Contacts of the helix formed by residues 153 - 169 (chain C) in PDB entry 3P8Z
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 SER 153 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C SER* 3.0 8.1 + - - -
152C PRO* 1.3 78.0 - - - +
154C PRO* 1.4 66.2 - - - +
155C THR* 3.1 22.5 + - - -
156C VAL* 3.2 26.8 + - - +
157C GLU* 3.0 24.1 + - - +
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Residues in contact with PRO 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU* 5.1 6.3 - - + +
14C LYS* 4.2 14.1 - - + -
18C ASN* 5.0 0.9 - - - +
152C PRO 3.2 11.4 - - - +
153C SER* 1.4 84.4 - - - +
155C THR* 1.3 60.9 + - + +
157C GLU* 3.7 6.3 - - - +
158C GLU* 2.8 28.2 + - - +
183C ASN* 3.8 10.1 + - - +
185C TYR* 3.8 21.3 - - + +
186C MET* 3.9 24.1 - - + +
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Residues in contact with THR 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C SER* 3.1 12.5 + - - -
154C PRO* 1.3 78.4 - - + +
156C VAL* 1.3 64.5 + - - +
158C GLU* 3.5 14.7 - - - +
159C SER* 3.1 25.8 + - - -
186C MET* 3.9 17.9 - - + -
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C SER* 3.6 12.3 - - - +
153C SER* 3.2 29.3 + - - +
155C THR* 1.3 76.5 + - - +
157C GLU* 1.3 62.7 + - - +
159C SER* 3.3 10.2 + - - -
160C ARG* 3.0 58.4 + - + +
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Residues in contact with GLU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TRP* 6.0 0.3 - - - -
14C LYS* 3.2 19.8 + - - -
150C SER* 3.4 12.5 + - - -
151C SER* 3.0 42.4 + - - +
153C SER 3.0 11.8 + - - +
154C PRO* 3.7 5.7 - - - +
156C VAL* 1.3 75.9 - - - +
158C GLU* 1.3 57.6 + - - +
160C ARG* 3.2 4.1 + - - +
161C THR* 2.8 35.9 + - - -
182C LEU* 3.8 27.3 - - + +
183C ASN* 2.9 27.8 + - + +
185C TYR* 4.0 1.9 + - - -
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Residues in contact with GLU 158 (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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154C PRO 2.8 21.0 + - - +
155C THR* 3.5 15.1 - - - +
157C GLU* 1.3 72.6 - - - +
159C SER* 1.3 58.1 + - - +
161C THR* 3.3 1.8 + - - -
162C ILE* 2.9 50.3 + - + +
183C ASN* 4.5 1.5 - - - +
186C MET* 3.8 30.6 - - + +
187C PRO* 4.7 1.2 - - - +
188C THR* 2.9 37.5 + - - -
189C VAL* 3.8 16.4 - - + -
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Residues in contact with SER 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C THR 3.1 13.9 + - - -
156C VAL* 3.4 10.9 - - - -
158C GLU* 1.3 75.6 - - - +
160C ARG* 1.3 65.8 + - - +
162C ILE* 3.4 5.6 + - - +
163C ARG* 3.0 25.2 + - - +
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Residues in contact with ARG 160 (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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133C PHE* 5.6 0.2 - - - -
148C GLY* 5.5 2.9 - - - -
149C GLU* 2.8 69.4 + - - +
150C SER 3.3 16.8 + - - -
151C SER* 3.9 5.9 - - - -
156C VAL* 3.0 40.3 + - + +
157C GLU* 3.7 7.2 - - - +
159C SER* 1.3 76.6 - - - +
161C THR* 1.3 62.6 + - - +
163C ARG* 3.3 9.4 + - - +
164C VAL* 3.1 28.1 + - + +
182C LEU* 4.4 7.6 - - + -
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Residues in contact with THR 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C GLU 2.8 23.3 + - - -
158C GLU 3.7 3.4 - - - -
160C ARG* 1.3 71.5 - - - +
162C ILE* 1.3 66.6 + - - +
164C VAL* 3.2 9.8 + - + +
165C LEU* 3.0 28.0 + - + +
180C LYS 5.7 0.2 - - - +
181C VAL* 3.7 31.6 - - + -
182C LEU* 3.4 13.8 - - - +
183C ASN* 3.1 31.9 + - - +
189C VAL* 3.8 13.9 - - + -
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Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C GLU* 2.9 36.9 + - + +
159C SER* 4.0 5.8 - - - +
161C THR* 1.3 75.0 - - - +
163C ARG* 1.3 57.7 + - - +
165C LEU* 3.2 8.3 + - + +
166C LYS* 2.9 58.1 + - + +
188C THR* 3.5 32.8 - - + -
189C VAL* 4.1 15.0 - - + -
192C HIS* 4.1 17.7 - - + +
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Residues in contact with ARG 163 (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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131C ASP* 5.0 4.4 + - - -
133C PHE* 3.3 56.2 - - + +
134C TYR* 5.6 5.1 + - - -
159C SER 3.0 17.3 + - - +
160C ARG* 3.5 8.5 - - - +
161C THR 3.1 0.2 - - - -
162C ILE* 1.3 78.5 - - - +
164C VAL* 1.3 61.5 + - - +
166C LYS* 3.4 9.0 + - + +
167C MET* 3.0 24.8 + - - +
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Residues in contact with VAL 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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133C PHE* 4.2 10.1 - - + -
145C CYS* 4.2 14.1 - - - -
147C ILE* 3.8 36.6 - - + +
148C GLY* 4.9 2.7 - - - +
160C ARG* 3.1 16.1 + - + +
161C THR* 3.2 10.3 + - - +
163C ARG* 1.3 75.1 - - - +
165C LEU* 1.3 59.6 + - + +
167C MET* 3.2 9.3 + - + +
168C VAL* 2.9 44.4 + - + +
179C ILE* 4.4 4.9 - - + -
180C LYS 4.3 16.8 - - - +
182C LEU* 6.6 0.2 - - + -
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Residues in contact with LEU 165 (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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161C THR* 3.0 36.0 + - + +
162C ILE* 3.2 6.5 + - + +
164C VAL* 1.3 78.5 - - + +
166C LYS* 1.3 61.3 + - - +
168C VAL* 3.5 4.8 - - + +
169C GLU* 3.3 24.4 + - - +
179C ILE* 4.7 10.1 - - + -
180C LYS 5.4 0.9 - - - +
181C VAL* 4.4 11.7 - - + -
189C VAL* 4.3 6.7 - - + -
192C HIS* 3.9 34.0 + - + +
193C LEU* 3.9 37.2 - - + -
196C LEU* 4.0 14.9 - - + +
219C TRP* 4.3 13.7 - - + -
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Residues in contact with LYS 166 (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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162C ILE* 2.9 40.4 + - + +
163C ARG* 3.8 7.6 - - - +
165C LEU* 1.3 74.5 - - - +
167C MET* 1.3 63.1 + - - +
169C GLU* 3.9 4.3 + - - +
170C PRO* 3.4 17.0 - - - +
192C HIS* 3.9 20.0 - - + -
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Residues in contact with MET 167 (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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80C LEU* 3.9 20.4 - - + -
132C VAL* 3.5 41.5 - - + +
133C PHE* 3.4 32.5 - - + -
145C CYS* 4.1 15.3 - - - -
147C ILE* 4.3 3.4 - - + -
163C ARG 3.0 18.0 + - - +
164C VAL* 3.2 7.2 + - + +
166C LYS* 1.3 76.8 - - - +
168C VAL* 1.3 79.3 + - + +
170C PRO* 3.2 13.9 - - - +
171C TRP* 3.4 13.6 + - - +
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Residues in contact with VAL 168 (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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80C LEU* 4.7 0.9 - - + -
143C LEU* 4.5 7.4 - - + -
145C CYS* 4.0 25.1 - - + -
164C VAL* 2.9 26.2 + - + +
165C LEU* 3.5 16.6 - - + +
167C MET* 1.3 93.2 - - + +
169C GLU* 1.3 71.8 + - - +
171C TRP* 2.9 26.2 + - - +
172C LEU* 3.7 5.8 - - + +
179C ILE* 3.8 33.2 - - + -
219C TRP* 4.4 10.3 - - + -
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Residues in contact with GLU 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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165C LEU 3.3 13.8 + - - +
166C LYS* 4.2 4.7 - - - +
168C VAL* 1.3 82.7 - - - +
170C PRO* 1.4 77.5 - - + +
172C LEU* 3.1 26.7 + - - +
173C LYS* 5.7 0.2 - - - -
196C LEU* 3.5 24.0 - - + -
199C LYS* 2.6 34.1 + - + -
200C HIS* 2.8 24.6 + - + +
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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