Contacts of the helix formed by residues 204 - 213 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197D TYR* 4.6 0.4 - - - -
200D ASP 3.8 8.7 + - - -
201D PHE* 2.9 49.8 + - + +
202D GLU* 3.1 8.9 + - - -
203D ASN* 1.3 89.8 + - - +
205D ARG* 1.3 64.8 + - - +
206D ALA 3.3 2.5 - - - -
207D ASP* 2.8 60.6 + - + +
208D TYR* 3.1 12.3 + - - +
211D GLU* 5.1 2.6 + - - -
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Residues in contact with ARG 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C TRP* 5.6 2.6 - - - -
148D GLY 2.9 27.0 + - - -
149D VAL* 3.7 18.2 + - + +
151D ASN 2.8 25.1 + - - -
153D GLY* 3.1 25.1 + - - +
192D VAL* 3.2 26.1 + - + +
194D GLU* 4.4 8.1 + - - +
197D TYR* 2.9 52.1 + - + +
203D ASN 2.8 12.8 + - - +
204D ARG* 1.3 72.5 - - - +
206D ALA* 1.3 63.9 + - - +
208D TYR* 3.2 7.0 + - + +
209D LEU* 3.0 30.0 + - + +
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D GLN* 5.3 2.3 + - - +
149D VAL* 3.7 29.9 - - + +
204D ARG 3.3 1.0 - - - -
205D ARG* 1.3 78.3 - - - +
207D ASP* 1.3 64.5 + - - +
209D LEU* 3.4 4.0 + - - +
210D LYS* 3.1 24.7 + - - +
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Residues in contact with ASP 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D PHE* 4.0 7.4 - - + -
204D ARG* 2.8 54.9 + - - +
206D ALA* 1.3 75.9 - - - +
208D TYR* 1.3 60.6 + - - +
210D LYS* 3.3 5.4 + - - +
211D GLU* 2.9 42.2 + - - +
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Residues in contact with TYR 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL* 5.0 4.2 - - + +
50D MET* 4.5 9.4 - - + +
111D PHE* 3.5 22.9 - - - -
191D ASP 2.8 30.9 + - - -
192D VAL* 4.5 2.5 - - + -
196D ALA* 3.8 16.4 - - + +
197D TYR* 3.5 42.8 - + + -
201D PHE* 3.7 28.8 - + + -
204D ARG 3.1 7.9 + - - +
205D ARG* 3.3 12.3 - - + +
207D ASP* 1.3 78.9 - - - +
209D LEU* 1.3 80.0 + - + +
211D GLU* 3.3 1.7 + - - +
212D LEU* 2.8 55.6 + - + +
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Residues in contact with LEU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 4.5 12.6 - - + -
145D GLN* 3.8 23.5 - - + +
148D GLY* 3.7 10.3 - - - -
149D VAL* 3.6 33.0 - - + +
190D ALA* 3.9 27.6 - - + -
192D VAL* 4.0 11.9 - - + -
205D ARG* 3.0 27.9 + - + +
206D ALA* 3.9 4.5 - - - +
207D ASP 3.3 0.4 - - - -
208D TYR* 1.3 88.1 - - + +
210D LYS* 1.3 62.4 + - - +
212D LEU* 3.5 19.9 + - + +
213D TRP* 3.6 16.3 + - - -
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Residues in contact with LYS 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D GLN* 4.0 25.2 - - - +
206D ALA 3.1 17.4 + - - +
207D ASP* 3.8 6.5 - - - +
209D LEU* 1.3 76.5 - - - +
211D GLU* 1.3 61.9 + - + +
213D TRP* 3.2 21.7 + - - +
214D GLN* 5.6 0.9 - - - +
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Residues in contact with GLU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D PRO 5.3 1.7 - - - +
49D VAL* 3.2 25.9 - - + +
201D PHE* 3.6 34.2 - - + -
204D ARG* 5.1 2.6 + - - -
207D ASP* 2.9 25.7 + - - +
208D TYR 4.0 2.2 - - - +
210D LYS* 1.3 74.2 - - + +
212D LEU* 1.3 65.6 + - - +
213D TRP 3.0 4.9 + - - -
214D GLN* 3.1 35.3 + - - +
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Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL* 4.5 6.9 - - + +
50D MET* 4.5 6.5 - - + -
111D PHE* 4.6 3.8 - - + -
115D LEU* 4.0 11.0 - - + -
144D PHE* 5.4 0.9 - - + -
188D PHE* 4.4 11.2 - - + -
190D ALA* 3.6 33.7 - - + -
208D TYR* 2.8 44.3 + - + +
209D LEU* 3.5 14.1 - - + +
210D LYS 3.3 0.4 - - - -
211D GLU* 1.3 77.1 - - - +
213D TRP* 1.3 65.2 + - + +
215D ILE* 3.0 41.5 + - + +
216D VAL* 3.5 12.2 - - + +
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Residues in contact with TRP 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D GLY* 5.6 0.2 - - - -
140D PHE* 3.6 18.6 - + - -
141D MET* 3.7 52.2 - - + +
144D PHE* 3.6 31.0 - + - -
145D GLN* 2.7 28.8 + - + -
188D PHE* 3.8 17.0 - + - -
209D LEU 3.6 8.7 + - - -
210D LYS 3.2 23.6 - - - +
211D GLU 3.0 0.8 + - - -
212D LEU* 1.3 79.9 - - + +
214D GLN* 1.3 62.5 + - + +
215D ILE 3.2 1.0 + - - -
216D VAL* 3.4 22.1 + - + +
218D TRP* 3.5 45.8 + + - +
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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