Contacts of the helix formed by residues 152 - 172 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A TYR* 3.4 52.5 - - + -
149A LEU* 4.2 19.1 - - - +
150A GLU 4.0 1.9 + - - +
151A ASP* 1.3 69.6 + - - +
153A ASN* 1.3 59.7 + - - +
154A GLU 3.1 1.3 - - - -
155A PHE* 3.1 39.1 + - + +
156A THR 3.4 1.7 + - - -
87B PHE* 3.7 40.6 - - + -
88B LYS 4.2 20.0 + - - +
92B HIS 5.5 1.2 + - - -
94B PHE* 3.1 31.2 - - + -
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Residues in contact with ASN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASP* 3.0 19.4 + - - +
152A MET* 1.3 76.8 - - - +
154A GLU* 1.3 58.2 + - - +
155A PHE 3.2 0.2 - - - -
156A THR* 3.5 8.0 + - - -
157A THR* 3.0 32.0 + - - +
92B HIS* 4.9 4.2 - - - +
93B PRO 3.5 20.0 + - - -
94B PHE* 3.4 15.6 - - - -
95B ASP* 2.9 37.3 + - - +
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Residues in contact with GLU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 5.0 1.3 - - - +
127A LYS* 4.9 10.6 + - + +
149A LEU* 3.0 32.4 - - + +
150A GLU* 4.7 2.4 + - - +
151A ASP* 2.9 33.0 + - + +
153A ASN* 1.3 77.6 - - - +
155A PHE* 1.3 58.7 + - - +
157A THR* 3.6 9.0 - - + +
158A HIS* 2.9 28.8 + - - +
151C ASP* 5.4 1.6 - - - +
92D HIS* 3.1 37.7 + - - -
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Residues in contact with PHE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL* 4.1 15.0 - - + -
125A TYR* 4.2 13.0 - + - -
149A LEU* 3.8 22.9 - - + +
152A MET* 3.1 32.5 + - + +
154A GLU* 1.3 76.2 - - - +
156A THR* 1.3 75.8 + - - +
158A HIS* 3.2 12.4 + - - +
159A ILE* 3.3 23.9 + - + +
11B ARG* 3.3 46.9 - - - -
68B GLU* 4.3 1.3 - - - -
87B PHE* 3.9 21.5 - + - -
94B PHE* 4.3 0.4 - + - -
99B TYR* 3.6 28.7 - + - -
113B TYR* 5.6 0.9 - - - -
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A MET 3.4 1.4 + - - -
153A ASN* 3.7 11.4 + - - -
154A GLU 3.4 0.2 - - - -
155A PHE* 1.3 80.5 - - - +
157A THR* 1.3 65.6 + - - +
159A ILE* 3.1 26.2 + - - +
160A LEU* 3.5 12.4 + - + +
94B PHE* 3.2 32.2 - - - -
95B ASP 4.8 0.8 + - - +
98B LEU* 3.8 15.0 - - + +
99B TYR* 3.7 30.5 - - + +
102B ALA* 3.8 10.7 - - + +
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Residues in contact with THR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASN* 3.0 22.2 + - - +
154A GLU* 3.6 10.3 - - - +
155A PHE 3.2 0.2 - - - -
156A THR* 1.3 77.7 - - - +
158A HIS* 1.3 61.9 + - - +
160A LEU* 3.0 16.5 + - + +
161A GLU* 2.9 47.1 + - + +
154C GLU* 5.4 6.5 - - - +
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Residues in contact with HIS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 3.5 11.3 - - + +
49A CYS 3.4 17.3 - - - -
75A THR* 3.3 30.2 + - - -
76A ILE* 3.5 20.6 - - + +
77A VAL* 3.4 28.7 - - + +
127A LYS* 4.5 7.9 - - - +
154A GLU 2.9 18.6 + - - +
155A PHE 3.5 5.6 - - - +
157A THR* 1.3 77.8 - - - +
159A ILE* 1.3 54.6 + - + +
161A GLU* 3.1 16.9 + - - +
162A VAL* 2.7 56.1 + - + +
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PHE* 3.3 41.0 + - + +
156A THR* 3.1 13.2 + - - +
158A HIS* 1.3 78.3 - - + +
160A LEU* 1.3 58.7 + - - +
162A VAL* 3.3 5.7 + - - +
163A ILE* 2.9 38.8 + - + +
11B ARG* 4.4 11.4 - - - -
99B TYR* 4.4 7.0 - - + -
102B ALA* 4.5 14.8 - - + -
106B ILE* 3.6 27.1 - - + -
113B TYR* 3.7 31.6 - - + +
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A THR* 4.0 16.4 - - + +
157A THR* 3.0 13.7 + - + +
159A ILE* 1.3 79.5 - - - +
161A GLU* 1.3 58.0 + - + +
163A ILE* 3.3 6.8 + - + +
164A ASN* 2.8 33.3 + - - +
98B LEU* 5.8 2.2 - - + +
101B GLU* 6.3 0.4 - - + -
102B ALA* 4.0 23.1 - - + +
105B ILE* 3.8 35.7 - - + -
145C LYS* 3.6 28.5 - - - +
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 3.5 15.8 - - + +
127A LYS* 4.5 10.9 + - - -
157A THR* 2.9 37.3 + - + +
158A HIS* 3.4 25.0 - - - +
160A LEU* 1.3 73.4 - - + +
162A VAL* 1.3 65.6 + - - +
164A ASN* 4.3 3.1 - - - +
165A ALA* 2.9 27.7 + - - +
127C LYS* 4.7 16.4 + - - +
154C GLU* 4.7 10.6 - - - +
161C GLU* 5.7 5.2 - - - +
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PRO* 3.9 10.2 - - - +
49A CYS 3.9 14.4 - - - +
50A THR* 4.0 13.5 - - + +
53A GLN* 3.2 35.7 - - - +
158A HIS* 2.7 51.6 + - + +
159A ILE* 3.3 9.6 + - - +
161A GLU* 1.3 72.5 - - - +
163A ILE* 1.3 63.8 + - - +
166A HIS* 3.1 32.0 + - + -
112B PHE 3.8 5.4 - - - +
113B TYR* 4.3 5.4 - - + -
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 2.9 38.7 + - + +
160A LEU* 3.3 8.5 + - + +
162A VAL* 1.3 78.2 - - - +
164A ASN* 1.3 58.5 + - - +
166A HIS* 3.3 0.9 + - - -
167A MET* 2.9 47.6 + - + +
102B ALA 4.8 0.2 - - - +
105B ILE* 3.6 35.2 - - + +
106B ILE* 4.0 17.9 - - + +
109B PHE* 4.9 8.3 - - + +
112B PHE* 4.0 30.7 - - + +
113B TYR* 4.2 10.5 - - + -
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Residues in contact with ASN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU 2.8 20.4 + - - +
161A GLU* 4.3 2.9 - - - +
163A ILE* 1.3 73.9 - - - +
165A ALA* 1.3 63.9 + - - +
167A MET* 3.2 15.0 + - + +
168A VAL* 3.0 25.0 + - - +
45C HIS* 3.6 9.9 - - - +
46C ILE* 2.7 64.0 - - + +
48C PRO* 5.3 1.6 - - - +
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.4 5.4 - - + -
48A PRO* 3.6 26.7 - - + -
161A GLU 2.9 19.8 + - - +
162A VAL 3.8 3.1 - - - +
164A ASN* 1.3 76.8 + - - +
166A HIS* 1.3 63.1 + - + +
168A VAL* 3.3 9.4 + - - +
169A LEU* 3.2 31.5 + - + +
161C GLU* 5.8 1.6 - - - +
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Residues in contact with HIS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.5 13.8 - - + +
48A PRO 3.1 24.5 + - - -
49A CYS* 3.6 7.0 - - - -
53A GLN* 3.4 45.5 + - + +
66A ILE* 3.9 28.6 - - + +
162A VAL 3.1 27.3 + - - +
163A ILE 4.1 0.9 - - - +
165A ALA* 1.3 76.2 - - - +
167A MET* 1.3 64.3 + - - +
168A VAL 3.1 0.9 - - - -
169A LEU* 4.3 12.9 - - + +
170A SER* 3.1 24.4 + - - -
112B PHE* 3.3 21.1 - - + -
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Residues in contact with MET 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE* 2.9 31.4 + - + +
164A ASN* 3.2 37.0 + - + +
166A HIS* 1.3 77.3 - - - +
168A VAL* 1.3 64.9 + - - +
170A SER* 3.3 13.0 - - - -
171A LYS* 3.4 12.3 + - - +
105B ILE* 6.2 0.7 - - + -
109B PHE* 5.2 11.0 - - + -
112B PHE* 3.7 32.0 - - + -
44C GLN* 3.7 42.2 - - + +
45C HIS* 3.6 16.1 - - + +
46C ILE* 5.9 1.6 - - + -
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASN* 3.0 23.9 + - - +
165A ALA* 3.4 10.8 - - - +
166A HIS 3.1 0.2 - - - -
167A MET* 1.3 73.3 - - - +
169A LEU* 1.3 71.2 + - + +
171A LYS* 3.2 16.0 + - - +
172A ALA* 3.6 6.2 + - - +
45C HIS* 4.6 17.3 - - + -
46C ILE 3.9 21.5 - - - +
47C VAL* 5.3 0.9 - - + -
48C PRO* 5.3 4.3 - - + -
165C ALA* 4.4 15.3 - - + -
168C VAL* 4.6 8.1 - - + -
169C LEU* 4.0 30.6 - - + +
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Residues in contact with LEU 169 (chain A).
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 3.4 - - + +
47A VAL* 4.5 28.9 - - + -
66A ILE* 4.8 21.8 - - + +
69A VAL* 3.8 40.0 - - + +
71A ILE* 5.9 2.2 - - + -
165A ALA 3.2 18.1 + - - +
166A HIS* 4.3 22.9 - - + +
167A MET 3.6 0.2 - - - -
168A VAL* 1.3 78.4 - - + +
170A SER* 1.3 56.1 + - - +
172A ALA* 2.8 35.6 + - - +
168C VAL* 4.7 12.3 - - + -
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Residues in contact with SER 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A HIS 3.1 21.2 + - - -
167A MET 3.3 7.4 - - - -
168A VAL 3.2 0.2 - - - -
169A LEU* 1.3 76.7 - - - +
171A LYS* 1.3 62.7 + - - +
172A ALA 3.4 4.5 + - - -
112B PHE* 3.4 25.4 - - - -
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A MET 3.4 9.4 + - - +
168A VAL* 3.2 10.4 + - - +
169A LEU 3.1 0.8 - - - -
170A SER* 1.3 77.7 - - - +
172A ALA* 1.3 63.6 + - - +
44C GLN* 5.9 2.9 - - - -
45C HIS* 3.7 34.6 - - + +
70C GLU* 5.0 9.5 + - - -
169C LEU* 4.2 15.1 - - + +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN* 4.9 18.4 + - - +
69A VAL* 4.1 15.4 - - + +
168A VAL 3.6 2.0 + - - +
169A LEU 2.8 18.1 + - - +
170A SER 4.2 4.0 - - - -
171A LYS* 1.3 82.0 - - - +
168C VAL* 3.5 42.6 - - + +
169C LEU* 4.7 3.8 - - + +
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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