Contacts of the helix formed by residues 152 - 163 (chain C) in PDB entry 2PI8
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 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C TYR* 3.4 7.7 - - - -
150C SER* 3.1 15.3 + - - -
151C ASN* 1.3 85.0 + - - +
153C LEU* 1.3 61.7 + - - +
154C MSE 3.3 12.0 + - - +
155C ASP* 3.3 39.9 + - - +
156C ASN* 3.4 13.3 + - - +
212C ARG* 5.5 0.2 + - - -
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Residues in contact with LEU 153 (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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118C TYR* 3.7 32.5 - - + -
119C PRO* 6.4 0.4 - - + -
137C TYR* 3.8 33.9 + - + +
152C SER* 1.3 71.6 + - - +
154C MSE 1.3 59.0 + - - +
155C ASP 3.4 0.2 - - - -
156C ASN* 3.5 10.6 + - + +
157C PHE* 3.1 25.6 + - - +
220C GLU* 3.2 31.8 + - - +
223C VAL* 4.7 3.6 - - + -
224C ARG* 3.8 31.9 - - + +
227C LEU* 3.8 16.3 - - + +
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Residues in contact with MSE 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C SER* 3.1 9.7 + - - +
153C LEU* 1.3 77.3 - - - +
155C ASP* 1.3 62.2 + - - +
157C PHE* 3.2 9.0 + - - +
158C ILE* 2.9 56.1 + - + +
211C ILE* 3.4 41.5 - - + +
212C ARG* 4.3 18.6 - - + +
214C TRP* 4.9 3.6 - - + -
215C GLY* 3.8 20.0 - - - -
216C GLU* 6.5 0.2 - - + -
223C VAL* 4.0 20.3 - - + +
226C LEU* 5.5 0.4 - - + -
227C LEU* 4.3 19.5 - - + +
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Residues in contact with ASP 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C PRO* 5.3 1.2 - - - +
105C VAL 5.6 0.3 - - - +
106C ILE* 3.3 38.9 - - + +
151C ASN* 4.1 7.6 - - - +
152C SER* 3.3 29.0 + - - +
154C MSE 1.3 77.7 - - - +
156C ASN* 1.3 58.2 + - - +
158C ILE* 3.4 2.8 + - - +
159C MSE 2.9 23.6 + - - +
212C ARG* 2.9 40.6 + - - +
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Residues in contact with ASN 156 (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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106C ILE* 4.0 8.1 - - - +
118C TYR* 3.2 27.3 + - - +
119C PRO 3.7 13.3 + - - +
120C ILE* 4.0 12.9 - - - +
133C ARG* 5.5 2.7 - - - +
137C TYR* 6.1 0.4 - - - +
150C SER* 2.6 37.6 + - - -
152C SER 3.4 2.8 + - - +
153C LEU* 3.6 14.8 - - + +
154C MSE 3.2 0.6 - - - -
155C ASP* 1.3 76.5 - - - +
157C PHE* 1.3 57.9 + - - +
159C MSE 3.4 14.6 + - + +
160C ASP* 2.9 29.2 + - - +
236C PHE* 5.5 0.2 - - - -
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Residues in contact with PHE 157 (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 ARG* 3.5 31.8 - - - +
137C TYR* 5.0 0.4 + - - +
153C LEU 3.1 14.4 + - - +
154C MSE 3.2 15.9 + - - +
156C ASN* 1.3 75.5 - - - +
158C ILE* 1.3 67.9 + - + +
160C ASP* 3.1 9.0 - - - +
161C VAL* 3.0 42.6 + - + +
188C TYR* 5.3 3.6 - + - -
191C ILE* 3.3 33.2 - - + -
208C MSE 5.5 5.8 - - + -
211C ILE* 6.4 1.3 - - + -
227C LEU* 3.8 42.4 - - + -
230C ASN* 3.5 29.8 - - + -
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Residues in contact with ILE 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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102C TYR* 3.5 25.4 - - + +
104C PRO* 5.1 2.2 - - + -
154C MSE 2.9 34.9 + - + +
155C ASP 3.8 3.8 - - - +
157C PHE* 1.3 75.3 - - + +
159C MSE 1.3 61.8 + - - +
161C VAL* 3.1 7.7 + - - +
162C GLN* 2.9 50.2 + - + +
208C MSE 4.8 11.0 - - - +
209C GLN* 6.1 0.4 - - - -
212C ARG* 3.1 47.1 - - + +
2G NAG 5.4 1.1 - - + +
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Residues in contact with MSE 159 (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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104C PRO* 3.8 14.8 - - + +
106C ILE* 3.5 25.6 - - + -
120C ILE* 3.9 26.0 - - + -
155C ASP 2.9 19.0 + - - +
156C ASN* 4.1 13.7 - - + +
158C ILE* 1.3 76.4 - - - +
160C ASP* 1.3 62.2 + - - +
162C GLN* 3.3 0.8 + - - -
163C GLY* 3.1 19.4 + - - -
164C SER 3.4 24.6 + - - +
165C GLY* 4.1 15.3 - - - +
167C ILE* 4.0 17.0 - - - -
178C PHE* 5.0 3.8 - - - -
236C PHE* 3.6 31.9 - - + -
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Residues in contact with ASP 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 ARG* 3.0 31.8 + - - +
156C ASN 2.9 15.1 + - - +
157C PHE* 3.1 15.3 - - - +
159C MSE 1.3 79.7 - - - +
161C VAL* 1.3 60.7 + - + +
163C GLY* 3.6 6.6 + - - -
188C TYR* 6.1 1.2 - - - -
230C ASN* 4.9 2.8 + - - -
232C SER* 4.4 2.1 + - - +
233C PHE* 3.9 6.8 - - - -
234C VAL* 2.9 57.0 + - - +
236C PHE* 4.0 12.1 - - + -
3G NAG 5.2 3.1 + - - +
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Residues in contact with VAL 161 (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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157C PHE* 3.0 37.9 + - + +
158C ILE* 3.1 8.5 + - - +
160C ASP* 1.3 79.5 - - + +
162C GLN* 1.3 63.1 + - - +
163C GLY 3.5 0.2 + - - -
188C TYR* 4.2 27.8 - - + +
208C MSE 5.5 5.2 - - + -
230C ASN* 5.3 0.7 - - - +
1G NAG 4.6 0.7 - - - +
2G NAG 3.0 45.3 + - - +
3G NAG 2.7 38.3 + - + -
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Residues in contact with GLN 162 (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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101C TYR* 3.2 22.9 - - - +
102C TYR* 2.9 58.6 + - + +
104C PRO* 3.8 12.6 - - + -
158C ILE* 2.9 37.9 + - - +
159C MSE 3.3 5.1 + - - +
161C VAL* 1.3 79.5 - - - +
163C GLY* 1.3 58.4 + - - +
164C SER 3.4 10.2 + - - +
2G NAG 3.0 35.3 + - - +
3G NAG 3.3 22.2 + - - +
4G NAG 4.2 3.8 - - - +
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Residues in contact with GLY 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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159C MSE 3.1 6.0 + - - -
160C ASP 3.6 6.5 + - - -
161C VAL 3.3 2.8 - - - -
162C GLN* 1.3 78.0 - - - +
164C SER* 1.3 61.5 + - - +
180C TYR* 3.2 35.1 + - - +
234C VAL* 5.2 0.2 - - - -
236C PHE* 3.6 12.1 - - - -
3G NAG 3.7 11.9 - - - -
4G NAG 3.2 12.1 - - - +
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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