Contacts of the helix formed by residues 150 - 157 (chain I) in PDB entry 2WQT
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 GLN 150 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27I ARG* 3.3 33.9 - - + +
32I ILE* 4.0 26.1 - - + +
71I GLN 4.4 12.4 + - - +
72I LEU* 3.8 28.6 - - - +
149I ILE* 1.3 86.8 + - - +
151I PHE* 1.3 68.0 + - - +
152I VAL* 3.2 4.0 - - + +
153I ASP* 3.0 25.9 + - - +
154I THR* 3.0 15.8 + - - -
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Residues in contact with PHE 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I ILE 5.4 5.2 - - - +
33I ASP* 6.2 1.6 - - - -
35I ALA* 3.9 27.6 - - + -
39I TYR* 4.5 11.7 - + - -
63I LEU* 3.5 24.9 - - + -
72I LEU* 3.9 29.0 + - + +
74I VAL* 3.7 32.1 - - + -
76I GLN* 4.6 6.1 - - + -
77I PRO 3.8 22.9 - - - -
78I ASP* 3.9 7.4 - - - -
150I GLN* 1.3 76.2 - - - +
152I VAL* 1.3 73.3 + - + +
154I THR* 3.3 6.4 + - - -
155I VAL* 3.1 44.0 + - + +
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Residues in contact with VAL 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I ARG* 3.8 23.8 - - + +
30I ILE* 3.5 28.2 - - + +
31I GLY 3.9 7.4 - - - +
32I ILE 3.8 20.6 + - - +
33I ASP 4.7 0.2 - - - -
34I ASN 3.2 35.2 - - - +
35I ALA* 4.1 3.8 - - - +
38I ALA* 3.4 19.8 - - + +
150I GLN* 3.2 2.1 - - + +
151I PHE* 1.3 84.8 - - + +
153I ASP* 1.3 64.2 + - - +
156I ALA* 3.3 21.8 + - - +
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Residues in contact with ASP 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I PRO* 3.8 5.5 - - - +
26I LEU* 2.8 34.4 + - - +
27I ARG* 2.9 43.3 + - - +
144I ILE* 3.7 18.3 - - + +
148I SER 4.7 0.2 - - - -
149I ILE* 3.6 16.8 - - + -
150I GLN* 3.0 19.1 + - - +
152I VAL* 1.3 75.9 - - - +
154I THR* 1.3 65.2 + - - +
156I ALA* 3.6 4.0 + - - +
157I ASP* 3.1 23.4 + - - +
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Residues in contact with THR 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I LEU* 5.1 7.7 - - + +
72I LEU* 4.7 4.5 - - - +
78I ASP* 4.2 12.3 - - - +
147I TRP* 5.6 0.9 - - + -
149I ILE* 3.8 20.4 - - + +
150I GLN 3.0 15.4 + - - -
151I PHE* 3.4 6.6 + - - -
153I ASP* 1.3 73.0 - - - +
155I VAL* 1.3 68.8 + - - +
157I ASP* 2.8 14.2 + - - +
159I ALA* 2.8 33.7 + - - +
160I SER* 2.5 34.8 - - - +
1262I PO4 5.5 2.9 - - - +
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Residues in contact with VAL 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ALA* 3.7 9.0 - - + -
39I TYR* 3.4 56.3 - - + +
42I GLN* 3.1 20.7 + - - +
78I ASP* 3.1 25.4 - - - +
79I PHE 5.0 0.2 - - - +
151I PHE* 3.1 40.7 + - + +
154I THR* 1.3 77.1 - - - +
156I ALA* 1.3 63.2 + - - +
158I ASN 3.0 11.8 + - - -
159I ALA* 4.0 5.6 - - - +
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Residues in contact with ALA 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I LEU* 3.6 12.0 - - - +
26I LEU* 4.1 18.8 - - + -
30I ILE* 5.0 1.3 - - + -
38I ALA* 3.3 20.3 + - - +
41I ILE* 3.9 23.1 - - + +
42I GLN* 3.8 14.0 + - - -
45I ASN* 4.9 4.0 + - - +
152I VAL 3.3 16.9 + - - +
153I ASP 3.8 4.5 - - - +
154I THR 3.2 0.4 - - - -
155I VAL* 1.3 78.7 - - - +
157I ASP* 1.3 56.7 + - - +
158I ASN* 3.0 5.4 + - - +
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Residues in contact with ASP 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I LEU* 4.0 14.2 - - + +
141I GLY 4.2 0.9 - - - +
142I SER* 3.7 8.8 + - - -
143I ARG* 2.7 80.9 + - - +
144I ILE* 4.0 9.4 + - + +
149I ILE* 5.4 1.0 - - + +
153I ASP 3.1 17.9 + - - +
154I THR* 2.8 10.1 + - - +
156I ALA* 1.3 74.5 - - - +
158I ASN* 1.3 64.0 + - - +
160I SER* 3.1 7.0 + - - +
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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