Contacts of the helix formed by residues 204 - 213 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ARG* 4.9 2.0 - - - +
197B TYR* 4.6 0.7 - - - -
200B ASP 3.5 22.8 + - - -
201B PHE* 2.7 45.7 + - + +
202B GLU* 3.1 27.7 + - - +
203B ASN* 1.3 87.2 + - - +
205B ARG* 1.3 62.7 + - - +
206B ALA 3.2 3.1 - - - +
207B ASP* 3.2 30.8 + - + +
208B TYR 3.1 17.0 + - - -
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Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TRP* 5.6 2.8 - - - -
148B GLY 2.9 27.8 + - - -
149B VAL* 3.8 17.9 + - + +
151B ASN 2.8 23.6 + - - -
153B GLY 2.9 26.3 + - - +
192B VAL* 3.2 28.3 + - + +
194B GLU* 4.5 8.1 + - - +
197B TYR* 2.9 52.6 + - + +
203B ASN 2.9 12.0 + - - +
204B ARG* 1.3 72.1 - - - +
206B ALA* 1.3 62.2 + - - +
208B TYR* 3.2 5.6 + - + +
209B LEU* 3.0 29.9 + - + +
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLN* 5.1 3.3 + - - +
149B VAL* 3.8 29.2 - - + +
204B ARG 3.2 1.4 - - - -
205B ARG* 1.3 79.5 - - - +
207B ASP* 1.3 61.6 + - - +
209B LEU* 3.4 2.8 + - - +
210B LYS* 3.0 27.9 + - - +
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Residues in contact with ASP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B PHE* 4.1 15.7 - - + -
204B ARG* 3.2 36.2 + - + +
206B ALA* 1.3 77.5 - - - +
208B TYR* 1.3 61.2 + - - +
210B LYS* 3.3 6.1 + - - +
211B GLU* 2.9 40.5 + - - +
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Residues in contact with TYR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B VAL* 4.9 4.6 - - + +
50B MET* 4.6 8.5 - - + -
111B PHE* 3.5 22.0 - - - -
191B ASP 2.7 30.7 + - - -
192B VAL* 4.3 2.7 - - + -
196B ALA* 3.8 13.2 - - + +
197B TYR* 3.4 48.0 - + + -
201B PHE* 3.8 27.5 - + + -
204B ARG 3.1 9.7 + - - +
205B ARG* 3.2 11.6 + - + +
207B ASP* 1.3 78.9 - - - +
209B LEU* 1.3 78.6 + - + +
211B GLU* 3.1 2.3 + - - +
212B LEU* 2.8 55.8 + - + +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PHE* 4.6 11.2 - - + -
145B GLN* 3.6 38.8 - - + +
148B GLY* 3.7 10.8 - - - -
149B VAL* 3.6 21.3 - - + +
190B ALA* 4.0 21.5 - - + -
192B VAL* 3.9 19.1 - - + -
205B ARG* 3.0 27.9 + - + +
206B ALA* 3.9 3.8 - - - +
208B TYR* 1.3 86.1 - - + +
210B LYS* 1.3 62.7 + - - +
212B LEU* 3.5 18.7 + - + +
213B TRP* 3.6 15.8 + - - -
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Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B GLN* 3.9 24.8 - - - +
206B ALA 3.0 17.1 + - - +
207B ASP* 3.8 7.4 - - - +
209B LEU* 1.3 76.1 - - - +
211B GLU* 1.3 66.1 + - + +
213B TRP* 3.3 18.8 + - - +
214B GLN* 4.9 2.8 + - - +
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PRO 5.2 4.9 - - - +
49B VAL* 3.2 22.7 - - + +
201B PHE* 3.4 34.9 - - + -
207B ASP* 2.9 25.0 + - - +
208B TYR 3.9 2.5 - - - +
210B LYS* 1.3 76.1 - - + +
212B LEU* 1.3 65.8 + - - +
213B TRP 3.1 3.1 - - - -
214B GLN* 3.0 35.8 + - - +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B VAL* 4.3 7.6 - - + +
50B MET* 4.4 7.2 - - + -
111B PHE* 4.5 5.6 - - + -
115B LEU* 4.0 13.0 - - + -
144B PHE* 5.5 1.1 - - + -
188B PHE* 4.6 10.1 - - + -
190B ALA* 3.6 33.0 - - + -
208B TYR* 2.8 44.7 + - + +
209B LEU* 3.6 13.9 - - + +
210B LYS 3.3 0.4 - - - -
211B GLU* 1.3 76.2 - - - +
213B TRP* 1.3 65.7 + - + +
215B ILE* 2.9 44.8 + - + +
216B VAL* 3.5 9.7 - - + +
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Residues in contact with TRP 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLY* 5.5 0.2 - - - -
140B PHE* 3.7 15.3 - + - -
141B MET* 3.6 49.7 - - + +
144B PHE* 3.4 39.7 - + - -
145B GLN* 2.7 28.5 + - + -
188B PHE* 3.7 22.0 - + - -
209B LEU 3.6 9.0 + - - -
210B LYS* 3.3 22.2 - - - +
211B GLU 3.0 0.8 + - - -
212B LEU* 1.3 79.2 - - + +
214B GLN* 1.3 61.3 + - + +
215B ILE 3.1 1.7 + - - -
216B VAL* 3.3 21.4 + - + +
218B TRP* 3.6 42.1 + + + -
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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