Contacts of the helix formed by residues 204 - 213 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197F TYR* 4.6 0.7 - - - -
200F ASP 4.0 6.9 + - - -
201F PHE* 3.0 49.7 + - - +
202F GLU* 3.2 8.1 + - - -
203F ASN* 1.3 93.4 + - - +
205F ARG* 1.3 63.2 + - - +
206F ALA* 3.3 3.4 - - - +
207F ASP* 2.8 52.3 + - + +
208F TYR* 3.1 20.4 + - - +
211F GLU* 5.6 1.0 + - - -
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Residues in contact with ARG 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E TRP* 5.6 2.0 - - - -
148F GLY 3.0 27.2 + - - -
149F VAL* 3.9 18.2 + - + +
151F ASN* 2.7 26.5 + - - +
153F GLY* 3.0 24.5 + - - +
192F VAL* 3.0 29.5 + - + +
194F GLU* 4.3 9.1 + - - +
197F TYR* 2.9 50.0 + - + +
203F ASN 2.9 10.8 + - - +
204F ARG* 1.3 73.4 - - - +
206F ALA* 1.3 57.1 + - - +
208F TYR* 3.3 5.3 + - + +
209F LEU* 3.0 36.6 + - + +
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Residues in contact with ALA 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F GLN* 5.3 2.6 + - - +
149F VAL* 3.7 30.7 - - + +
204F ARG* 3.3 1.7 - - + +
205F ARG* 1.3 77.4 - - - +
207F ASP* 1.3 61.5 + - - +
209F LEU* 3.4 2.5 + - - +
210F LYS* 3.1 27.2 + - - +
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Residues in contact with ASP 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F PHE* 4.0 6.5 - - + -
204F ARG* 2.8 55.5 + - - +
206F ALA* 1.3 77.9 - - - +
208F TYR* 1.3 58.9 + - - +
210F LYS* 3.3 7.2 + - - +
211F GLU* 2.9 38.9 + - + +
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Residues in contact with TYR 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F VAL* 4.9 3.4 - - + -
50F MET* 4.7 8.6 - - + +
111F PHE* 3.5 23.4 - - - -
191F ASP 2.8 30.8 + - - -
192F VAL* 4.4 1.8 - - + -
196F ALA* 3.8 16.2 - - + +
197F TYR* 3.4 44.9 - + + -
201F PHE* 3.7 26.7 - + + -
204F ARG 3.1 9.7 + - - +
205F ARG* 3.4 11.4 - - + +
207F ASP* 1.3 77.6 - - - +
209F LEU* 1.3 75.4 + - + +
211F GLU* 3.3 1.9 + - - +
212F LEU* 2.8 56.4 + - + +
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Residues in contact with LEU 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F PHE* 4.5 11.9 - - + -
145F GLN* 3.8 23.6 - - + +
148F GLY* 3.7 12.1 - - - -
149F VAL* 3.7 31.4 - - + +
190F ALA* 3.9 22.7 - - + -
192F VAL* 3.8 19.1 - - + -
205F ARG* 3.0 29.2 + - + +
206F ALA* 4.0 3.6 - - - +
208F TYR* 1.3 86.6 - - + +
210F LYS* 1.3 62.3 + - - +
212F LEU* 3.5 16.9 + - + +
213F TRP* 3.6 17.7 + - - -
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Residues in contact with LYS 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F GLN* 3.7 31.8 - - - +
206F ALA 3.1 17.2 + - - +
207F ASP* 3.6 9.2 - - - +
208F TYR 3.3 0.2 - - - -
209F LEU* 1.3 75.8 - - - +
211F GLU* 1.3 64.8 + - + +
213F TRP* 3.4 20.1 + - + +
214F GLN* 5.0 2.3 + - - +
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Residues in contact with GLU 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F PRO* 4.7 4.2 - - - +
49F VAL* 3.2 29.4 - - + +
201F PHE* 3.6 31.1 - - + -
204F ARG* 5.6 1.0 + - - -
207F ASP* 2.9 24.7 + - + +
208F TYR 3.9 2.7 - - - +
210F LYS* 1.3 75.1 - - + +
212F LEU* 1.3 67.9 + - - +
213F TRP 3.1 2.9 - - - -
214F GLN* 2.9 35.0 + - - +
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Residues in contact with LEU 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F VAL* 4.3 7.2 - - + +
50F MET* 4.3 6.7 - - + -
111F PHE* 4.5 4.3 - - + -
115F LEU* 4.1 12.3 - - + -
144F PHE* 5.4 1.1 - - + -
188F PHE* 4.3 13.7 - - + -
190F ALA* 3.5 34.3 - - + -
208F TYR* 2.8 49.6 + - + +
209F LEU* 3.7 14.6 - - + +
210F LYS 3.4 0.8 - - - -
211F GLU* 1.3 72.5 - - - +
213F TRP* 1.3 64.8 + - + +
214F GLN 2.9 1.4 + - - -
215F ILE* 2.9 39.2 + - + +
216F VAL* 3.5 9.1 - - + +
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Residues in contact with TRP 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F PHE* 3.6 19.5 - + - -
141F MET* 3.6 50.4 - - + +
144F PHE* 3.5 36.3 - + + -
145F GLN* 2.7 29.3 + - + -
188F PHE* 3.7 18.2 - + - -
209F LEU 3.6 11.0 + - - -
210F LYS* 3.4 22.9 - - + +
211F GLU 3.0 1.0 + - - -
212F LEU* 1.3 77.3 - - + +
214F GLN* 1.3 60.6 + - + +
215F ILE 3.4 0.9 + - - -
216F VAL* 3.4 22.3 + - + +
218F TRP* 3.6 45.5 + + - -
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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