Contacts of the helix formed by residues 163 - 173 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D SER* 6.4 0.2 - - - -
161D PRO 4.0 0.4 + - - -
162D VAL* 1.3 85.5 - - - +
164D ILE* 1.3 78.9 + - - +
165D CYS* 2.8 37.5 + - - +
166D TRP* 3.0 13.6 + - - +
167D HIS* 3.9 0.9 - - - -
208D THR* 5.0 5.0 + - + +
212D THR* 3.3 26.6 + - + +
213D TYR* 3.8 5.2 - - - +
243D ASP* 4.5 15.0 + - - +
276D LYS* 5.7 3.9 - - - +
465D HIS* 3.0 27.5 + - - +
466D THR* 4.6 1.8 - - - -
467D PO4 4.3 12.0 + - - -
317E PHE* 3.7 24.3 - - - -
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Residues in contact with ILE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D VAL 3.9 0.4 + - - -
163D GLN* 1.3 91.0 + - - +
165D CYS* 1.3 68.4 + - + +
166D TRP 3.1 0.2 - - - -
167D HIS* 3.0 17.0 + - + -
168D LYS* 2.9 32.6 + - + +
213D TYR* 4.1 4.8 + - - -
465D HIS* 4.1 16.4 + - + +
301E PHE* 3.9 35.4 - - + -
302E ASN 5.5 0.9 - - - +
303E VAL* 3.6 30.3 - - + -
312E THR* 6.1 0.4 - - - +
317E PHE* 3.8 26.7 - - + -
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Residues in contact with CYS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D SER* 4.3 4.0 - - - -
127D SER* 3.9 30.7 - - - +
130D CYS* 3.2 41.4 - - + +
131D MET* 4.1 4.8 - - - +
163D GLN* 2.8 19.8 + - - +
164D ILE* 1.3 82.8 - - + +
166D TRP* 1.3 70.7 + - - +
168D LYS* 3.4 9.5 + - - +
169D PHE* 2.8 26.7 + - - +
243D ASP* 4.3 3.1 - - - -
317E PHE* 6.1 0.9 - - + -
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Residues in contact with TRP 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D CYS* 3.5 43.1 - - + -
134D GLY* 4.2 7.2 - - - -
137D MET* 4.2 11.9 - - + -
157D LEU* 4.3 11.7 - - + -
162D VAL* 3.6 41.5 - - + -
163D GLN 3.0 6.1 + - - -
165D CYS* 1.3 81.0 - - - +
167D HIS* 1.3 60.5 + - - +
168D LYS 3.1 1.3 - - - -
169D PHE* 3.6 22.7 - + + +
170D ALA* 2.9 29.1 + - - +
177D LEU* 4.3 11.0 - - + +
206D VAL* 3.7 24.6 - - + +
241D HIS* 3.5 36.6 - + - -
243D ASP* 2.7 31.2 + - + +
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Residues in contact with HIS 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D VAL* 3.9 20.3 + - + +
163D GLN 3.9 15.0 - - - -
164D ILE* 3.0 17.5 + - + +
166D TRP* 1.3 75.9 - - - +
168D LYS* 1.3 62.5 + - - +
170D ALA* 3.3 3.1 + - - +
171D ARG* 3.0 27.4 + - - +
177D LEU* 3.5 19.3 - - + +
179D GLU* 3.3 28.1 + - - -
213D TYR* 5.2 2.0 + - - -
301E PHE* 3.6 22.0 - + + -
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Residues in contact with LYS 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D SER* 4.2 7.6 + - - -
131D MET* 4.2 9.9 - - + -
164D ILE* 2.9 30.2 + - + +
165D CYS* 3.6 10.8 - - - +
167D HIS* 1.3 79.7 - - - +
169D PHE* 1.3 62.9 + - - +
171D ARG* 3.9 0.2 - - - +
172D TYR* 2.8 45.5 + - + +
301E PHE* 3.8 33.0 - - + -
312E THR* 4.9 9.2 + - - -
314E ALA* 3.1 33.7 + - - +
316E ASN 3.2 20.4 + - - -
317E PHE* 3.8 22.0 - - - -
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Residues in contact with PHE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D CYS 5.6 0.2 - - - -
131D MET* 4.0 23.0 - - - +
134D GLY* 3.2 41.7 - - - -
135D MET* 3.5 6.5 - - - -
138D LYS* 4.7 3.4 - - + -
157D LEU* 4.7 9.4 - - + -
165D CYS 2.8 17.9 + - - +
166D TRP* 3.6 28.3 - + + +
168D LYS* 1.3 76.6 - - - +
170D ALA* 1.3 61.4 + - + +
173D TRP* 2.9 77.7 + + + +
175D VAL* 4.0 22.0 - - + -
203D ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D LEU* 5.9 0.7 - - + -
166D TRP 2.9 17.0 + - - +
167D HIS* 3.8 4.9 - - - +
168D LYS 3.2 0.4 - - - -
169D PHE* 1.3 81.7 - - + +
171D ARG* 1.3 58.4 + - - +
174D ASP* 2.8 11.4 + - - -
175D VAL* 2.8 50.2 + - + +
177D LEU* 3.8 26.9 - - + +
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Residues in contact with ARG 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D HIS 3.0 15.4 + - - +
168D LYS 3.9 2.5 - - - +
170D ALA* 1.3 78.5 - - - +
172D TYR* 1.3 76.0 + - + +
173D TRP 3.3 0.3 + - - -
174D ASP* 3.5 6.5 + - - +
139E TRP* 3.3 30.3 - - + +
298E GLU* 3.2 43.0 + - - +
299E LEU* 4.8 1.1 - - + -
300E VAL 5.2 2.4 + - - -
301E PHE* 3.5 34.1 - - + -
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Residues in contact with TYR 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D MET* 4.5 5.4 - - + -
168D LYS* 2.8 40.2 + - + +
171D ARG* 1.3 77.9 - - + +
173D TRP* 1.3 80.8 + + + +
174D ASP* 3.5 1.8 - - - +
135E MET* 3.4 32.3 - - + -
139E TRP* 3.8 11.1 - - - -
173E TRP* 3.1 24.4 + - - +
299E LEU* 2.7 46.8 + - + -
301E PHE* 3.5 27.3 - + - -
312E THR 4.7 0.3 + - - -
313E PHE* 3.3 19.6 - + - -
314E ALA 3.9 21.7 + - - -
315E ILE* 4.9 2.7 - - + -
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Residues in contact with TRP 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D MET* 3.8 44.4 - - + -
135D MET* 3.4 37.0 - - + +
138D LYS* 2.7 41.3 + - + +
139D TRP* 4.8 5.2 - + - -
169D PHE* 2.9 53.0 + + + +
170D ALA 3.6 0.4 - - - -
172D TYR* 1.3 94.0 - + + +
174D ASP* 1.3 66.9 + - - +
175D VAL* 3.3 4.1 + - + +
315D ILE* 4.1 7.0 - - + -
172E TYR 2.7 29.4 + - - -
173E TRP* 3.4 38.7 - + - -
174E ASP* 6.1 0.4 - - - -
315E ILE* 5.2 2.2 - - + -
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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