Contacts of the helix formed by residues 157 - 173 (chain C) in PDB entry 1D5Z
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 ALA 157 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C VAL 3.7 1.8 + - - -
156C THR* 1.3 72.1 - - - +
158C GLN* 1.3 53.2 + - - +
160C LEU* 3.2 3.4 + - - +
161C ASP* 2.7 38.3 + - - +
189C PHE* 3.7 14.5 - - + -
196C PHE* 3.8 25.1 - - + -
198C TYR* 3.8 27.8 - - + +
221C LYS* 2.8 16.6 + - + +
222C MET* 4.3 1.0 - - - +
223C VAL* 4.8 6.1 - - + -
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Residues in contact with GLN 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE 4.0 0.4 - - - +
86C GLY* 3.0 15.7 - - - -
87C ALA* 2.8 32.1 + - + +
114C MET* 4.4 0.2 - - - +
115C TYR 2.6 29.8 + - - +
117C GLY* 3.3 17.2 - - - +
156C THR* 3.0 8.9 - - - +
157C ALA* 1.3 79.7 - - - +
159C GLU* 1.3 53.0 + - - +
161C ASP* 3.3 1.4 + - - +
162C TYR* 2.8 34.1 + - + +
217C TYR* 3.3 56.9 + - + +
221C LYS 4.6 0.4 + - - -
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Residues in contact with GLU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C PHE* 3.5 49.1 - - + +
149C GLN 4.7 1.4 - - - +
150C THR* 4.4 9.6 + - - -
152C LYS* 2.9 38.9 + - - +
155C VAL* 3.9 13.3 - - + +
156C THR* 3.1 24.4 + - - +
158C GLN* 1.3 75.3 - - - +
160C LEU* 1.3 60.4 + - + +
162C TYR* 3.2 2.6 + - - +
163C LEU* 2.8 49.6 + - + +
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Residues in contact with LEU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ILE* 3.6 33.2 - - + -
148C VAL* 4.3 13.4 - - + +
149C GLN 5.1 0.4 - - - +
150C THR* 4.6 7.9 - - + -
155C VAL* 4.0 14.4 - - + -
156C THR 3.4 8.7 + - - +
157C ALA* 3.2 6.1 + - - +
159C GLU* 1.3 77.8 - - + +
161C ASP* 1.3 52.1 + - - +
163C LEU* 3.3 14.3 + - + +
164C THR* 2.8 42.6 + - - -
189C PHE* 3.8 15.5 - - + -
223C VAL* 3.6 31.4 - - + -
228C VAL* 4.0 5.6 - - + -
230C ILE* 3.9 13.7 - - + -
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Residues in contact with ASP 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C ALA 2.7 21.9 + - - +
158C GLN* 3.5 6.1 - - - +
160C LEU* 1.3 72.5 - - - +
162C TYR* 1.3 58.2 + - - +
164C THR* 3.2 1.4 + - - -
165C ARG* 2.7 68.9 + - - +
187C ILE* 3.4 31.5 - - - +
189C PHE* 3.8 8.2 - - + -
198C TYR* 3.9 1.7 - - - -
216C MET* 3.8 2.6 - - - +
217C TYR* 2.3 33.6 + - + +
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Residues in contact with TYR 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU 3.7 23.1 - - - -
28C TYR* 3.8 21.7 - + + -
29C ASP 2.5 29.2 + - - -
30C ASP* 2.8 19.2 + - - -
31C ASN 3.9 1.6 - - - -
32C HIS* 3.0 34.7 + + + -
85C PHE* 3.4 29.8 - + + -
87C ALA* 4.5 12.1 - - + +
158C GLN* 2.8 23.6 + - + +
159C GLU 3.5 2.5 - - - +
161C ASP* 1.3 74.2 - - - +
163C LEU* 1.3 68.3 + - + +
165C ARG* 4.1 0.2 - - - +
166C HIS* 2.8 44.8 + + + +
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Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C HIS* 6.0 0.9 - - + +
85C PHE* 4.0 19.5 - - + -
148C VAL* 4.0 23.8 - - + +
149C GLN 3.5 26.0 - - - +
159C GLU* 2.8 44.1 + - + +
160C LEU* 3.8 10.5 - - + +
162C TYR* 1.3 83.6 - - + +
164C THR* 1.3 61.9 + - - +
166C HIS* 4.0 2.5 + - - +
167C TYR* 3.3 23.0 + - - +
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Residues in contact with THR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C VAL* 3.6 42.1 - - + +
146C PHE* 3.9 6.9 - - + -
148C VAL* 3.9 8.2 - - - +
160C LEU 2.8 27.1 + - - -
161C ASP 3.6 3.6 - - - -
163C LEU* 1.3 74.2 - - - +
165C ARG* 1.3 64.7 + - + +
167C TYR* 3.3 5.2 + - - +
168C LEU* 3.1 25.4 + - + +
187C ILE* 3.9 11.8 - - + +
200C MET* 5.8 0.2 - - + -
230C ILE* 3.6 9.9 - - + +
232C VAL* 3.7 19.3 - - + -
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Residues in contact with ARG 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C MET* 4.2 0.2 - - - -
28C TYR* 3.3 45.5 + - + -
161C ASP* 2.7 54.1 + - - +
164C THR* 1.3 75.1 - - - +
166C HIS* 1.3 58.0 + - - +
168C LEU* 3.1 4.1 + - - +
169C VAL* 2.7 33.1 + - - +
174C LEU* 4.0 10.0 - - + +
175C TYR* 2.9 28.9 + - - -
187C ILE* 4.5 0.6 - - + +
198C TYR* 4.2 4.2 - - - +
199C ASP 4.0 1.2 + - - -
200C MET* 3.5 37.4 + - + +
213C TYR* 2.6 32.7 + - - -
216C MET* 3.6 13.1 - - - +
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Residues in contact with HIS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 2.8 30.4 + - - +
29C ASP* 3.2 18.3 - - - -
30C ASP* 3.3 29.3 + - - -
162C TYR* 2.8 33.7 + - + +
163C LEU* 4.0 4.5 - - - +
165C ARG* 1.3 76.9 - - - +
167C TYR* 1.3 63.0 + - - +
169C VAL* 3.3 3.5 + - + +
170C LYS* 3.2 61.1 + - + +
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Residues in contact with TYR 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 4.4 17.7 - - + +
146C PHE* 3.5 56.7 - + + +
148C VAL* 5.8 0.2 - - + -
163C LEU 3.3 16.1 + - - +
164C THR 3.6 4.7 - - - +
165C ARG 3.2 0.2 - - - -
166C HIS* 1.3 80.0 + - - +
168C LEU* 1.3 57.8 + - - +
170C LYS* 3.4 10.6 + - + -
171C ASN* 2.7 70.9 + - + +
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C VAL* 3.8 23.8 - - + -
144C LEU* 3.9 20.0 - - + -
146C PHE* 4.0 7.2 - - + -
164C THR* 3.1 19.7 + - + +
165C ARG 3.1 8.6 + - - +
167C TYR* 1.3 77.1 - - - +
169C VAL* 1.3 58.5 + - - +
172C LYS* 2.7 40.5 + - + +
173C LYS 3.1 5.7 + - - -
174C LEU* 3.2 26.4 + - + -
200C MET* 4.4 2.5 - - + -
232C VAL* 3.9 39.0 - - + -
234C LEU* 4.8 7.2 - - + -
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LYS* 3.7 35.9 - - + +
28C TYR* 4.0 16.8 - - + +
29C ASP* 3.8 8.1 - - - +
165C ARG 2.7 24.8 + - - +
166C HIS* 3.3 6.9 + - + +
168C LEU* 1.3 73.7 - - - +
170C LYS* 1.3 65.1 + - + +
173C LYS* 3.1 25.8 + - - +
174C LEU* 3.8 9.0 - - + +
175C TYR* 3.6 37.9 - - + +
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ASP* 5.6 3.6 - - - -
166C HIS* 3.2 46.5 + - + +
167C TYR* 3.8 11.8 - - + +
169C VAL* 1.3 85.2 - - + +
171C ASN* 1.3 71.2 + - - +
173C LYS* 4.4 16.3 + - - +
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Residues in contact with ASN 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LEU* 5.0 4.7 - - + -
167C TYR* 2.7 74.0 + - + +
168C LEU* 4.9 0.2 - - - -
170C LYS* 1.3 89.0 - - - +
172C LYS* 1.3 69.5 + - + +
173C LYS* 3.7 1.9 - - - +
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Residues in contact with LYS 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C VAL* 5.4 4.9 - - + -
138C GLU* 2.6 30.1 + - - +
143C LEU* 4.2 19.4 + - - +
144C LEU* 3.8 29.8 - - + +
168C LEU* 2.7 41.6 + - + +
171C ASN* 1.3 79.9 - - - +
173C LYS* 1.3 71.8 + - - +
174C LEU 3.0 1.2 + - - +
181C PRO* 4.0 2.6 - - - +
182C TYR* 3.4 30.4 + - + +
234C LEU* 5.4 1.3 - - + -
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Residues in contact with LYS 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LYS* 6.3 3.0 - - - +
168C LEU 3.1 2.2 + - - -
169C VAL 3.1 17.6 + - - +
170C LYS* 4.4 13.6 + - - +
171C ASN 5.4 0.9 - - - -
172C LYS* 1.3 80.4 - - - +
174C LEU* 1.3 66.0 + - - +
175C TYR 3.0 8.8 + - - +
176C GLU* 3.5 30.2 - - + +
181C PRO* 3.0 22.3 - - + +
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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
------------------------------------------------------------
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