Contacts of the helix formed by residues 50 - 60 (chain F) in PDB entry 1WOH
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 PHE 50 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PHE* 4.1 8.7 - + - -
45A ARG* 4.1 21.5 - - + -
46A PRO* 3.7 31.9 - - + -
9C TYR* 3.9 23.6 - - + -
47F GLY* 2.9 27.8 + - - +
49F ARG* 1.3 89.7 - - + +
51F ALA* 1.3 61.6 + - - +
52F PRO* 3.4 1.8 - - - -
53F ARG* 3.4 12.2 + - + +
54F ALA* 3.2 21.0 + - - +
277F PRO* 3.9 11.7 - - + -
278F ASN* 4.6 16.2 - - + -
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Residues in contact with ALA 51 (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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47F GLY 3.9 1.2 + - - -
48F ALA 3.1 10.1 + - - +
50F PHE* 1.3 75.3 - - - +
52F PRO* 1.3 66.6 - - - +
54F ALA* 3.7 0.2 - - - +
55F LEU* 2.8 31.2 + - + +
118F GLY 3.1 23.1 - - - +
275F LEU* 3.3 39.0 - - + +
277F PRO* 3.8 10.5 - - - +
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Residues in contact with PRO 52 (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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35F GLY* 4.2 2.9 - - - -
36F VAL 4.0 8.7 - - - +
37F PRO* 4.0 10.5 - - + -
48F ALA 3.6 3.6 - - - +
49F ARG 3.5 15.0 - - - +
50F PHE 3.6 0.7 - - - -
51F ALA* 1.3 88.6 - - + +
53F ARG* 1.3 56.1 + - - +
55F LEU* 3.7 1.7 - - - +
56F ARG* 3.0 52.7 + - - +
85F ASP* 4.1 10.5 - - - +
117F LEU* 3.4 37.8 - - + +
118F GLY 3.3 12.3 - - - +
119F GLY 4.1 0.2 - - - +
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Residues in contact with ARG 53 (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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44A PHE* 6.2 0.8 - - - -
8C PRO 3.4 14.3 + - - -
9C TYR* 3.4 27.6 + - - +
10C GLY 3.3 15.0 + - - -
11C GLY 2.9 28.6 + - - +
13C PRO* 3.9 17.0 - - + +
57C GLU* 3.9 34.0 + - - +
60C LEU* 3.4 18.7 - - - +
13F PRO* 5.5 1.3 - - + -
50F PHE* 3.4 12.9 + - + +
51F ALA 3.2 0.4 - - - -
52F PRO* 1.3 79.6 - - - +
54F ALA* 1.3 58.7 + - - +
56F ARG* 3.3 12.2 + - - +
57F GLU* 3.0 48.3 + - + +
85F ASP* 5.2 0.4 + - - -
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Residues in contact with ALA 54 (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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50F PHE 3.2 9.1 + - - +
51F ALA 3.2 2.4 + - - +
53F ARG* 1.3 76.9 - - - +
55F LEU* 1.3 57.5 + - - +
57F GLU* 3.4 13.1 + - - +
58F ALA* 2.8 31.4 + - - +
275F LEU* 4.7 0.2 - - + -
277F PRO* 3.4 37.9 - - + -
286F GLU* 3.9 20.2 - - + +
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Residues in contact with LEU 55 (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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15F PHE* 4.1 5.7 - - + -
51F ALA* 2.8 24.5 + - + +
52F PRO 3.7 3.8 - - - +
54F ALA* 1.3 74.2 - - - +
56F ARG* 1.3 60.8 + - - +
58F ALA* 3.7 3.0 - - - +
59F SER* 2.9 30.9 + - - -
117F LEU* 4.0 38.8 - - + -
118F GLY 4.5 4.5 - - - +
272F LEU* 3.8 23.3 - - + -
275F LEU* 3.8 22.4 - - + -
286F GLU 4.0 6.1 - - - +
289F MET* 4.1 9.9 - - + +
290F ALA* 3.8 30.8 - - - +
293F VAL* 5.7 1.1 - - + -
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Residues in contact with ARG 56 (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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11C GLY 5.0 2.6 + - - -
12C ILE* 3.3 16.2 - - - +
13C PRO* 6.0 2.2 - - - -
13F PRO* 3.6 26.5 - - + +
14F THR 3.8 4.6 - - - +
15F PHE* 3.8 17.4 - - + +
33F ALA* 4.9 0.8 + - - +
34F LEU* 4.4 2.4 - - - +
35F GLY* 3.6 8.8 - - - +
52F PRO* 3.0 38.4 + - - +
53F ARG* 3.6 9.6 - - - +
55F LEU* 1.3 77.0 - - - +
57F GLU* 1.3 63.3 + - - +
59F SER* 2.6 25.1 + - - -
60F LEU* 3.6 8.5 + - - +
82F ASP* 2.6 33.9 + - - -
84F GLY 2.9 29.7 + - - -
85F ASP* 2.9 26.4 + - - -
117F LEU* 4.4 9.4 - - + +
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Residues in contact with GLU 57 (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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53C ARG* 4.1 21.9 + - - +
57C GLU* 2.5 30.9 - - - +
44D PHE* 5.7 3.9 - - - -
8F PRO* 4.8 1.7 - - - +
13F PRO* 3.9 23.0 - - + +
53F ARG* 3.0 33.7 + - + +
54F ALA* 3.7 9.1 - - - +
56F ARG* 1.3 76.4 - - - +
58F ALA* 1.3 61.1 + - - +
60F LEU* 3.3 23.2 + - - +
61F ARG* 4.6 1.9 + - - +
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Residues in contact with ALA 58 (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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44D PHE* 5.9 1.1 - - - -
54F ALA 2.8 17.6 + - - +
55F LEU 4.3 0.2 - - - -
57F GLU* 1.3 72.4 - - - +
59F SER* 1.3 62.1 + - - +
60F LEU 3.1 6.3 + - - -
61F ARG* 3.2 21.1 + - - +
62F SER* 4.2 2.4 + - - -
286F GLU* 3.3 39.0 - - + +
287F LEU* 3.8 20.4 - - + +
290F ALA* 3.8 9.3 - - + +
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Residues in contact with SER 59 (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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14F THR 3.5 1.2 + - - -
15F PHE* 3.5 22.7 - - - -
16F ALA* 2.8 31.1 + - - -
55F LEU 2.9 15.7 + - - -
56F ARG 2.6 17.7 + - - -
58F ALA* 1.3 71.3 - - - +
60F LEU* 1.3 56.5 + - - +
61F ARG 3.0 6.1 - - - -
62F SER* 2.9 33.8 + - - +
63F VAL* 3.7 3.5 + - - +
290F ALA* 3.8 9.2 - - - +
294F MET* 5.4 2.7 - - - -
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Residues in contact with LEU 60 (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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53C ARG* 3.4 22.9 - - - +
8F PRO* 3.3 41.7 - - + +
10F GLY 4.2 0.7 - - - +
13F PRO* 4.1 13.7 - - + -
14F THR 3.7 24.7 - - - +
17F ARG* 3.8 49.5 + - + +
56F ARG 3.6 5.2 - - - +
57F GLU 3.4 16.6 - - - +
58F ALA 3.1 0.8 - - - -
59F SER* 1.3 76.9 - - - +
61F ARG* 1.3 58.5 + - - +
62F SER 3.3 1.3 - - - -
63F VAL* 3.6 16.0 - - - +
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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