Contacts of the helix formed by residues 163 - 173 (chain E) in PDB entry 3FZ7
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 GLN 163 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317D PHE* 3.6 16.3 - - - -
126E SER* 5.9 0.4 - - - -
162E VAL* 1.3 86.1 - - - +
164E ILE* 1.3 89.0 + - - +
165E CYS* 3.0 36.0 + - - +
166E TRP* 3.2 13.3 + - - -
167E HIS* 3.8 1.1 + - - -
208E THR* 5.0 3.7 + - + +
212E THR* 3.5 27.2 + - + +
213E TYR* 4.4 4.0 - - - -
243E ASP* 4.3 16.2 + - - +
245E ALA* 6.0 5.8 - - + -
276E LYS* 5.7 5.3 - - - +
465E HIS* 2.9 28.1 + - - +
466E THR* 4.7 1.4 + - - -
467E PO4 4.0 14.4 + - - +
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Residues in contact with ILE 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D PHE* 4.2 35.9 - - + -
302D ASN 5.5 1.8 - - - +
303D VAL* 3.9 26.0 - - + -
312D THR* 6.0 0.4 - - - +
317D PHE* 3.7 29.6 - - + -
162E VAL 4.1 0.2 + - - -
163E GLN* 1.3 93.9 - - - +
165E CYS* 1.3 66.7 + - + +
167E HIS* 2.9 25.1 + - + +
168E LYS* 3.1 20.0 + - + +
213E TYR* 4.6 1.4 + - - -
465E HIS* 4.0 20.3 + - + +
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Residues in contact with CYS 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D PHE* 6.3 0.2 - - + -
126E SER* 5.0 2.7 - - - -
127E SER* 3.7 29.8 - - - +
130E CYS* 2.8 43.1 - - + -
131E MET* 4.3 4.4 - - + +
163E GLN* 3.0 21.4 + - - +
164E ILE* 1.3 80.3 - - + +
166E TRP* 1.3 70.4 + - - +
168E LYS* 3.4 9.9 + - - +
169E PHE* 2.8 29.0 + - - +
243E ASP* 4.5 3.1 - - - -
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Residues in contact with TRP 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E CYS* 3.5 49.3 - - + -
134E GLY* 4.2 5.8 - - - -
137E MET* 4.1 20.9 - - + -
157E LEU* 4.6 7.2 - - + -
159E CYS* 5.3 0.2 - - - -
162E VAL* 3.6 42.4 - - + -
163E GLN 3.2 6.1 + - - -
165E CYS* 1.3 82.1 - - - +
167E HIS* 1.3 58.0 + - - +
169E PHE* 3.6 23.4 - + + +
170E ALA* 2.9 29.5 + - - +
177E LEU* 4.3 12.7 - - + +
206E VAL* 3.8 23.3 - - + +
241E HIS* 3.8 30.7 - + - -
243E ASP* 3.0 28.8 + - + +
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Residues in contact with HIS 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D PHE* 3.6 21.5 - + + -
162E VAL* 3.7 24.2 - - + +
163E GLN 3.8 10.7 + - - -
164E ILE* 2.9 17.1 + - + +
166E TRP* 1.3 78.4 - - - +
168E LYS* 1.3 58.1 + - - +
170E ALA* 3.5 6.4 - - - +
171E ARG* 3.0 30.1 + - - +
177E LEU* 3.7 15.2 - - + +
179E GLU* 3.1 28.7 + - - -
213E TYR* 5.3 3.1 - - - -
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Residues in contact with LYS 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D PHE* 3.7 30.3 - - + +
312D THR* 4.2 14.3 + - - -
314D ALA* 3.2 38.0 + - - +
316D ASN 3.7 14.3 + - - -
317D PHE* 3.9 23.3 - - - -
127E SER* 4.5 7.9 - - - -
131E MET* 4.1 11.2 - - + -
164E ILE* 3.1 27.7 + - + +
165E CYS* 3.5 8.3 - - - +
167E HIS* 1.3 74.6 - - - +
169E PHE* 1.3 56.1 + - - +
172E TYR* 2.7 57.8 + - + +
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Residues in contact with PHE 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E CYS 5.2 0.4 - - - +
131E MET* 4.0 18.3 - - - -
134E GLY* 3.3 45.1 - - - -
135E MET* 3.6 5.2 - - - -
138E LYS* 4.9 2.7 - - + -
157E LEU* 4.7 7.2 - - + -
165E CYS 2.8 20.0 + - - +
166E TRP* 3.6 30.5 - + + +
168E LYS* 1.3 71.5 - - - +
170E ALA* 1.3 69.9 + - + +
173E TRP* 2.9 65.3 + + + +
175E VAL* 3.9 32.1 - - + -
203E ILE* 4.1 12.3 - - + -
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Residues in contact with ALA 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E LEU* 6.4 0.2 - - + -
166E TRP 2.9 17.9 + - - +
167E HIS* 3.5 6.1 - - - +
169E PHE* 1.3 82.7 - - + +
171E ARG* 1.3 57.6 + - - +
174E ASP* 2.9 26.5 + - - -
175E VAL* 2.9 32.9 + - + +
177E LEU* 3.8 27.4 - - + +
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Residues in contact with ARG 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D TRP* 3.4 21.4 - - + +
298D GLU* 3.1 36.8 + - - +
299D LEU* 4.6 6.1 - - + -
300D VAL 5.1 3.4 + - - -
301D PHE* 3.6 34.8 - - + -
167E HIS 3.0 16.2 + - - +
168E LYS 3.9 2.5 - - - +
170E ALA* 1.3 77.9 - - - +
172E TYR* 1.3 74.0 + - + +
173E TRP 3.4 0.5 + - - -
174E ASP* 3.5 6.2 + - - +
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Residues in contact with TYR 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D MET* 3.5 29.2 - - + -
139D TRP* 3.8 9.6 - - - -
173D TRP* 2.7 30.2 + - - +
299D LEU* 2.7 48.8 + - + -
301D PHE* 3.4 25.8 - + - -
312D THR 4.7 0.3 + - - -
313D PHE* 3.2 21.2 - + - -
314D ALA 3.8 14.5 + - - -
315D ILE* 4.8 5.4 - - + -
131E MET* 4.9 1.8 - - + -
168E LYS* 2.7 48.1 + - + +
171E ARG* 1.3 77.9 - - + +
173E TRP* 1.3 78.1 + + + +
174E ASP* 3.6 1.3 - - - +
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Residues in contact with TRP 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D TYR 3.1 29.0 + - - -
173D TRP* 3.4 38.0 - + - -
315D ILE* 5.1 3.4 - - + -
131E MET* 3.5 43.7 - - + -
135E MET* 3.4 39.6 - - + +
138E LYS* 2.9 38.7 + - + +
139E TRP* 5.0 0.4 - + - -
169E PHE* 2.9 50.6 + + + +
170E ALA 3.7 0.2 - - - -
172E TYR* 1.3 97.5 - + + +
174E ASP* 1.3 68.5 + - - +
175E VAL* 3.3 6.8 + - + +
315E ILE* 4.0 6.3 - - + -
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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