Contacts of the helix formed by residues 150 - 157 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27T ARG* 3.4 35.0 - - + +
32T ILE* 4.0 25.5 - - + +
71T GLN 4.3 12.4 + - - +
72T LEU* 3.8 28.8 - - - +
149T ILE* 1.3 84.1 + - - +
151T PHE* 1.3 68.7 + - - +
152T VAL* 3.2 4.0 - - + +
153T ASP* 3.0 25.8 + - - +
154T THR* 3.1 15.7 + - - -
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Residues in contact with PHE 151 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32T ILE 5.4 4.9 - - - +
33T ASP* 6.2 1.6 - - + -
35T ALA* 4.0 27.4 - - + -
39T TYR* 4.5 11.4 - + - -
63T LEU* 3.5 24.5 - - + -
72T LEU* 3.9 27.9 + - + +
74T VAL* 3.7 31.4 - - + -
76T GLN* 4.6 6.3 - - + -
77T PRO 3.8 23.6 - - - -
78T ASP* 4.0 1.8 - - - -
150T GLN* 1.3 75.4 - - - +
152T VAL* 1.3 72.5 + - + +
154T THR* 3.3 6.4 + - - -
155T VAL* 3.1 50.8 + - + +
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Residues in contact with VAL 152 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T ARG* 3.8 23.1 - - + +
30T ILE* 3.5 28.2 - - + +
31T GLY 3.9 7.9 - - - +
32T ILE 3.8 20.1 + - - +
33T ASP 4.7 0.4 - - - -
34T ASN 3.3 35.4 - - - +
35T ALA* 4.2 2.9 - - - +
38T ALA* 3.4 19.8 - - + +
150T GLN* 3.2 2.5 - - + +
151T PHE* 1.3 84.3 - - + +
153T ASP* 1.3 64.2 + - - +
156T ALA* 3.3 21.7 + - - +
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Residues in contact with ASP 153 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25T PRO* 3.8 5.5 - - - +
26T LEU* 2.8 35.4 + - - +
27T ARG* 2.9 44.2 + - - +
144T ILE* 3.7 17.4 - - + +
148T SER 4.7 0.2 - - - -
149T ILE* 3.6 16.4 - - + -
150T GLN* 3.0 19.1 + - - +
152T VAL* 1.3 76.2 - - - +
154T THR* 1.3 63.7 + - - +
156T ALA* 3.8 4.8 - - - +
157T ASP* 3.1 22.9 + - - +
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Residues in contact with THR 154 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63T LEU* 5.0 6.4 - - + +
72T LEU* 4.7 4.3 - - - +
78T ASP* 4.2 12.1 - - - +
147T TRP* 5.7 0.7 - - + -
149T ILE* 3.8 18.7 - - + +
150T GLN 3.1 15.6 + - - -
151T PHE* 3.4 7.0 + - - -
153T ASP* 1.3 74.1 - - - +
155T VAL* 1.3 61.1 + - - +
157T ASP* 2.9 14.2 + - - -
159T ALA* 2.7 41.4 + - - +
160T SER* 2.5 32.0 + - - +
1262T PO4 4.9 6.3 - - - +
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Residues in contact with VAL 155 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T ALA* 3.7 9.2 - - + -
39T TYR* 3.4 56.5 - - + +
42T GLN* 3.1 20.9 + - - +
78T ASP* 3.1 24.5 - - - +
79T PHE 5.0 0.2 - - - +
151T PHE* 3.1 41.1 + - + +
154T THR* 1.3 78.6 - - - +
156T ALA* 1.3 63.4 + - - +
158T ASN 3.1 11.4 + - - -
159T ALA* 4.0 6.1 - - - +
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Residues in contact with ALA 156 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T LEU* 3.7 12.0 - - - +
26T LEU* 4.0 18.8 - - + -
30T ILE* 5.0 1.6 - - + -
38T ALA* 3.4 20.1 + - - +
41T ILE* 3.8 24.8 - - + +
42T GLN* 3.8 13.0 - - - -
45T ASN* 4.8 3.8 + - - -
152T VAL 3.3 17.3 + - - +
153T ASP 3.8 4.3 - - - +
154T THR 3.3 0.2 - - - -
155T VAL* 1.3 77.8 - - - +
157T ASP* 1.3 57.0 + - - +
158T ASN* 3.0 5.9 + - - +
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Residues in contact with ASP 157 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T LEU* 4.0 15.2 - - + +
141T GLY 4.2 0.9 - - - +
142T SER* 3.7 8.5 + - - -
143T ARG* 2.7 78.6 + - - +
144T ILE* 4.0 9.3 + - + +
149T ILE* 5.4 1.0 - - + +
153T ASP 3.1 17.3 + - - +
154T THR* 2.9 10.8 + - - +
156T ALA* 1.3 73.2 - - - +
158T ASN* 1.3 66.1 + - - +
160T SER* 3.1 7.2 + - - +
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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