Contacts of the helix formed by residues 178 - 193 (chain S) in PDB entry 1RZZ
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 GLY 178 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74S PHE* 4.4 6.1 - - - -
92S PHE 3.9 11.0 - - - -
176S PRO 3.3 4.2 + - - -
177S TYR* 1.3 75.3 - - - +
179S ILE* 1.3 66.1 + - - -
180S PHE 3.6 0.4 - - - -
181S SER* 3.1 15.7 + - - -
182S HIS* 3.0 24.9 + - - -
2010S SPO 3.3 14.4 - - - +
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Residues in contact with ILE 179 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74S PHE* 5.4 0.4 - - - -
89S LEU* 4.8 4.2 + - + +
90S PHE* 3.7 57.7 + - + +
92S PHE 4.7 1.2 + - - -
178S GLY* 1.3 70.0 - - - +
180S PHE* 1.3 67.0 + - + +
182S HIS* 2.8 26.0 + - + -
183S LEU* 3.4 10.0 - - - +
2001S BCL 3.5 43.1 - - + -
2010S SPO 3.7 34.5 - - + +
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Residues in contact with PHE 180 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169R TYR* 3.5 36.3 + + - +
174R MET* 3.8 20.0 - - + -
260R VAL* 5.9 1.1 - - + -
263R TRP* 3.5 36.1 - + + -
90S PHE* 3.2 44.3 + + + +
91S PHE* 3.7 39.5 - + + -
179S ILE* 1.3 85.5 - - + +
181S SER* 1.3 66.3 + - - +
183S LEU* 3.0 14.4 + - + +
184S ASP* 3.0 26.6 + - - +
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Residues in contact with SER 181 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90S PHE 4.6 1.2 + - - -
91S PHE 5.4 2.6 + - - -
92S PHE 4.8 0.9 - - - -
93S SER* 2.9 35.1 + - - -
95S GLU* 4.0 9.2 - - - -
176S PRO* 3.9 8.5 - - - +
178S GLY* 3.1 23.3 + - - -
179S ILE 3.4 0.2 - - - -
180S PHE* 1.3 78.3 - - - +
182S HIS* 1.3 56.9 + - - +
184S ASP* 3.1 15.7 + - - +
185S TRP* 2.9 26.7 + - - +
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Residues in contact with HIS 182 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175S VAL* 3.8 8.5 - - + -
176S PRO* 3.6 19.5 - - - +
178S GLY 3.0 18.2 + - - +
179S ILE* 2.8 27.4 + - - -
181S SER* 1.3 77.3 + - - +
183S LEU* 1.3 68.1 + - + +
185S TRP* 3.7 9.7 - - - +
186S THR* 2.7 33.6 + - - -
2001S BCL 2.4 76.7 + + + -
2010S SPO 3.5 23.6 - - + -
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Residues in contact with LEU 183 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166R ASN* 4.3 2.7 - - - +
168R HIS* 3.3 32.1 + - + +
169R TYR* 5.1 4.9 - - + +
174R MET* 3.9 19.7 - - + -
179S ILE 3.4 16.8 - - - +
180S PHE* 3.0 16.2 + - + +
182S HIS* 1.3 84.7 - - + +
184S ASP* 1.3 65.4 + - - +
186S THR* 3.1 7.0 + - - -
187S ASN* 3.0 19.4 + - - +
2001S BCL 3.4 68.0 - - + +
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Residues in contact with ASP 184 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166R ASN* 4.4 6.5 + - - +
169R TYR* 3.0 29.7 + - - -
180S PHE* 3.0 17.8 + - - +
181S SER* 3.3 15.5 - - - +
183S LEU* 1.3 77.1 - - - +
185S TRP* 1.3 58.2 + - - +
187S ASN* 3.1 5.1 + - - +
188S ASN* 2.8 32.4 + - - +
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Residues in contact with TRP 185 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160S LEU* 3.5 32.1 - - + -
164S ARG* 5.2 1.3 - - - -
172S SER 5.3 1.9 + - - -
173S GLU 3.4 19.6 + - - -
174S ALA 3.3 15.4 + - - -
175S VAL* 3.7 24.2 - - + -
176S PRO* 3.7 27.6 - - + -
181S SER 2.9 15.4 + - - +
182S HIS* 3.7 6.1 - - - +
184S ASP* 1.3 75.3 - - - +
186S THR* 1.3 73.0 + - - +
188S ASN* 3.7 10.4 + - - +
189S PHE* 2.8 66.6 + + + +
2001S BCL 4.3 6.7 - - + -
2003S BCL 4.3 8.7 - - + -
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Residues in contact with THR 186 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168R HIS* 3.9 15.9 - - + -
2002R BCL 4.1 6.5 - - + +
182S HIS 2.7 18.6 + - - -
183S LEU* 3.1 11.1 + - - -
185S TRP* 1.3 89.1 - - - +
187S ASN* 1.3 64.4 + - - +
189S PHE* 3.5 3.8 + - - +
190S SER 3.4 14.7 + - - -
2001S BCL 3.6 29.0 - - + -
2003S BCL 3.7 41.2 - - + +
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Residues in contact with ASN 187 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162R TYR* 2.7 36.6 + - - -
166R ASN* 3.4 39.6 - - - +
168R HIS* 4.1 1.1 - - + -
183S LEU 3.0 5.5 + - - -
184S ASP* 3.1 5.7 + - - +
186S THR* 1.3 74.1 - - - +
188S ASN* 1.3 67.8 + - - +
190S SER* 3.2 5.2 + - - -
191S LEU* 3.1 34.1 + - - +
2003S BCL 3.2 16.0 - - + +
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Residues in contact with ASN 188 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184S ASP 2.8 18.2 + - - +
185S TRP* 3.7 11.0 + - - +
187S ASN* 1.3 77.4 - - - +
189S PHE* 1.3 55.6 + - - +
191S LEU* 3.0 15.2 + - - +
192S VAL* 2.7 57.4 + - - +
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Residues in contact with PHE 189 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164S ARG* 3.4 36.8 - - - -
185S TRP* 2.8 48.7 + + + +
186S THR 3.6 5.4 - - - +
187S ASN 3.3 0.2 - - - -
188S ASN* 1.3 79.8 - - - +
190S SER* 1.3 60.5 + - - +
192S VAL* 3.6 2.6 + - - -
193S HIS* 2.8 46.2 + + - +
196S LEU* 4.2 10.5 - - + -
284S ILE* 3.7 28.7 - - + -
287S SER* 3.6 31.0 - - - -
2003S BCL 3.5 20.2 - - + -
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Residues in contact with SER 190 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162R TYR* 5.1 1.2 + - - -
186S THR 3.4 2.9 + - - -
187S ASN 3.2 9.3 + - - -
188S ASN 3.2 0.6 - - - -
189S PHE* 1.3 77.4 - - - +
191S LEU* 1.3 70.3 + - - +
193S HIS 3.0 11.8 + - - -
195S ASN* 3.0 23.5 + - - -
196S LEU* 2.8 40.1 + - - +
2003S BCL 3.6 36.9 - - - +
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Residues in contact with LEU 191 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162R TYR* 3.0 37.7 - - + +
187S ASN* 3.1 30.5 + - - +
188S ASN* 3.0 15.8 + - - +
190S SER* 1.3 78.1 - - - +
192S VAL* 1.3 64.6 + - + +
193S HIS 3.3 0.3 + - - -
194S GLY* 3.5 9.4 + - - -
195S ASN* 4.5 2.6 + - - +
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Residues in contact with VAL 192 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188S ASN* 2.7 46.0 + - - +
189S PHE* 3.8 6.1 - - - +
191S LEU* 1.3 74.9 - - + +
193S HIS* 1.3 76.9 + - + +
194S GLY 3.5 1.0 + - - -
292S ASP 3.6 8.1 - - - +
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Residues in contact with HIS 193 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164S ARG* 3.3 31.3 + - - -
168S MET* 5.3 0.8 - - - +
189S PHE* 2.8 42.7 + + - +
190S SER 3.0 5.3 + - - +
192S VAL* 1.3 94.7 - - + +
194S GLY* 1.3 60.0 + - - +
195S ASN 3.5 2.2 + - - -
196S LEU* 4.7 5.4 - - + -
287S SER* 3.6 10.1 - - - -
288S GLY* 3.4 29.4 + - - -
291S VAL 3.9 5.8 - - - -
292S ASP* 3.3 18.2 - - - +
293S ASN* 3.4 0.6 - - - -
294S TRP* 2.8 41.0 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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