Contacts of the helix formed by residues 152 - 170 (chain C) in PDB entry 2PQA
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 MET 152 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C TYR* 3.5 51.8 - - + -
149C LEU* 4.2 17.5 - - - +
150C GLU 4.0 1.7 + - - +
151C ASP* 1.3 72.9 + - - +
153C ASN* 1.3 56.9 + - - +
154C GLU 3.1 0.2 - - - -
155C PHE* 2.9 46.1 + - + +
156C THR 3.4 0.7 + - - -
87D PHE* 3.5 39.3 - - + -
88D LYS* 4.1 22.5 + - + +
89D GLU* 6.4 0.4 - - + -
94D PHE* 3.5 22.4 - - + -
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Residues in contact with ASN 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LYS* 4.5 11.7 + - - +
151C ASP* 3.1 23.7 + - - +
152C MET* 1.3 76.8 - - - +
154C GLU* 1.3 55.2 + - - +
156C THR* 3.0 9.1 + - - +
157C THR* 2.9 32.5 + - + +
92D HIS* 4.4 2.8 - - - +
93D PRO 2.8 33.7 + - - -
94D PHE* 3.7 9.0 - - - +
95D ASP* 3.1 33.7 + - - +
98D LEU* 5.1 6.6 - - + +
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Residues in contact with GLU 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 5.4 5.1 - - - +
161A GLU* 4.7 11.9 - - - +
77C VAL* 4.8 2.6 - - - +
127C LYS* 3.5 34.1 + - + +
147C MET* 5.5 4.0 - - - +
149C LEU* 3.8 27.6 - - + +
150C GLU 5.0 1.2 + - - -
151C ASP* 2.8 30.1 + - + +
153C ASN* 1.3 78.4 - - - +
155C PHE* 1.3 55.9 + - - +
157C THR* 3.5 8.9 + - - +
158C HIS* 3.2 24.9 + - - +
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Residues in contact with PHE 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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77C VAL* 3.9 20.4 - - + -
125C TYR* 4.1 18.6 - + - -
149C LEU* 3.8 19.4 - - + +
151C ASP 4.1 0.6 + - - -
152C MET* 2.9 33.6 + - + +
154C GLU* 1.3 77.4 - - - +
156C THR* 1.3 68.1 + - - +
158C HIS* 3.3 10.0 + - - +
159C ILE* 3.4 23.9 + - + +
11D ARG* 3.3 44.6 - - - -
68D GLU* 4.0 2.7 - - - -
87D PHE* 3.8 22.0 - + - -
94D PHE* 4.1 1.8 - + - -
99D TYR* 3.8 25.1 - + - -
113D TYR* 6.1 0.2 - - - -
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Residues in contact with THR 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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152C MET 3.4 1.6 + - - -
153C ASN* 3.0 12.7 + - - -
155C PHE* 1.3 78.7 - - - +
157C THR* 1.3 63.2 + - - +
159C ILE* 3.1 22.6 + - - +
160C LEU* 3.3 12.5 + - + +
94D PHE* 3.4 29.3 - - - -
95D ASP 5.2 0.6 + - - -
98D LEU* 3.8 35.9 - - + +
99D TYR* 3.7 24.4 + - + +
102D ALA* 4.0 11.0 - - + -
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Residues in contact with THR 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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46A ILE* 4.5 17.7 - - + -
153C ASN* 2.9 17.7 + - + +
154C GLU* 3.5 13.2 + - - +
156C THR* 1.3 76.8 - - - +
158C HIS* 1.3 56.4 + - - +
160C LEU* 3.3 22.4 + - + +
161C GLU* 2.8 42.9 + - - +
98D LEU* 4.6 11.0 - - + -
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Residues in contact with HIS 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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48C PRO* 3.5 12.3 - - + +
49C CYS 3.4 26.7 - - - -
75C THR* 3.3 37.0 + - + +
76C ILE* 3.7 11.2 - - - -
77C VAL* 3.6 28.4 + - + +
127C LYS* 4.5 10.1 - - + +
154C GLU 3.2 18.3 + - - +
155C PHE 3.6 7.0 - - - +
156C THR 3.1 0.8 - - - -
157C THR* 1.3 75.6 - - - +
159C ILE* 1.3 60.6 + - - +
161C GLU* 3.1 12.2 + - - +
162C VAL* 2.8 45.2 + - + +
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Residues in contact with ILE 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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155C PHE* 3.4 37.4 + - + +
156C THR* 3.1 10.0 + - - +
158C HIS* 1.3 76.7 + - - +
160C LEU* 1.3 63.0 + - + +
162C VAL* 3.4 3.6 + - - +
163C ILE* 3.3 30.3 + - + +
11D ARG* 4.3 7.2 - - - -
99D TYR* 4.4 10.5 - - + -
102D ALA* 3.8 18.8 - - + +
106D ILE* 3.7 40.2 - - + -
113D TYR* 3.9 27.5 - - + +
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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
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44A GLN* 4.1 31.9 - - + +
45A HIS* 5.9 1.1 - - - -
46A ILE* 3.8 29.6 - - + +
156C THR 3.3 10.5 + - - +
157C THR* 3.6 17.9 - - + +
158C HIS 3.2 0.4 - - - -
159C ILE* 1.3 76.1 - - - +
161C GLU* 1.3 58.8 + - + +
163C ILE* 3.5 0.7 + - - +
164C ASN* 3.0 38.5 + - - +
98D LEU* 4.2 12.3 - - + -
102D ALA* 3.7 27.4 - - + +
105D ILE* 3.5 28.9 - - + -
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Residues in contact with GLU 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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46A ILE 4.5 14.7 - - - +
48A PRO* 4.7 13.3 - - - +
161A GLU* 5.7 4.7 - - - +
165A ALA* 5.8 1.4 - - - +
48C PRO* 3.7 17.4 - - + +
127C LYS* 4.9 8.1 + - - -
157C THR* 2.8 34.2 + - - +
158C HIS* 3.1 13.1 + - - +
160C LEU* 1.3 73.5 - - + +
162C VAL* 1.3 56.9 + - - +
164C ASN* 4.8 2.5 - - - -
165C ALA* 2.8 38.5 + - - +
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Residues in contact with VAL 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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48C PRO* 3.6 9.8 - - + +
49C CYS 3.6 27.6 - - - +
50C THR* 4.2 13.9 - - + +
53C GLN* 3.5 24.2 - - - +
158C HIS* 2.8 39.1 + - + +
159C ILE* 3.7 7.2 - - - +
161C GLU* 1.3 73.7 - - - +
163C ILE* 1.3 65.4 + - - +
166C HIS* 2.9 32.1 + - + -
112D PHE 3.5 16.2 - - - +
113D TYR* 4.4 5.2 - - + -
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Residues in contact with ILE 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 ALA 5.5 1.1 - - - +
159C ILE* 3.3 16.8 + - + +
160C LEU 4.0 2.7 - - - +
162C VAL* 1.3 79.0 - - - +
164C ASN* 1.3 63.3 + - - +
167C MET* 2.9 34.0 + - + +
105D ILE* 3.4 41.7 - - + +
106D ILE* 3.8 25.1 - - + +
109D PHE* 3.9 29.8 - - + -
112D PHE* 3.8 28.3 - - + +
113D TYR* 4.0 15.7 - - + -
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Residues in contact with ASN 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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43A ALA 4.5 9.1 + - - -
44A GLN 3.5 15.6 + - - +
45A HIS* 3.0 47.0 + - + +
160C LEU* 3.0 26.3 + - - +
161C GLU* 4.3 2.7 - - - +
163C ILE* 1.3 77.0 - - - +
165C ALA* 1.3 59.3 + - - +
167C MET* 3.3 31.4 - - + +
168C VAL* 2.9 34.9 + - - +
105D ILE* 4.6 5.0 - - - +
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Residues in contact with ALA 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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168A VAL* 4.4 17.3 - - + -
47C VAL* 5.0 0.4 - - + -
48C PRO* 3.7 26.5 - - + -
161C GLU 2.8 23.9 + - - +
162C VAL 3.7 0.9 - - - +
164C ASN* 1.3 73.6 - - - +
166C HIS* 1.3 61.4 + - + +
168C VAL* 3.8 3.7 - - - +
169C LEU* 2.8 41.8 + - + +
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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
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47C VAL* 3.8 9.6 - - + +
48C PRO 2.9 25.1 + - - -
49C CYS* 3.5 15.5 - - - -
53C GLN* 3.0 41.6 + - - +
66C ILE* 4.1 16.2 + - + +
69C VAL* 4.1 13.0 - - + +
71C ILE* 4.2 9.6 - - + -
162C VAL* 2.9 27.8 + - + +
163C ILE 4.1 1.1 - - - +
165C ALA* 1.3 75.3 - - + +
167C MET* 1.3 53.8 + - - +
169C LEU* 4.7 4.3 - - - -
170C SER* 2.8 42.7 + - - -
112D PHE* 3.9 18.8 - - + -
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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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42A ARG* 3.9 27.6 - - - +
43A ALA 5.5 1.1 - - - +
45A HIS* 5.6 4.9 - - + +
163C ILE* 2.9 23.7 + - - +
164C ASN* 3.3 33.2 - - - +
166C HIS* 1.3 77.9 - - - +
168C VAL* 1.3 72.2 + - + +
170C SER* 3.6 12.6 + - - +
109D PHE* 4.5 15.7 - - - -
112D PHE* 3.6 29.3 - - + -
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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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45A HIS* 5.1 8.5 - - + +
69A VAL* 4.3 25.4 - - + -
168A VAL* 4.6 13.5 - - + +
169A LEU* 4.7 12.3 - - + -
172A ALA* 3.5 33.1 - - + +
164C ASN 2.9 21.8 + - - +
165C ALA* 3.9 4.0 - - - +
167C MET* 1.3 85.5 - - + +
169C LEU* 1.3 71.5 + - + +
170C SER 3.8 4.2 - - - +
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Residues in contact with LEU 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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168A VAL* 4.0 36.1 - - + +
171A LYS* 4.2 17.7 - - + +
172A ALA* 4.7 6.1 - - - +
45C HIS* 5.3 6.3 - - + +
47C VAL* 4.1 31.2 - - + -
68C ASN* 5.2 1.4 - - - +
69C VAL* 4.0 31.2 - - + +
165C ALA* 2.8 29.3 + - + +
166C HIS 4.1 1.3 - - - +
168C VAL* 1.3 76.6 - - + +
170C SER* 1.3 67.2 + - - +
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Residues in contact with SER 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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68C ASN* 4.0 38.8 - - - -
69C VAL* 5.0 6.0 - - - +
166C HIS* 2.8 27.8 + - - -
167C MET 3.6 8.8 + - - +
168C VAL 3.5 6.5 - - - +
169C LEU* 1.3 79.3 - - - +
112D PHE* 3.4 23.7 - - - -
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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
------------------------------------------------------------
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