Contacts of the helix formed by residues 51 - 62 (chain B) in PDB entry 1OFD
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 PRO 51 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B ALA 3.3 6.7 - - - +
50B ILE* 1.3 86.2 - - + +
52B ARG* 1.3 64.2 + - - +
53B GLU* 3.4 2.7 - - - -
54B LEU* 3.2 15.1 + - + -
55B LEU* 3.1 32.8 + - + +
130B GLN* 5.9 0.2 - - - +
173B ILE* 3.8 20.4 - - + -
175B TYR* 4.7 8.3 - - + +
195B GLY 5.7 0.4 - - - -
196B TYR* 3.8 43.3 - - + +
197B THR* 4.2 13.0 - - - +
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Residues in contact with ARG 52 (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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50B ILE* 3.0 20.8 + - + +
51B PRO* 1.3 71.2 - - - +
53B GLU* 1.3 64.4 + - - +
55B LEU* 3.1 5.8 + - - +
56B ALA* 2.9 24.2 + - - +
66B MET* 3.8 37.9 + - + +
67B PRO 2.7 33.7 + - - -
68B ASP* 3.8 6.8 + - - +
69B GLY* 3.2 30.1 - - - +
72B LEU* 4.7 8.9 - - + +
197B THR* 5.7 1.8 + - - -
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Residues in contact with GLU 53 (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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51B PRO 3.4 0.4 - - - -
52B ARG* 1.3 77.9 - - - +
54B LEU* 1.3 62.6 + - - +
56B ALA* 3.5 16.9 - - - +
57B GLN* 3.8 10.2 - - - +
194B PRO 5.3 0.2 - - - +
195B GLY* 3.4 34.2 - - - +
197B THR* 4.2 18.1 + - - +
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Residues in contact with LEU 54 (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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51B PRO* 3.2 19.4 + - + +
52B ARG 3.2 0.4 - - - -
53B GLU* 1.3 80.9 - - - +
55B LEU* 1.3 64.2 + - + +
57B GLN* 3.3 31.3 + - - +
58B TRP 4.2 1.6 + - - -
108B ARG* 4.4 15.0 + - - +
175B TYR* 5.0 0.4 - - - +
190B ASP* 3.6 33.7 - - + +
193B ASN* 3.4 36.8 - - + +
195B GLY* 4.0 6.0 + - - +
196B TYR* 3.6 40.8 - - + +
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Residues in contact with LEU 55 (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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50B ILE* 3.7 28.9 - - + -
51B PRO* 3.1 21.3 + - + +
52B ARG* 3.9 7.0 - - - +
54B LEU* 1.3 72.7 - - + +
56B ALA* 1.3 65.6 + - - +
57B GLN 3.1 2.7 - - - -
58B TRP* 3.0 19.0 + - + +
59B PHE* 3.3 23.5 + - + -
66B MET* 4.6 1.6 - - - -
72B LEU* 4.3 8.1 - - + -
74B VAL* 4.0 21.1 - - + -
108B ARG* 3.6 32.1 - - - +
130B GLN* 3.8 13.5 - - - +
132B LEU* 4.2 16.8 - - + -
173B ILE* 6.1 0.4 - - + -
175B TYR* 6.0 0.2 - - - +
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Residues in contact with ALA 56 (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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52B ARG 2.9 10.9 + - - +
53B GLU* 3.5 15.5 - - + +
54B LEU 3.2 0.2 - - - -
55B LEU* 1.3 77.5 - - - +
57B GLN* 1.3 57.1 + - + +
59B PHE* 3.2 3.8 + - - +
60B ASN* 2.9 36.6 + - - +
66B MET* 3.3 34.8 - - + +
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Residues in contact with GLN 57 (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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53B GLU 3.8 11.0 - - - +
54B LEU* 3.5 31.2 - - - +
55B LEU 3.1 0.6 - - - -
56B ALA* 1.3 77.1 - - + +
58B TRP* 1.3 56.2 + - - +
60B ASN* 3.3 8.0 + - - +
61B THR* 3.0 35.4 + - - +
193B ASN* 4.4 7.6 + - - +
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Residues in contact with TRP 58 (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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54B LEU 4.2 1.2 + - - -
55B LEU* 3.0 13.7 + - - +
57B GLN* 1.3 79.1 - - - +
59B PHE* 1.3 88.0 + + - +
61B THR* 4.6 0.9 - - - -
62B ARG* 3.1 75.9 + - - +
64B LEU* 4.1 9.0 - - + -
105B LEU* 3.8 12.3 - - + -
106B GLY* 3.8 17.5 - - - -
107B TRP 3.0 39.3 + - - -
108B ARG* 3.4 38.3 - - + +
109B GLU 5.3 0.2 - - - -
132B LEU* 3.3 31.2 - - + -
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Residues in contact with PHE 59 (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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55B LEU* 3.3 24.3 + - + -
56B ALA* 3.2 8.4 + - - +
58B TRP* 1.3 98.2 - + - +
60B ASN* 1.3 66.1 + - - +
62B ARG* 3.0 3.5 + - - -
63B ASN 3.0 17.8 + - - -
64B LEU* 3.0 37.5 + - + +
65B PRO 3.5 26.0 - - - -
66B MET* 3.8 26.2 - - + -
67B PRO* 3.7 12.6 - - + -
72B LEU* 3.9 19.3 - - + -
105B LEU* 3.6 30.5 - - + -
132B LEU* 4.0 10.5 - - + -
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Residues in contact with ASN 60 (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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56B ALA* 2.9 26.4 + - - +
57B GLN* 3.5 8.3 - - - +
59B PHE* 1.3 77.6 - - - +
61B THR* 1.3 63.1 + - - +
63B ASN* 3.2 14.2 + - - +
64B LEU 5.2 0.2 - - - -
66B MET* 5.9 0.7 - - - +
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Residues in contact with THR 61 (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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57B GLN* 3.0 19.4 + - - +
58B TRP* 3.8 5.6 - - - -
59B PHE 3.3 0.2 - - - -
60B ASN* 1.3 77.6 - - - +
62B ARG* 1.3 76.8 + - + +
63B ASN 3.8 0.5 + - - -
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Residues in contact with ARG 62 (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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58B TRP* 3.1 85.5 + - - +
59B PHE 3.0 4.9 + - - +
61B THR* 1.3 97.0 - - + +
63B ASN* 1.3 69.5 + - - +
64B LEU* 3.3 23.8 + - + +
107B TRP 4.4 5.1 + - - -
108B ARG* 5.7 0.2 - - - +
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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