Contacts of the helix formed by residues 42 - 48 (chain F) in PDB entry 1W88
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 GLY 42 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D GLN* 5.3 11.1 - - - +
11D ASP* 5.3 0.3 - - - +
14D ARG* 5.5 1.2 + - - -
14F ARG* 5.5 3.7 + - - -
31F GLY 5.8 1.6 + - - -
34F GLY* 5.1 1.4 - - - -
40F THR 3.3 0.8 + - - -
41F GLU* 1.3 70.9 - - - +
43F LEU* 1.3 64.2 + - - +
44F GLN 3.4 2.0 - - - +
45F ALA* 3.6 15.0 + - - +
46F GLU* 3.1 24.9 + - - +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F THR* 4.0 17.3 - - + -
13F LEU* 3.6 27.8 - - + -
14F ARG* 4.1 36.6 - - + +
17F LEU* 4.1 6.1 - - + -
25F ILE* 3.9 16.2 - - + -
39F ALA 4.7 1.1 - - - +
40F THR* 3.1 37.7 + - - +
41F GLU 4.2 0.2 - - - +
42F GLY* 1.3 76.2 - - - +
44F GLN* 1.3 60.7 + - - +
46F GLU* 3.3 1.3 + - - +
47F PHE* 2.8 41.1 + - + +
52F VAL* 3.8 16.6 - - + -
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Residues in contact with GLN 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ALA* 3.6 15.4 - - + +
2D GLN* 4.7 6.4 + - - +
31F GLY* 3.6 32.5 + - - +
32F VAL* 3.7 21.9 + - - +
40F THR 4.5 1.0 + - - -
42F GLY 3.4 0.6 - - - +
43F LEU* 1.3 78.7 - - - +
45F ALA* 1.3 58.5 + - - +
48F GLY* 2.7 39.8 + - - +
49F GLU* 3.9 16.7 - - - +
52F VAL* 2.7 44.3 + - + +
53F PHE* 3.9 5.7 - - - +
54F ASP* 4.9 1.6 + - - +
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Residues in contact with ALA 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ALA* 3.9 11.2 - - - +
3D MET* 3.6 39.8 - - + +
7D GLN* 5.3 9.6 - - + +
11D ASP* 4.0 11.9 - - + +
185D GLU* 3.2 23.0 - - - +
42F GLY* 3.6 17.1 + - - +
43F LEU 3.4 0.8 - - - -
44F GLN* 1.3 77.2 - - - +
46F GLU* 1.3 58.1 + - - +
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Residues in contact with GLU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASP* 4.1 0.6 + - - +
14D ARG* 3.3 50.3 + - - +
46D GLU* 5.5 0.2 - - - +
185D GLU* 3.8 13.6 - - - +
186D GLY 4.9 2.3 + - - +
14F ARG* 3.4 30.2 + - - +
18F LYS* 4.9 7.3 + - - +
42F GLY 3.1 17.8 + - - +
43F LEU* 5.5 0.7 - - - +
45F ALA* 1.3 78.0 - - - +
47F PHE* 1.3 96.8 + - + +
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Residues in contact with PHE 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D GLU* 4.3 3.8 - - - +
14F ARG* 3.7 30.3 - - + -
17F LEU* 3.8 30.1 - - + -
18F LYS* 3.6 32.1 - - + -
43F LEU* 2.8 26.9 + - + +
46F GLU* 1.3 115.2 - - + +
48F GLY* 1.3 57.8 + - - +
50F ASP* 3.9 2.4 - - - +
51F ARG* 3.2 44.9 - - + +
52F VAL* 4.3 4.7 - - + -
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Residues in contact with GLY 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D GLU* 3.7 21.9 - - - +
44F GLN* 2.7 27.4 + - - +
46F GLU 3.8 0.8 - - - -
47F PHE* 1.3 72.0 - - - +
49F GLU* 1.3 57.3 + - - -
50F ASP* 3.2 11.7 - - - -
51F ARG 3.3 1.9 + - - -
52F VAL* 3.0 28.2 + - - +
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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