Contacts of the helix formed by residues 204 - 213 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C TYR* 4.6 0.2 - - - -
200C ASP 3.9 7.1 + - - -
201C PHE* 2.9 52.6 + - - +
202C GLU* 3.2 8.1 + - - -
203C ASN* 1.3 94.4 + - - +
205C ARG* 1.3 62.1 + - - +
206C ALA* 3.2 3.8 - - - +
207C ASP* 2.8 56.7 + - + +
208C TYR* 3.1 17.3 + - - +
211C GLU* 5.2 2.0 + - - -
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Residues in contact with ARG 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C GLY 2.9 27.2 + - - -
149C VAL* 3.7 18.8 + - + +
151C ASN 2.7 25.3 + - - -
153C GLY* 2.9 27.3 + - - +
192C VAL* 3.1 29.9 + - + +
194C GLU* 4.5 7.3 + - - +
197C TYR* 3.0 47.4 + - + +
203C ASN 2.8 12.2 + - - +
204C ARG* 1.3 72.1 - - - +
206C ALA* 1.3 62.4 + - - +
208C TYR* 3.3 8.1 + - + +
209C LEU* 3.0 28.7 + - + +
193D TRP* 5.6 2.2 - - - -
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Residues in contact with ALA 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C GLN* 5.0 2.9 + - - +
149C VAL* 3.7 29.0 - - + +
204C ARG* 3.2 1.7 - - - +
205C ARG* 1.3 79.9 - - - +
207C ASP* 1.3 61.2 + - - +
209C LEU* 3.4 3.6 + - - +
210C LYS* 3.0 29.0 + - - +
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Residues in contact with ASP 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C PHE* 4.0 7.4 - - + -
204C ARG* 2.8 53.3 + - - +
206C ALA* 1.3 78.9 - - - +
208C TYR* 1.3 58.1 + - - +
210C LYS* 3.7 6.2 - - - +
211C GLU* 2.9 40.5 + - - +
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Residues in contact with TYR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL* 4.9 4.2 - - + +
50C MET* 4.6 9.6 - - + -
111C PHE* 3.5 21.3 - - - -
191C ASP 2.8 31.2 + - - -
192C VAL* 4.4 2.2 - - + -
196C ALA* 3.9 12.4 - - + +
197C TYR* 3.5 40.4 - + + -
201C PHE* 3.7 33.9 - + + -
204C ARG 3.1 10.7 + - - +
205C ARG* 3.4 12.3 - - + +
207C ASP* 1.3 75.6 - - - +
209C LEU* 1.3 75.1 + - + +
211C GLU* 3.2 2.9 + - - +
212C LEU* 2.8 59.6 + - + +
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Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 4.5 11.5 - - + -
145C GLN* 3.6 37.9 - - + +
148C GLY* 3.7 11.7 - - - -
149C VAL* 3.6 20.4 - - + +
190C ALA* 3.9 27.6 - - + -
192C VAL* 3.9 12.8 - - + -
205C ARG* 3.0 27.0 + - + +
206C ALA* 3.9 3.8 - - - +
208C TYR* 1.3 85.2 - - + +
210C LYS* 1.3 65.9 + - - +
212C LEU* 3.5 18.2 + - + +
213C TRP* 3.6 17.2 + - - -
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Residues in contact with LYS 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C GLN* 3.9 24.6 - - - +
206C ALA 3.0 18.3 + - - +
207C ASP* 3.7 8.7 - - - +
209C LEU* 1.3 76.0 - - - +
211C GLU* 1.3 64.2 + - + +
213C TRP* 3.3 19.6 + - - +
214C GLN* 5.0 1.4 + - - +
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Residues in contact with GLU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PRO 5.1 4.5 - - - +
49C VAL* 3.3 24.1 - - + +
201C PHE* 3.4 33.8 - - + -
204C ARG* 5.2 1.7 + - - -
207C ASP* 2.9 23.4 + - - +
208C TYR 3.8 2.9 - - - +
210C LYS* 1.3 75.5 - - + +
212C LEU* 1.3 66.1 - - - +
213C TRP 3.1 2.5 - - - -
214C GLN* 2.9 37.5 + - - +
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C VAL* 4.5 7.2 - - + +
50C MET* 4.6 5.6 - - + -
111C PHE* 4.6 3.8 - - + -
115C LEU* 4.0 20.2 - - + -
144C PHE* 5.2 1.8 - - + -
188C PHE* 4.3 11.4 - - + -
190C ALA* 3.5 34.5 - - + -
208C TYR* 2.8 49.7 + - + +
209C LEU* 3.6 15.3 - - + +
210C LYS 3.4 0.4 - - - -
211C GLU* 1.3 73.3 - - - +
213C TRP* 1.3 64.0 + - + +
215C ILE* 3.0 34.0 + - + +
216C VAL* 3.6 13.1 - - + +
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Residues in contact with TRP 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLY* 5.5 0.2 - - - -
140C PHE* 3.6 19.3 - + - -
141C MET* 3.6 52.4 - - + +
144C PHE* 3.5 32.5 - + - -
145C GLN* 2.8 26.1 + - + -
188C PHE* 3.8 16.8 - + - -
209C LEU 3.6 10.7 + - - -
210C LYS 3.3 24.0 - - - +
211C GLU 3.0 0.4 + - - -
212C LEU* 1.3 79.7 - - + +
214C GLN* 1.3 63.3 + - + +
215C ILE 3.1 1.2 + - - -
216C VAL* 3.3 22.5 + - + +
218C TRP* 3.5 45.6 + + + -
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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