Contacts of the helix formed by residues 150 - 157 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27L ARG* 3.3 34.5 - - + +
32L ILE* 4.0 24.6 - - + +
71L GLN 4.4 12.3 + - - -
72L LEU* 3.7 29.0 - - - +
149L ILE* 1.3 86.1 + - - +
151L PHE* 1.3 68.2 + - - +
152L VAL* 3.2 4.7 - - + +
153L ASP* 2.9 26.7 + - - +
154L THR* 3.1 15.5 + - - -
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Residues in contact with PHE 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L ILE 5.4 5.2 - - - +
33L ASP* 6.2 1.6 - - - -
35L ALA* 4.0 27.4 - - + -
39L TYR* 4.4 11.4 - + - -
63L LEU* 3.5 25.4 - - + -
72L LEU* 3.9 27.7 + - + +
74L VAL* 3.7 32.1 - - + -
76L GLN* 4.6 4.9 - - + -
77L PRO 3.8 23.3 - - - -
78L ASP* 4.0 2.0 - - - -
150L GLN* 1.3 75.6 - - - +
152L VAL* 1.3 72.4 + - + +
154L THR* 3.3 6.8 + - - -
155L VAL* 3.1 50.6 + - + +
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Residues in contact with VAL 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L ARG* 3.8 24.2 - - + +
30L ILE* 3.5 28.2 - - + +
31L GLY 3.9 7.9 - - - +
32L ILE 3.8 19.9 + - - +
33L ASP 4.7 0.4 - - - -
34L ASN 3.2 35.2 - - - +
35L ALA* 4.2 4.0 - - - +
38L ALA* 3.4 18.6 - - + +
150L GLN* 3.2 1.9 - - + +
151L PHE* 1.3 84.5 - - + +
153L ASP* 1.3 63.1 + - - +
156L ALA* 3.3 22.2 + - - +
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Residues in contact with ASP 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L PRO* 3.8 5.5 - - - +
26L LEU* 2.8 35.3 + - - +
27L ARG* 2.9 42.5 + - - +
144L ILE* 3.7 17.1 - - + +
148L SER 4.7 0.4 - - - -
149L ILE* 3.6 16.2 - - + -
150L GLN* 2.9 20.6 + - - +
152L VAL* 1.3 76.1 - - - +
154L THR* 1.3 64.7 + - - +
156L ALA* 3.5 4.3 + - - +
157L ASP* 3.1 23.2 + - - +
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Residues in contact with THR 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L LEU* 5.1 6.8 - - + +
72L LEU* 4.7 4.5 - - - +
78L ASP* 4.2 11.7 - - - +
147L TRP* 5.7 0.9 - - + -
149L ILE* 3.7 20.7 - - + +
150L GLN 3.1 14.8 + - - -
151L PHE* 3.4 7.0 + - - -
153L ASP* 1.3 73.4 - - - +
155L VAL* 1.3 66.3 + - - +
157L ASP* 2.9 14.6 + - - -
159L ALA* 2.8 37.0 + - - +
160L SER* 2.5 31.0 - - - +
1262L PO4 4.7 5.6 - - - +
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Residues in contact with VAL 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ALA* 3.8 8.7 - - + -
39L TYR* 3.4 55.9 - - + +
42L GLN* 3.2 21.0 + - - +
78L ASP* 3.1 25.6 - - - +
151L PHE* 3.1 41.6 + - + +
154L THR* 1.3 77.5 - - - +
156L ALA* 1.3 64.2 + - - +
158L ASN 3.1 11.3 + - - -
159L ALA 4.0 5.2 - - - +
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Residues in contact with ALA 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L LEU* 3.6 11.6 - - - +
26L LEU* 4.1 18.4 - - + -
30L ILE* 4.9 1.6 - - + -
38L ALA* 3.4 19.9 + - - +
41L ILE* 3.9 24.5 - - + +
42L GLN* 3.8 13.7 + - - -
45L ASN* 4.8 4.0 + - - -
152L VAL 3.3 16.2 + - - +
153L ASP 3.8 4.3 - - - +
155L VAL* 1.3 79.5 - - - +
157L ASP* 1.3 55.7 + - - +
158L ASN 3.0 5.9 + - - -
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Residues in contact with ASP 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L LEU* 4.0 14.4 - - + +
141L GLY 4.2 0.7 - - - +
142L SER* 3.6 9.4 + - - -
143L ARG* 2.7 79.0 + - - +
144L ILE* 4.1 10.0 + - + +
149L ILE* 5.4 0.6 - - + +
153L ASP 3.1 16.0 + - - +
154L THR* 2.9 10.3 + - - +
156L ALA* 1.3 74.5 - - - +
158L ASN* 1.3 65.2 + - - +
160L SER* 3.1 7.1 + - - +
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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