Contacts of the helix formed by residues 151 - 163 (chain R) 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 TRP 151 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62R GLN* 3.2 51.7 + - + +
150R ILE* 1.3 88.0 - - + +
152R THR* 1.3 67.1 + - + +
153R HIS 3.2 2.5 - - - -
154R LEU* 3.1 27.2 + - + +
155R ASP* 3.1 19.4 + - - +
197S PHE* 3.4 27.4 - - + -
198S TYR* 4.5 30.1 - + + -
199S ASN 6.2 0.2 - - - -
200S PRO* 6.2 3.8 - - + -
2004S BCL 4.1 20.4 - - - -
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Residues in contact with THR 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62R GLN 6.1 0.2 - - - +
63R LEU 5.1 3.6 - - - +
64R ILE 5.2 0.2 - - - +
65R SER* 2.8 29.9 + - - +
67R TYR* 3.1 27.5 - - - +
147R PRO* 3.5 16.3 - - - +
149R GLY* 3.0 23.3 + - - -
151R TRP* 1.3 80.2 - - + +
153R HIS* 1.3 60.0 + - - +
155R ASP* 3.4 14.0 + - - +
156R TRP* 3.2 17.2 + - - +
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Residues in contact with HIS 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146R PHE* 3.8 12.1 - - + -
147R PRO* 3.3 25.1 - - - +
149R GLY 2.7 26.7 + - - +
150R ILE* 2.9 21.9 + - + -
152R THR* 1.3 76.4 + - - +
154R LEU* 1.3 69.8 + - + +
156R TRP* 3.4 5.5 + - - +
157R VAL* 3.1 30.7 + - - +
2006R BPH 3.7 21.9 - - + +
2004S BCL 2.4 74.5 + + + -
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Residues in contact with LEU 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150R ILE 3.7 12.6 - - - +
151R TRP* 3.1 25.0 + - + +
153R HIS* 1.3 97.4 - - + +
155R ASP* 1.3 60.3 + - - +
157R VAL* 3.3 6.4 + - - +
158R SER* 3.0 27.9 + - - -
197S PHE* 3.8 36.5 - - + +
2004S BCL 3.4 64.6 - - + +
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Residues in contact with ASP 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151R TRP* 3.1 19.3 + - - +
152R THR* 3.6 17.0 - - - +
153R HIS 3.3 0.2 - - - -
154R LEU* 1.3 75.7 - - - +
156R TRP* 1.3 53.2 + - - +
158R SER* 3.2 6.7 + - - -
159R ASN* 2.6 52.2 + - - +
195S ASN* 5.4 2.4 - - - +
198S TYR* 3.7 21.6 + - - -
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Residues in contact with TRP 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131R LEU* 3.8 28.0 - - + -
135R ARG* 4.0 13.2 - - - +
143R GLY 5.2 1.1 + - - -
144R TYR* 3.4 19.1 + - - +
145R ALA* 3.2 23.1 + - - -
146R PHE* 3.3 29.6 - + + -
147R PRO* 3.7 20.2 - - + -
152R THR 3.2 6.7 + - - +
153R HIS* 3.5 8.5 - - - +
154R LEU 3.2 0.2 - - - -
155R ASP* 1.3 74.4 - - - +
157R VAL* 1.3 97.3 + - + +
159R ASN* 4.2 6.1 - - - +
160R THR* 2.5 55.0 + - - -
248R MET* 4.0 11.0 - - + -
2002R BCL 4.0 13.0 - - + -
2004S BCL 4.5 6.7 - - + -
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Residues in contact with VAL 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153R HIS 3.1 16.9 + - - +
154R LEU* 3.3 9.4 + - + +
156R TRP* 1.3 95.8 - - + +
158R SER* 1.3 55.2 + - - +
161R GLY* 2.8 32.2 + - - -
2002R BCL 3.5 25.0 - - + +
197S PHE* 4.2 5.4 - - + -
2003S BCL 3.4 34.8 - - + +
2004S BCL 4.0 30.7 - - + -
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Residues in contact with SER 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154R LEU 3.0 13.7 + - - -
155R ASP* 3.5 11.2 - - - -
156R TRP 3.2 0.2 - - - -
157R VAL* 1.3 78.0 - - - +
159R ASN* 1.3 58.9 + - - +
161R GLY* 3.2 0.9 + - - -
162R TYR* 2.9 54.9 + - - -
2002R BCL 4.2 11.2 - - - +
195S ASN* 4.5 11.8 + - - -
197S PHE* 4.0 14.5 - - - -
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Residues in contact with ASN 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155R ASP* 2.6 42.6 + - - +
156R TRP* 4.0 5.1 - - - +
158R SER* 1.3 74.1 + - - +
160R THR* 1.3 56.6 + - - +
162R TYR* 3.6 4.0 + - - +
163R THR* 2.7 34.2 + - - +
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Residues in contact with THR 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135R ARG* 3.6 27.4 - - - +
156R TRP* 2.5 51.3 + - + -
159R ASN* 1.3 73.1 - - - +
161R GLY* 1.3 65.0 + - - +
163R THR* 3.1 22.1 + - - -
164R TYR* 3.2 22.9 - - + +
167R PHE* 5.8 0.7 - - + -
248R MET* 4.2 8.5 - - + -
251R THR* 5.7 0.4 - - + -
2002R BCL 3.9 17.0 - - + -
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Residues in contact with GLY 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157R VAL 2.8 19.2 + - - -
158R SER 3.6 0.9 - - - -
160R THR* 1.3 78.8 - - - +
162R TYR* 1.3 61.1 + - - +
163R THR 3.3 0.5 + - - -
164R TYR* 3.3 6.6 + - - -
165R GLY 3.0 12.1 - - - +
167R PHE* 3.5 25.7 - - - +
2002R BCL 3.8 24.1 - - - +
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Residues in contact with TYR 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R SER* 2.9 40.4 + - - +
159R ASN* 3.9 4.0 - - - +
161R GLY* 1.3 68.7 - - - +
163R THR* 1.3 60.7 + - - +
164R TYR 2.9 6.7 + - - -
165R GLY* 3.1 27.9 + - - -
166R ASN* 4.9 4.3 - - - -
167R PHE 5.7 0.4 - - - -
258R GLN* 5.0 0.7 + - - -
2002R BCL 3.5 21.1 - - + -
187S ASN* 2.7 34.7 + - - -
190S SER* 5.1 1.4 + - - -
191S LEU* 3.0 26.7 - - + +
2003S BCL 3.4 12.7 - - + +
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Residues in contact with THR 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159R ASN* 2.7 21.2 + - - +
160R THR* 3.1 16.8 + - - -
162R TYR* 1.3 77.0 - - - +
164R TYR* 1.3 83.4 + - + +
165R GLY 3.5 0.2 - - - -
256R PHE 5.0 2.3 - - - +
258R GLN* 3.6 10.6 + - - -
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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