Contacts of the helix formed by residues 147 - 152 (chain B) in PDB entry 2QFI
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 VAL 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ASN* 3.7 26.4 + - - +
60B VAL* 3.9 12.3 - - + -
79B GLU* 2.8 53.8 - - + +
82B ALA* 3.9 9.8 - - + +
83B ALA* 4.2 1.1 - - + -
144B SER* 2.7 23.7 + - - +
145B GLN 2.7 1.0 + - - -
146B ALA* 1.3 68.4 - - - +
148B ARG* 1.3 67.4 + - - +
149B ALA 3.0 1.0 + - - -
150B ASP* 3.3 20.3 + - - +
197B MET* 4.0 4.9 - - - +
200B GLU* 3.4 16.2 - - - +
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE 2.2 33.9 + - - -
15B ALA* 2.8 23.0 + - - +
16B ALA 3.2 6.3 + - - -
17B THR 2.4 32.3 + - - +
18B ALA* 2.6 28.0 - - - +
19B MET* 3.8 21.6 - - - +
20B ALA* 3.9 6.3 - - - +
56B ASN* 4.1 9.2 - - - +
60B VAL* 4.5 7.1 - - - +
135B GLN* 3.4 16.5 + - + +
138B VAL* 3.5 19.7 - - + +
139B VAL 5.9 0.7 - - - +
144B SER* 2.3 48.6 + - - +
146B ALA* 5.6 0.2 - - - -
147B VAL* 1.3 68.7 - - - +
149B ALA* 1.3 49.3 + - - +
150B ASP* 2.4 22.5 + - - +
151B MET* 2.5 20.3 + - + +
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 6.0 7.4 - - + -
146B ALA* 3.1 15.5 + - - +
147B VAL 3.0 2.0 - - - -
148B ARG* 1.3 74.8 - - - +
150B ASP* 1.3 56.7 + - - +
151B MET* 3.2 17.0 - - - -
152B LEU* 4.0 6.1 + - + +
192B TYR* 3.5 8.8 + - - -
196B ARG* 2.9 39.6 + - - +
197B MET* 3.0 18.3 - - - +
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Residues in contact with ASP 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B MET* 2.5 46.0 - - - +
52B ALA* 5.4 1.2 - - - +
56B ASN* 4.2 8.4 - - - +
86B GLN* 3.6 35.8 - - + +
147B VAL 3.3 10.5 + - - +
148B ARG 2.4 17.8 + - - +
149B ALA* 1.3 66.2 - - - +
151B MET* 1.3 60.4 + - - -
152B LEU 3.0 2.0 - - - -
153B HIS* 2.4 47.5 + - + +
154B TYR* 4.3 0.6 - - - -
192B TYR* 3.4 5.6 - - - -
197B MET* 3.4 23.2 - - + +
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Residues in contact with MET 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B VAL* 3.8 11.2 - - + -
135B GLN* 3.2 52.7 - - + +
136B ARG* 3.4 38.4 - - + -
139B VAL* 6.3 1.6 - - - -
148B ARG* 2.5 18.3 + - + +
149B ALA* 3.9 12.1 - - - -
150B ASP* 1.3 71.8 + - - +
152B LEU* 1.3 68.9 + - + +
154B TYR* 2.3 41.9 + - - +
155B GLN* 3.1 37.8 + - + +
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ARG* 5.5 5.6 - - - +
149B ALA* 4.0 8.2 + - + +
150B ASP 2.8 3.6 + - - -
151B MET* 1.3 100.0 - - + +
153B HIS* 1.3 61.0 + - - +
154B TYR 3.1 0.4 - - - -
155B GLN* 2.9 37.2 - - + +
156B SER* 3.2 26.2 + - - +
188B ILE* 5.3 12.8 - - + -
192B TYR* 2.9 48.3 + - + +
196B ARG* 5.2 8.3 - - - +
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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