Contacts of the helix formed by residues 217 - 230 (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 ASP 217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B LYS 3.8 7.7 - - - +
114B CYS 2.7 23.9 + - - +
115B LEU 4.0 11.1 - - - +
116B SER* 4.1 6.4 - - - -
120B LYS* 3.2 39.2 - - - +
215B ILE 3.4 2.4 + - - -
216B VAL* 1.3 68.7 - - - +
218B TRP* 1.3 61.8 + - - +
219B GLU* 3.1 14.0 + - - +
220B PHE* 3.2 19.4 + - - +
221B VAL* 3.2 22.3 + - - +
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Residues in contact with TRP 218 (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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120B LYS 3.2 25.7 + - - +
121B PRO* 3.7 1.6 - - + +
122B MET* 3.3 54.9 - - + +
123B PRO* 3.6 4.3 - - + +
126B LEU* 3.6 21.6 - - + +
130B ILE* 4.4 6.7 - - + -
140B PHE* 4.2 12.3 - + - -
141B MET* 3.9 12.5 - - + +
159B LEU* 5.3 1.8 - - + -
188B PHE* 5.0 6.3 - + + -
213B TRP* 3.6 48.3 + + - -
216B VAL* 3.1 31.5 + - + +
217B ASP* 1.3 69.6 + - - +
219B GLU* 1.3 59.4 + - - +
220B PHE 3.4 0.2 - - - -
221B VAL* 3.7 24.1 - - + +
222B CYS* 2.8 30.8 + - - +
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Residues in contact with GLU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LYS* 3.6 32.8 - - + +
121B PRO* 4.0 18.1 - - - +
123B PRO* 4.3 14.4 - - + -
217B ASP* 3.1 7.1 + - - +
218B TRP* 1.3 76.8 - - - +
220B PHE* 1.3 61.1 + - - +
222B CYS* 3.4 1.7 + - - +
223B HIS* 2.9 27.9 + - - +
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Residues in contact with PHE 220 (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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26B LEU* 4.4 6.7 - - + -
28B HIS* 6.2 0.2 - + - -
110B PHE* 3.7 23.1 - + - -
113B LYS* 3.3 68.9 - - + +
114B CYS* 4.0 17.3 - - - -
187B ILE 4.5 0.2 - - - -
217B ASP* 3.2 19.9 + - - +
219B GLU* 1.3 71.5 - - - +
221B VAL* 1.3 70.7 + - - +
223B HIS* 3.2 14.2 + + - +
224B MET* 2.9 58.4 + - + +
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Residues in contact with VAL 221 (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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114B CYS* 4.8 1.1 - - - -
126B LEU* 3.6 17.3 - - + -
159B LEU* 5.0 2.0 - - + -
187B ILE* 3.4 44.3 - - + +
188B PHE* 3.9 26.7 - - + -
216B VAL* 4.0 2.5 - - + -
217B ASP 3.2 14.9 + - - +
218B TRP* 3.7 28.3 - - + +
220B PHE* 1.3 81.7 - - + +
222B CYS* 1.3 56.5 + - - +
224B MET* 3.2 3.3 + - - +
225B TYR* 2.8 27.0 + - - +
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Residues in contact with CYS 222 (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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123B PRO* 3.7 28.7 - - + -
125B THR* 4.1 5.8 - - - -
126B LEU* 3.8 33.0 - - + +
218B TRP 2.8 18.7 + - - +
219B GLU 3.8 3.1 - - - +
220B PHE 3.2 0.2 - - - -
221B VAL* 1.3 75.1 - - - +
223B HIS* 1.3 64.2 + - - +
225B TYR* 3.2 5.7 + - - +
226B GLU* 2.9 44.7 + - - +
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Residues in contact with HIS 223 (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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219B GLU 2.9 18.7 + - - +
220B PHE* 3.5 15.3 - + + +
222B CYS* 1.3 75.5 - - - +
224B MET* 1.3 73.0 + - - +
226B GLU* 3.4 11.3 + - - +
227B ARG* 3.2 45.5 + - + +
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Residues in contact with MET 224 (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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23B TYR* 3.6 13.2 + - - +
25B THR* 3.5 25.6 - - + +
26B LEU* 5.2 0.7 - - - -
110B PHE* 4.2 4.0 - - + -
186B PRO 3.7 15.3 - - - +
187B ILE* 3.8 18.8 - - + +
220B PHE* 2.9 55.8 + - + +
221B VAL 3.4 7.2 - - - +
223B HIS* 1.3 77.5 - - - +
225B TYR* 1.3 60.6 + - - +
227B ARG* 3.4 33.9 - - - +
228B ALA* 2.8 33.8 + - - +
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Residues in contact with TYR 225 (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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125B THR* 4.3 19.5 - - + -
126B LEU* 4.1 15.3 - - + -
129B ALA* 3.4 34.4 - - + +
132B LYS* 5.7 3.8 + - - -
161B VAL* 3.9 13.2 - - + -
166B LYS 5.3 4.1 + - - -
168B LEU* 4.1 21.3 - - + -
187B ILE* 3.8 17.6 - - + +
221B VAL 2.8 17.4 + - - +
222B CYS* 3.2 7.6 + - - +
224B MET* 1.3 73.3 - - - +
226B GLU* 1.3 74.0 + - + +
228B ALA* 3.9 0.4 - - - -
229B THR* 2.9 56.5 + - + +
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Residues in contact with GLU 226 (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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125B THR* 3.8 20.8 + - + +
222B CYS* 2.9 36.6 + - - +
223B HIS* 3.9 11.4 + - - +
225B TYR* 1.3 86.9 - - + +
227B ARG* 1.3 62.0 + - - +
229B THR* 3.5 5.7 + - - -
230B LYS* 3.3 21.1 + - - +
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Residues in contact with ARG 227 (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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23B TYR* 3.2 42.8 + - + +
24B HIS 2.9 31.1 + - - +
25B THR 3.2 17.7 + - - -
27B PRO* 3.9 18.2 - - - +
185B ARG* 4.2 2.6 + - - -
223B HIS* 3.2 42.4 + - + +
224B MET* 3.4 15.9 - - - +
226B GLU* 1.3 80.0 - - - +
228B ALA* 1.3 64.2 + - - +
229B THR 3.5 0.3 + - - -
230B LYS* 3.6 19.5 + - + +
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Residues in contact with ALA 228 (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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23B TYR* 3.5 21.1 - - - +
161B VAL* 3.9 22.6 - - + +
163B PRO* 4.4 4.5 - - - +
166B LYS* 5.1 0.2 + - - -
185B ARG* 2.9 45.3 + - + +
187B ILE* 4.2 5.6 - - + -
224B MET 2.8 19.1 + - - +
225B TYR 4.0 1.8 - - - +
227B ARG* 1.3 77.7 - - - +
229B THR* 1.3 58.6 + - - +
230B LYS* 4.5 0.3 - - - +
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Residues in contact with THR 229 (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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161B VAL* 3.6 23.3 - - + -
166B LYS* 3.0 39.8 + - + +
225B TYR* 2.9 58.7 + - + +
226B GLU* 3.5 6.8 + - - -
228B ALA* 1.3 74.1 - - - +
230B LYS* 1.3 69.7 + - - +
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Residues in contact with LYS 230 (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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166B LYS* 3.5 14.2 + - - -
185B ARG* 4.7 6.3 + - - +
226B GLU 3.3 13.5 + - - +
227B ARG* 3.7 16.6 - - - +
228B ALA 3.4 4.9 - - - +
229B THR* 1.3 83.0 - - - +
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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