Contacts of the helix formed by residues 51 - 59 (chain A) in PDB entry 2R4S
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 ASN 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ALA 4.0 0.8 + - - -
47A ILE* 3.3 34.3 + - - +
49A PHE 3.0 1.4 + - - +
50A GLY* 1.3 79.0 - - - +
52A VAL* 1.3 60.6 + - + +
54A VAL* 4.0 6.2 - - - +
55A ILE* 2.8 29.6 + - - +
75A LEU 4.4 1.2 - - - +
76A ALA* 3.6 25.9 - - - +
79A ASP* 2.7 43.7 + - - +
80A LEU* 4.0 10.1 - - + +
319A SER 3.6 6.6 + - - +
322A ASN* 5.8 0.9 + - - +
323A PRO* 4.4 9.2 - - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 2.8 28.3 - - + +
49A PHE* 2.8 6.4 + - - +
51A ASN* 1.3 77.1 - - - +
53A LEU* 1.3 57.9 + - - +
54A VAL 2.9 5.2 - - - -
55A ILE* 2.8 35.7 - - + +
56A THR* 2.9 21.0 + - + +
80A LEU* 3.2 29.4 - - + -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE 2.9 14.9 + - - +
50A GLY* 4.5 6.7 - - - +
52A VAL* 1.3 77.6 - - - +
54A VAL* 1.3 57.6 + - - +
56A THR* 3.2 14.7 - - - +
57A ALA* 3.0 21.1 - - - +
336A PHE* 3.8 26.4 - - + +
339A LEU* 3.9 8.3 - - + +
340A LEU* 6.3 3.8 - - + -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLY 2.8 26.2 - - - +
51A ASN* 4.1 8.3 - - - +
52A VAL 2.9 0.4 - - - -
53A LEU* 1.3 78.5 - - - +
55A ILE* 1.3 67.2 + - - +
56A THR 3.1 1.1 - - - -
57A ALA* 3.0 7.3 + - + +
58A ILE* 2.9 26.5 + - + +
72A ILE* 4.8 11.0 - - + +
73A THR* 4.7 13.9 - - - -
76A ALA* 4.7 12.6 - - + -
323A PRO* 4.1 15.5 - - + -
336A PHE* 4.3 15.7 - - + -
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASN 2.8 21.1 + - - +
52A VAL* 2.8 51.4 - - + +
54A VAL* 1.3 77.5 - - - +
56A THR* 1.3 58.9 + - - +
58A ILE* 2.9 9.5 - - - +
59A ALA* 2.8 34.6 + - + +
73A THR* 4.7 4.7 - - - +
76A ALA* 3.5 22.0 - - + -
77A CYS* 4.8 10.3 - - - -
80A LEU* 4.3 10.1 - - + -
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Residues in contact with THR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 2.9 24.5 + - + +
53A LEU* 3.2 17.7 - - - +
55A ILE* 1.3 76.2 - - - +
57A ALA* 1.3 78.9 + - - +
58A ILE 3.1 2.4 + - - -
59A ALA* 3.4 20.5 + - - +
61A PHE* 4.1 8.2 + - + -
339A LEU* 4.3 13.2 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A LEU 3.0 18.2 - - - +
54A VAL* 3.0 10.7 + - + +
56A THR* 1.3 84.1 - - - +
58A ILE* 1.3 52.2 + - - +
61A PHE* 2.5 39.0 + - - -
64A LEU* 3.1 29.6 - - + +
335A ALA* 4.8 3.4 - - + +
336A PHE* 4.4 15.0 - - + -
339A LEU* 5.0 0.4 - - - -
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A VAL* 2.9 14.7 + - + +
55A ILE* 2.9 25.6 - - - +
57A ALA* 1.3 75.4 - - - +
59A ALA* 1.3 72.5 + - + +
61A PHE 3.3 11.8 + - - +
64A LEU* 4.1 20.0 - - + +
65A GLN* 3.7 21.3 + - + +
69A ASN* 3.7 23.1 - - + +
70A TYR* 4.4 24.2 - - + -
73A THR* 3.7 20.0 - - - -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 2.8 25.3 + - + +
56A THR* 3.5 14.8 - - - +
58A ILE* 1.3 90.6 - - + +
61A PHE 4.4 5.2 - - - -
65A GLN* 5.0 6.4 + - - -
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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