I ASP* 3.2 55.2 + - - +
237I VAL* 3.5 28.8 - - + +
238I ASP* 3.6 13.7 + - - -
276I VAL* 3.8 13.7 - - + +
56K ARG* 3.5 21.4 - - - +
72K LEU* 5.8 0.2 - - - -
75K HIS* 5.8 4.7 - - + -
79K ASP* 3.4 23.8 - - - +
83K GLU* 5.1 1.0 + - - -
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Residues in contact with PHE 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I ILE* 4.0 21.3 - - + -
197I MET* 3.5 36.3 - - + -
199I PHE* 3.8 32.5 - + - -
204I MET* 4.7 6.1 - - + -
212I ASN 3.4 2.9 + - - +
213I ILE 3.2 8.8 + - - +
215I ARG* 1.3 76.2 - - - +
217I LEU* 1.3 72.8 + - + +
219I SER* 3.3 15.8 + - - -
220I LEU* 3.4 30.8 + - + +
72K LEU* 4.0 23.0 - - + +
73K MET* 5.2 4.3 - - + -
76K THR* 3.4 42.1 + - + +
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Residues in contact with LEU 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I ILE* 4.0 20.2 - - + -
124I ILE* 4.3 2.5 - - + -
135I LEU* 3.8 31.6 - - + +
138I LEU* 4.1 24.0 - - + -
142I LEU* 3.8 25.3 - - + +
185I PHE* 4.1 21.3 - - + -
197I MET* 4.8 1.1 - - - -
213I ILE* 3.0 20.0 + - + +
214I ALA 3.4 4.2 + - - +
216I PHE* 1.3 89.7 - - + +
218I PHE* 1.3 62.1 + - - +
220I LEU* 3.3 25.1 + - + +
221I PHE* 3.6 11.4 - - - -
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Residues in contact with PHE 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I LEU* 3.6 18.8 - - + +
141I LEU* 4.6 5.6 - - + -
214I ALA 3.1 14.7 + - - +
215I ARG 4.0 2.0 - - - +
217I LEU* 1.3 78.2 - - - +
219I SER* 1.3 52.6 + - - +
220I LEU 3.1 2.5 + - - -
221I PHE* 3.3 36.6 + + - -
222I GLY* 2.6 51.7 + - - -
223I GLN* 5.1 2.2 - - + -
225I HIS* 5.5 4.0 - + - -
274I LEU* 3.6 27.8 - - + -
275I THR* 3.6 16.4 - - + -
276I VAL* 3.6 37.2 - - + -
279I VAL* 4.4 9.6 - - + -
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Residues in contact with SER 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I ARG* 2.8 24.4 + - - +
216I PHE 3.6 6.7 - - - -
217I LEU 3.3 0.4 - - - -
218I PHE* 1.3 75.3 - - - +
220I LEU* 1.3 61.6 + - - +
221I PHE 3.2 1.6 + - - -
222I GLY* 3.9 14.1 + - - +
72K LEU* 3.6 32.1 - - - +
75K HIS* 5.2 6.4 + - - -
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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