Contacts of the helix formed by residues 204 - 213 (chain E) in PDB entry 4F2N
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 204 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197E TYR* 4.7 0.2 - - - -
200E ASP 3.8 7.9 + - - -
201E PHE* 2.9 51.6 + - - +
202E GLU* 3.2 8.9 + - - -
203E ASN* 1.3 91.3 + - - +
205E ARG* 1.3 63.1 + - - +
206E ALA* 3.2 4.3 - - + +
207E ASP* 2.9 57.7 + - - +
208E TYR 3.1 9.5 + - - -
211E GLU* 5.1 2.4 + - - -
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Residues in contact with ARG 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E GLY 2.9 27.5 + - - -
149E VAL* 3.8 18.1 + - + +
151E ASN 2.8 25.1 + - - -
153E GLY* 2.9 26.3 + - - +
192E VAL* 3.0 27.2 + - + +
194E GLU* 4.4 8.3 + - - +
197E TYR* 2.9 49.2 + - + +
203E ASN 2.9 11.0 + - - +
204E ARG* 1.3 71.8 - - - +
206E ALA* 1.3 62.4 + - - +
208E TYR* 3.3 8.6 + - + +
209E LEU* 3.0 32.0 + - + +
193F TRP* 5.6 2.4 - - - -
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Residues in contact with ALA 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E GLN* 5.1 2.5 + - - +
149E VAL* 3.8 27.1 - - + +
204E ARG* 3.2 1.9 - - - +
205E ARG* 1.3 78.7 - - - +
207E ASP* 1.3 62.2 + - - +
209E LEU* 3.4 2.8 + - - +
210E LYS* 3.0 29.0 + - - +
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Residues in contact with ASP 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E PHE* 3.8 6.5 - - + -
204E ARG* 2.9 54.2 + - - +
206E ALA* 1.3 78.2 - - - +
208E TYR* 1.3 61.3 + - - +
210E LYS* 3.8 5.5 - - - +
211E GLU* 2.9 43.5 + - - +
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Residues in contact with TYR 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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49E VAL* 5.1 3.8 - - + +
50E MET* 4.4 9.8 - - + +
111E PHE* 3.6 22.0 - - - -
191E ASP 2.7 31.6 + - - -
192E VAL* 4.3 2.2 - - + -
196E ALA* 3.8 15.5 - - + +
197E TYR* 3.4 37.5 - + + -
201E PHE* 3.6 36.3 - + + -
204E ARG 3.1 8.4 + - - +
205E ARG* 3.4 12.6 - - + +
207E ASP* 1.3 76.9 - - - +
209E LEU* 1.3 82.2 + - + +
211E GLU* 3.2 2.1 + - - +
212E LEU* 2.8 56.0 + - + +
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Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E PHE* 4.3 13.0 - - + -
145E GLN* 3.6 26.0 - - + +
148E GLY* 3.6 9.9 - - - -
149E VAL* 3.6 33.0 - - + +
190E ALA* 3.8 28.9 - - + -
192E VAL* 4.0 11.9 - - + -
205E ARG* 3.0 26.2 + - + +
206E ALA* 3.9 3.6 - - - +
208E TYR* 1.3 86.8 - - + +
210E LYS* 1.3 65.6 + - - +
211E GLU 3.5 0.2 + - - -
212E LEU* 3.5 16.2 + - + +
213E TRP* 3.5 17.7 + - - -
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Residues in contact with LYS 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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145E GLN* 3.9 25.6 - - - +
206E ALA 3.0 17.2 + - - +
207E ASP* 3.9 7.4 - - - +
209E LEU* 1.3 77.2 - - - +
211E GLU* 1.3 59.7 + - + +
213E TRP* 3.2 21.8 - - - +
214E GLN* 5.0 1.7 + - - +
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Residues in contact with GLU 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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48E PRO 5.2 4.2 - - - +
49E VAL* 3.3 22.1 - - + +
201E PHE* 3.5 34.6 - - + -
204E ARG* 5.1 2.3 + - - -
207E ASP* 2.9 26.7 + - - +
208E TYR 3.9 2.2 - - - +
210E LYS* 1.3 74.6 - - + +
212E LEU* 1.3 64.1 + - - +
213E TRP 3.2 3.1 - - - -
214E GLN* 3.0 37.6 + - - +
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Residues in contact with LEU 212 (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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49E VAL* 4.5 8.3 - - + +
50E MET* 4.5 7.2 - - + -
111E PHE* 4.6 3.6 - - + -
115E LEU* 3.9 21.8 - - + -
144E PHE* 5.4 1.3 - - + -
188E PHE* 4.4 11.7 - - + -
190E ALA* 3.7 32.8 - - + -
208E TYR* 2.8 42.3 + - + +
209E LEU* 3.7 14.1 - - + +
210E LYS 3.4 0.4 - - - -
211E GLU* 1.3 76.0 - - - +
213E TRP* 1.3 66.5 + - + +
214E GLN 2.9 1.7 + - - -
215E ILE* 3.0 29.9 + - + +
216E VAL* 3.4 11.8 - - + +
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Residues in contact with TRP 213 (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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140E PHE* 3.7 19.3 - + - -
141E MET* 3.6 51.8 - - + +
144E PHE* 3.5 31.2 - + - -
145E GLN* 2.7 26.8 + - + -
188E PHE* 3.8 17.3 - + - -
209E LEU 3.5 9.2 + - - -
210E LYS 3.2 23.8 - - - +
211E GLU 3.1 0.6 + - - -
212E LEU* 1.3 78.1 - - + +
214E GLN* 1.3 63.6 + - + +
215E ILE 3.2 1.0 + - - -
216E VAL* 3.4 22.4 + - + +
218E TRP* 3.5 44.9 + + + +
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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