Contacts of the helix formed by residues 153 - 164 (chain C) in PDB entry 2Q41
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 ASP 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C SER* 2.5 29.1 + - - -
75C TYR* 3.8 14.3 - - + +
76C GLN* 2.7 29.0 + - - +
78C VAL* 4.9 0.5 - - - +
151C GLU* 2.5 37.7 + - - +
152C ILE* 1.3 77.3 - - + +
154C LYS* 1.3 57.8 + - - +
155C MSE 2.9 24.2 + - - +
156C VAL* 3.0 23.4 + - + +
157C VAL 3.3 1.6 + - - -
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Residues in contact with LYS 154 (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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41A SER 5.8 2.0 - - - +
75C TYR* 5.6 0.6 - - - -
152C ILE 4.1 1.0 + - - -
153C ASP* 1.3 70.5 + - - +
155C MSE 1.3 60.2 + - - +
157C VAL* 3.5 2.1 + - + +
158C ASP* 2.9 66.2 + - - +
180C ILE* 3.3 42.1 - - + +
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Residues in contact with MSE 155 (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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51A MSE 4.3 17.5 - - + -
69C PHE* 3.8 20.2 - - + -
72C LYS 3.4 24.9 - - - +
73C SER* 3.5 28.9 - - - -
78C VAL* 3.8 17.0 - - + -
153C ASP* 2.9 15.2 + - - +
154C LYS* 1.3 78.1 - - - +
156C VAL* 1.3 52.1 + - + +
158C ASP* 3.2 4.4 + - - -
159C VAL* 2.6 54.3 + - + +
44D ILE* 4.6 8.7 - - + -
45D PRO* 3.9 14.4 - - + +
47D TRP* 6.1 2.0 - - - +
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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
----------------------------------------------------------
76C GLN* 3.7 26.5 - - - +
78C VAL* 4.8 10.1 - - + -
90C LEU* 4.8 7.9 - - + -
92C LEU* 3.9 24.7 - - + -
130C GLY* 3.4 37.0 - - - +
151C GLU* 4.2 7.2 - - + +
153C ASP* 3.0 16.5 + - + +
155C MSE 1.3 73.1 - - - +
157C VAL* 1.3 67.0 + - - +
158C ASP 3.0 1.3 - - - -
159C VAL* 4.6 2.0 - - - +
160C SER* 2.9 33.7 + - - +
171C TYR* 5.4 0.2 - - - +
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Residues in contact with VAL 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C GLU* 3.3 35.9 - - + -
153C ASP 3.3 3.9 + - - +
154C LYS* 3.9 5.8 - - + +
156C VAL* 1.3 77.5 - - - +
158C ASP* 1.3 58.8 + - - +
161C LYS* 3.1 29.5 - - + +
171C TYR* 3.6 31.4 - - + +
178C LEU* 3.4 33.2 - - + -
180C ILE* 4.0 16.6 - - + -
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Residues in contact with ASP 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER 4.2 24.5 + - - +
154C LYS* 2.9 55.4 + - - +
155C MSE 3.6 5.2 - - - +
157C VAL* 1.3 79.8 - - - +
159C VAL* 1.3 67.1 + - - +
161C LYS* 4.4 4.1 - - - +
162C GLN* 2.9 28.4 + - - +
45D PRO* 4.4 18.3 - - + +
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Residues in contact with VAL 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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43A VAL* 5.2 0.4 - - + -
69C PHE* 3.3 57.9 - - + -
78C VAL* 5.2 4.3 - - + -
80C VAL* 3.5 15.7 - - + -
90C LEU* 6.0 0.4 - - + -
155C MSE 2.6 29.4 + - + +
156C VAL* 4.5 1.8 - - - +
158C ASP* 1.3 71.4 - - - +
160C SER* 1.3 65.1 + - - +
162C GLN* 3.2 7.2 - - - +
163C PHE* 3.0 44.3 + - + -
45D PRO* 3.5 14.4 - - + -
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Residues in contact with SER 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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80C VAL* 5.1 0.4 - - - +
90C LEU* 4.1 11.6 - - - +
130C GLY 3.9 10.3 + - - -
131C ASP* 3.4 31.4 + - - +
156C VAL* 2.9 21.2 + - - +
157C VAL* 4.8 1.1 - - - -
159C VAL* 1.3 72.7 - - - +
161C LYS* 1.3 67.2 + - - -
162C GLN 2.6 5.1 + - - -
163C PHE 2.7 14.0 + - - -
164C PHE* 2.9 34.9 + - - -
171C TYR* 5.0 0.2 - - - -
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Residues in contact with LYS 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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131C ASP 4.8 1.3 - - - -
157C VAL* 3.1 24.3 + - + +
158C ASP* 4.4 3.4 - - - +
160C SER* 1.3 78.6 + - - +
162C GLN* 1.3 60.0 + - - +
164C PHE* 3.1 20.6 - - - +
168C ALA* 3.2 33.6 - - + +
171C TYR* 3.5 32.0 - - + +
172C GLU* 5.6 6.9 - - - +
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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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41A SER 2.9 24.9 - - - +
42A THR* 2.9 24.8 - - + +
43A VAL* 2.7 42.7 + - - +
158C ASP 2.9 20.9 + - - +
159C VAL* 3.2 5.6 - - - +
160C SER 2.6 4.6 + - - -
161C LYS* 1.3 79.3 - - - +
163C PHE* 1.3 77.8 + - + +
164C PHE 3.8 0.7 + - - +
45D PRO* 5.8 0.7 - - - +
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Residues in contact with PHE 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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43A VAL* 3.1 32.3 - - + -
45A PRO* 3.7 20.9 - - + -
68C LEU* 4.1 22.2 - - + -
69C PHE* 3.8 11.4 - + + -
80C VAL* 3.9 25.6 - - + -
88C LYS* 3.5 29.2 + - + +
159C VAL* 3.0 46.1 + - + +
160C SER 2.7 8.8 + - - +
162C GLN* 1.3 91.4 - - - +
164C PHE* 1.3 58.6 + - + -
165C PRO* 4.0 4.2 - - - +
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Residues in contact with PHE 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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80C VAL* 3.9 31.0 - - + -
88C LYS* 3.4 32.1 - - + -
89C VAL 3.9 11.9 - - - -
90C LEU* 4.1 17.3 - - + -
98C LEU* 4.2 10.8 - - + -
100C GLU* 3.5 22.9 - - + -
160C SER* 2.9 47.3 + - - +
161C LYS 3.1 17.3 - - - +
162C GLN 3.4 1.5 - - - +
163C PHE* 1.3 82.5 - - + +
165C PRO* 1.3 68.6 - - + +
167C VAL* 3.4 28.0 - - + -
168C ALA* 3.6 7.6 + - - +
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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