Contacts of the helix formed by residues 203 - 211 (chain E) in PDB entry 4Q9U
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 ARG 203 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200E PRO* 3.9 11.3 + - + +
201E PRO 3.1 0.4 - - - -
202E GLU* 1.3 86.2 - - + +
204E VAL* 1.3 54.8 + - - +
205E GLU 3.1 5.6 - - - -
206E LYS* 2.9 64.3 + - - +
207E ILE* 3.3 7.1 + - - +
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Residues in contact with VAL 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E MET* 5.5 11.2 - - + -
199E VAL* 5.9 4.7 - - + -
200E PRO 4.6 2.7 + - - +
201E PRO* 3.1 31.6 + - + +
203E ARG* 1.3 72.0 - - - +
205E GLU* 1.3 56.7 + - - +
206E LYS 2.9 5.6 - - - -
207E ILE* 2.8 43.4 + - + -
208E MET* 3.0 28.2 + - + +
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Residues in contact with GLU 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E PRO 3.7 5.3 + - - +
202E GLU* 2.9 28.8 - - - +
203E ARG 3.1 0.2 - - - -
204E VAL* 1.3 76.9 - - - +
206E LYS* 1.3 87.0 + - + +
208E MET* 4.2 13.0 - - - +
209E ASP* 4.3 8.1 - - - +
346E ARG* 5.5 4.7 + - - -
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Residues in contact with LYS 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E GLU* 4.8 1.2 + - - -
203E ARG* 2.9 58.1 + - - +
205E GLU* 1.3 111.8 - - + +
207E ILE* 1.3 60.3 + - - +
208E MET 3.2 2.2 - - - -
209E ASP* 3.2 28.8 + - - +
210E GLN* 3.5 5.7 + - - +
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Residues in contact with ILE 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E PHE* 4.1 14.8 - - + -
149E PHE* 5.8 5.8 - - + -
203E ARG 3.3 4.9 + - - +
204E VAL* 2.8 51.2 + - + +
206E LYS* 1.3 71.5 - - - +
208E MET* 1.3 71.1 + - - +
209E ASP 3.0 2.5 - - - -
210E GLN* 2.7 48.8 + - - +
211E ILE* 3.9 17.1 + - + +
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Residues in contact with MET 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E TYR* 6.2 0.2 - - + -
204E VAL* 3.0 35.2 + - + +
205E GLU* 4.2 12.1 - - - +
206E LYS 3.2 0.2 - - - -
207E ILE* 1.3 83.0 - - - +
209E ASP* 1.3 66.5 + - - +
211E ILE* 4.5 5.1 + - - +
212E GLU* 3.7 20.6 - - - +
343E ASN* 3.0 43.7 + - + +
345E SER* 3.6 12.3 - - - +
346E ARG* 5.6 7.9 - - + +
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Residues in contact with ASP 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E GLU 4.3 10.0 - - - +
206E LYS* 3.2 19.5 + - - +
207E ILE 3.0 1.4 - - - -
208E MET* 1.3 82.2 - - - +
210E GLN* 1.3 65.7 + - - +
211E ILE 3.1 3.4 + - - -
212E GLU* 3.5 14.5 + - - +
213E LYS* 4.6 1.7 + - - +
285E ARG* 4.0 37.7 + - - +
346E ARG* 4.8 13.9 + - - -
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Residues in contact with GLN 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E GLU* 6.2 0.2 - - - +
145E PHE* 3.8 31.8 - - + -
206E LYS 3.5 3.2 + - - +
207E ILE* 2.7 56.9 + - - +
209E ASP* 1.3 75.2 - - - +
211E ILE* 1.3 92.8 + - - +
212E GLU 3.5 0.5 + - - -
213E LYS* 3.6 21.4 + - - +
214E TYR* 4.6 2.3 + - - +
285E ARG* 5.6 3.4 - - - +
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Residues in contact with ILE 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E ILE* 6.4 2.2 - - + -
189E VAL* 6.3 3.1 - - + -
207E ILE* 3.9 21.5 - - + +
208E MET* 4.5 3.1 - - - +
209E ASP 3.1 1.0 + - - -
210E GLN* 1.3 104.9 - - - +
212E GLU* 1.3 77.4 + - + +
213E LYS 3.3 0.9 + - - -
214E TYR* 3.8 9.9 + - - +
215E ILE* 3.5 20.3 + - + +
343E ASN* 6.0 1.3 - - - +
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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