Contacts of the helix formed by residues 202 - 210 (chain I) in PDB entry 6AHU
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 ASP 202 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TRP* 4.4 5.9 - - - +
81E LEU* 4.1 9.7 - - - +
82E PRO* 3.3 45.0 - - - +
97E PHE 5.6 3.9 - - - +
98E PHE* 6.0 0.8 - - + -
99E ASN* 3.2 27.2 + - - +
198I ARG* 3.3 17.6 - - + +
199I GLY 3.4 18.8 + - - +
200I PRO 3.2 1.2 - - - -
201I TYR* 1.3 76.7 - - - +
203I VAL* 1.3 63.5 + - - +
204I ALA 3.5 0.2 + - - -
205I ASN* 3.6 5.1 + - - +
206I LEU* 3.3 20.1 + - - +
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Residues in contact with VAL 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I LEU* 4.1 18.8 - - + -
30I TYR* 4.2 4.3 - - + +
156I TYR* 4.2 15.3 - - - +
187I ILE* 3.8 31.1 - - + +
198I ARG* 4.9 4.7 - - + -
199I GLY 3.4 17.7 + - - +
200I PRO* 4.1 8.7 - - + +
201I TYR 3.3 0.8 - - - -
202I ASP* 1.3 79.3 - - - +
204I ALA* 1.3 54.1 + - - +
206I LEU* 4.0 7.0 - - + -
207I GLY* 2.8 32.2 + - - -
217I ALA 4.8 2.4 - - - +
221I VAL* 3.9 29.4 - - + -
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Residues in contact with ALA 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E TRP* 4.4 12.0 - - + -
4I PHE* 5.7 2.7 - - + -
200I PRO 4.5 1.9 + - - +
201I TYR* 3.4 19.4 + - + +
202I ASP 3.2 1.0 - - - -
203I VAL* 1.3 78.4 - - - +
205I ASN* 1.3 58.5 + - - +
208I LEU* 3.7 17.3 + - - +
217I ALA* 4.0 19.6 - - - +
218I LYS* 4.3 26.6 + - + +
221I VAL* 5.4 2.8 - - + +
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Residues in contact with ASN 205 (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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75E GLN* 3.5 10.5 + - - +
78E TRP* 3.1 48.6 - - + +
79E SER* 3.1 39.3 + - - -
201I TYR 4.1 2.0 + - - -
202I ASP 3.6 6.1 + - - +
203I VAL 3.3 0.2 - - - -
204I ALA* 1.3 76.7 - - - +
206I LEU* 1.3 55.1 + - - +
207I GLY 3.3 0.4 - - - -
208I LEU* 3.5 29.9 - - - +
209I LEU* 2.6 34.6 + - - +
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Residues in contact with LEU 206 (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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79E SER* 5.4 0.9 - - - +
82E PRO* 4.2 30.7 - - + +
83E PHE* 5.3 8.1 - - + -
156I TYR* 3.6 48.9 - - + +
187I ILE* 4.3 6.3 - - + -
198I ARG* 4.8 2.2 - - + -
202I ASP* 3.3 19.2 + - - +
203I VAL* 3.1 7.7 + - + +
205I ASN* 1.3 77.1 - - - +
207I GLY* 1.3 57.5 + - - +
209I LEU* 3.4 18.3 - - + +
210I PHE* 3.1 50.9 + - + -
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Residues in contact with GLY 207 (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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187I ILE* 3.8 18.9 - - - +
203I VAL 2.8 18.6 + - - -
206I LEU* 1.3 72.7 - - - +
208I LEU* 1.3 56.3 + - - +
210I PHE* 3.2 10.0 + - - +
211I GLY 2.9 26.6 + - - +
212I LEU* 4.3 7.2 - - - +
217I ALA* 3.9 17.1 - - - +
220I ALA* 6.2 0.4 - - - -
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Residues in contact with LEU 208 (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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75E GLN* 4.2 33.7 - - + +
78E TRP* 6.2 3.4 - - + -
204I ALA 3.7 13.9 + - - +
205I ASN* 3.1 28.0 + - - +
207I GLY* 1.3 73.7 - - - +
209I LEU* 1.3 61.2 + - - +
211I GLY* 2.9 23.6 + - - -
213I SER 4.3 13.5 - - - +
214I GLU* 4.2 22.7 - - + +
217I ALA* 3.9 5.8 - - + +
8L ARG* 6.6 0.4 - - - -
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Residues in contact with LEU 209 (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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40E VAL* 5.5 1.8 - - + -
41E HIS* 5.0 12.3 - - + +
79E SER* 3.4 28.5 - - - +
82E PRO* 5.5 1.6 - - + -
83E PHE* 3.7 34.1 - - + -
55H VAL* 3.8 33.3 - - + +
170I ILE* 3.7 13.2 - - + +
205I ASN* 2.6 19.4 + - - +
206I LEU* 3.4 20.6 - - + +
208I LEU* 1.3 75.5 - - - +
210I PHE* 1.3 65.9 + - + +
211I GLY 3.5 0.3 + - - -
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Residues in contact with PHE 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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83E PHE* 6.3 2.0 - + - -
154I LEU* 3.6 31.6 - - + -
156I TYR* 4.5 20.4 - + + -
169I THR* 4.6 15.7 - - - -
170I ILE* 3.6 26.9 - - + -
173I ALA* 4.8 9.9 - - + +
174I LEU* 3.4 24.7 - - - +
177I MET* 4.1 11.0 - - - +
187I ILE* 3.8 22.0 - - + -
206I LEU* 3.1 39.1 + - + -
207I GLY* 3.4 9.6 - - - +
208I LEU 3.2 0.4 - - - -
209I LEU* 1.3 81.9 - - + +
211I GLY* 1.3 59.4 + - - +
212I LEU* 3.7 8.2 + - + -
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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