Contacts of the helix formed by residues 136 - 150 (chain A) in PDB entry 2Q53
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 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A TRP* 2.7 29.6 + - - +
65A HIS* 3.7 9.2 - - - -
66A GLY* 3.8 6.1 - - - -
135A PRO* 1.3 75.3 - - - +
137A PRO* 1.3 68.3 - - - +
138A GLN* 3.0 14.0 + - - +
139A TYR* 3.1 23.6 + - - +
140A LYS* 3.0 21.3 + - - +
165A PRO* 4.2 0.2 - - - -
166A ASN* 3.0 14.8 - - - -
168A TYR* 4.4 3.6 - - - -
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Residues in contact with PRO 137 (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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135A PRO 3.8 0.2 - - - -
136A SER* 1.3 82.9 - - - +
138A GLN* 1.3 67.6 + - - +
140A LYS* 3.6 4.4 + - + +
141A LYS* 3.1 49.0 + - - +
165A PRO* 3.8 20.9 - - + -
166A ASN* 3.1 30.3 - - - +
168A TYR 3.5 17.3 - - - +
169A THR* 5.6 2.2 - - + -
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Residues in contact with GLN 138 (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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64A TRP* 4.4 9.4 - - + +
136A SER* 3.4 20.3 - - - +
137A PRO* 1.3 82.8 - - + +
139A TYR* 1.3 64.3 + - - +
141A LYS* 3.3 8.5 + - + +
142A ILE* 3.0 28.7 + - - +
168A TYR* 3.3 25.2 + - - -
169A THR* 4.3 4.2 - - - +
170A GLY 3.8 4.0 + - - -
172A VAL* 2.9 42.0 - - + +
176A ILE* 5.5 1.1 - - + -
180A ILE* 3.9 23.5 - - + +
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Residues in contact with TYR 139 (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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23A GLY* 4.7 0.2 - - - -
24A SER* 3.7 28.1 + - - -
53A PHE* 3.5 18.2 - + - -
64A TRP* 3.3 54.5 - + + -
67A GLY 3.5 17.5 - - - +
68A ILE* 4.0 6.9 - - + +
69A ALA* 3.0 41.4 + - + +
105A TYR* 4.9 1.7 + - - -
135A PRO* 3.7 13.0 - - + -
136A SER* 3.1 25.1 + - - +
138A GLN* 1.3 75.3 - - - +
140A LYS* 1.3 62.6 + - - +
142A ILE* 3.2 12.3 + - - +
143A ILE* 3.3 21.1 + - + +
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Residues in contact with LYS 140 (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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53A PHE* 6.2 0.9 - - - -
135A PRO* 4.6 11.4 - - + +
136A SER 3.0 15.7 + - - +
137A PRO* 3.7 7.0 - - + +
139A TYR* 1.3 80.0 - - - +
141A LYS* 1.3 62.6 + - + +
142A ILE 3.3 0.3 + - - -
143A ILE* 3.3 7.8 + - - +
144A CYS* 3.0 38.2 + - - -
160A LEU 3.4 20.2 - - - +
161A LYS* 2.7 27.0 + - - +
162A ALA 4.2 0.6 - - - -
163A ILE* 2.6 40.1 + - + +
165A PRO* 4.4 17.1 - - + +
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Residues in contact with LYS 141 (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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137A PRO* 3.1 43.7 + - - +
138A GLN* 3.3 9.3 + - + +
140A LYS* 1.3 77.2 - - + +
142A ILE* 1.3 57.5 + - - +
144A CYS* 3.8 6.7 - - - +
145A MSE 2.8 41.8 + - + +
180A ILE* 3.5 35.0 - - + -
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Residues in contact with ILE 142 (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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24A SER* 3.8 34.1 - - - +
27A LEU* 3.8 26.3 - - + +
30A ARG* 4.4 7.4 - - + -
64A TRP* 3.6 22.2 - - + -
138A GLN 3.0 15.8 + - - +
139A TYR* 3.3 7.2 - - + +
141A LYS* 1.3 77.9 - - - +
143A ILE* 1.3 63.6 + - - +
145A MSE 3.2 6.5 + - - +
146A GLY 3.0 16.6 + - - -
176A ILE* 3.7 15.5 - - + -
179A ILE* 4.7 6.5 - - + -
180A ILE* 3.6 27.4 - - + -
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Residues in contact with ILE 143 (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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22A TYR 4.6 2.7 - - - +
23A GLY* 3.5 38.4 - - - -
24A SER* 3.7 4.0 - - - +
26A LEU* 3.3 23.8 - - + +
51A LEU* 5.9 0.7 - - + -
53A PHE* 3.8 33.2 - - + -
69A ALA* 4.7 1.3 - - + -
139A TYR* 3.3 24.0 + - + +
140A LYS* 3.8 7.6 - - - +
142A ILE* 1.3 73.1 - - - +
144A CYS* 1.3 57.8 + - - +
146A GLY* 2.9 2.6 + - - -
147A ALA* 2.7 33.1 + - - +
160A LEU* 3.7 26.5 - - + -
163A ILE* 6.1 0.4 - - + -
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Residues in contact with CYS 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LYS* 3.0 45.3 + - - +
141A LYS* 3.8 7.0 - - - +
143A ILE* 1.3 77.1 - - - +
145A MSE 1.3 63.6 + - + +
147A ALA* 3.9 6.0 - - - +
148A LYS* 3.0 27.0 + - - +
157A GLN* 4.7 1.0 - - - +
160A LEU* 4.0 27.6 - - - -
161A LYS* 4.3 15.9 - - + -
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Residues in contact with MSE 145 (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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27A LEU* 3.7 19.3 - - + +
141A LYS* 2.8 33.8 + - + +
142A ILE* 3.5 5.4 - - - +
144A CYS* 1.3 76.0 - - + +
146A GLY* 1.3 58.4 + - - +
148A LYS* 4.2 5.6 - - - +
149A GLU* 3.1 27.5 + - - +
179A ILE* 3.0 43.3 - - + +
180A ILE* 4.0 24.0 - - - +
182A LYS* 4.9 10.3 - - + -
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Residues in contact with GLY 146 (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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26A LEU* 3.6 36.9 - - - +
27A LEU* 3.7 8.9 - - - +
142A ILE 3.0 7.2 + - - -
143A ILE 2.9 6.9 + - - -
145A MSE 1.3 77.0 - - - +
147A ALA* 1.3 64.3 + - - +
149A GLU* 3.6 1.6 - - - +
150A ASN* 3.0 25.8 + - - +
152A LEU* 4.9 0.5 - - - +
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Residues in contact with ALA 147 (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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26A LEU* 4.2 2.7 - - + +
143A ILE 2.7 13.4 + - - +
144A CYS* 3.9 4.9 - - - +
146A GLY* 1.3 71.3 - - - +
148A LYS* 1.3 62.0 + - - +
151A GLY* 3.3 2.6 + - - -
152A LEU* 2.9 48.8 + - + -
157A GLN* 3.7 19.5 - - + -
160A LEU* 3.4 33.0 - - + -
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Residues in contact with LYS 148 (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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144A CYS 3.0 17.7 + - - +
145A MSE 4.2 5.2 - - - +
147A ALA* 1.3 76.1 - - - +
149A GLU* 1.3 68.5 + - - +
151A GLY* 3.1 13.9 + - - -
157A GLN* 3.1 21.7 + - - +
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Residues in contact with GLU 149 (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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27A LEU* 3.9 7.2 - - - +
28A THR* 2.7 41.0 + - - -
29A GLU* 2.8 28.5 - - - +
145A MSE 3.1 17.7 + - - +
146A GLY 3.3 2.9 + - - +
148A LYS* 1.3 81.5 - - - +
150A ASN* 1.3 68.2 + - - +
151A GLY* 3.1 4.9 + - - -
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Residues in contact with ASN 150 (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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26A LEU 2.7 29.5 + - - -
28A THR* 3.8 15.4 + - - -
40A PHE* 3.8 26.7 - - + +
43A VAL* 3.2 16.8 - - - +
82A VAL* 3.7 26.3 - - + +
84A TRP* 4.1 7.7 - - - -
146A GLY 3.0 8.2 + - - +
149A GLU* 1.3 90.5 + - - +
151A GLY* 1.3 63.0 + - - +
152A LEU* 3.6 2.7 - - + -
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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
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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