Contacts of the helix formed by residues 51 - 57 (chain A) in PDB entry 2NYM
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 LEU 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.4 8.1 - - + -
35A LEU* 3.5 35.2 - - + +
38A ILE* 3.7 18.8 - - + -
39A ALA* 3.6 31.4 - - + -
42A LEU* 4.0 8.0 - - + +
46A ARG 4.0 0.8 + - - -
47A THR* 3.4 21.9 + - + +
50A GLU* 1.3 76.5 - - - +
52A LEU* 1.3 62.5 + - + +
54A PHE* 3.4 13.3 + - + +
55A LEU* 3.0 36.9 + - + +
76A PHE* 4.6 1.6 - - + -
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Residues in contact with LEU 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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47A THR* 3.2 23.8 + - + +
48A ARG* 4.6 4.0 - - - +
51A LEU* 1.3 76.2 - - + +
53A PRO* 1.3 68.7 - - + +
54A PHE 2.8 4.7 - - - -
55A LEU* 3.1 18.4 + - + +
56A THR* 2.6 38.5 + - - +
73A LEU* 4.4 13.9 - - + -
76A PHE* 4.5 13.9 - - + -
80A VAL* 4.4 2.9 - - + -
88A CYS* 2.9 48.7 - - + +
89A LEU* 3.7 16.4 - - + +
92A PRO* 5.2 6.0 - - + +
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Residues in contact with PRO 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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48A ARG 3.7 10.1 - - - +
49A SER* 3.7 19.1 - - - +
50A GLU* 3.6 22.0 - - - +
52A LEU* 1.3 94.0 - - + +
54A PHE* 1.3 56.3 + - - -
56A THR* 3.9 9.4 - - + +
57A ASP* 2.8 35.4 - - - +
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Residues in contact with PHE 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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20A LEU* 3.6 43.7 - - + -
21A ARG* 4.6 27.6 - - + -
50A GLU 3.3 19.5 + - - +
51A LEU* 3.4 7.8 + - + +
52A LEU 2.8 1.0 - - - -
53A PRO* 1.3 78.0 - - - +
55A LEU* 1.3 79.9 + - + +
56A THR 3.0 1.6 + - - -
57A ASP* 3.5 1.3 + - - -
58A THR* 2.7 50.0 + - + -
60A TYR* 3.6 22.9 - + - -
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Residues in contact with LEU 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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32A ILE* 3.7 28.5 - - + -
35A LEU* 3.3 25.4 - - + -
51A LEU* 3.0 31.4 + - + +
52A LEU* 3.1 17.9 + - + +
54A PHE* 1.3 90.5 - - + +
56A THR* 1.3 61.2 - - - +
58A THR* 3.7 16.0 - - - +
60A TYR* 4.5 6.2 - - + +
69A LEU* 3.8 29.2 - - + +
73A LEU* 4.3 5.2 - - + -
76A PHE* 5.3 0.4 - - + -
92A PRO* 4.3 16.4 - - + +
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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 LEU* 2.6 26.0 + - - +
53A PRO* 4.0 8.8 - - + +
55A LEU* 1.3 77.6 - - - +
57A ASP* 1.3 69.7 + - - +
58A THR 3.2 9.6 + - - +
91A PRO* 4.1 21.0 - - + +
92A PRO* 4.0 24.6 - - - +
95A SER* 5.4 4.5 + - - -
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Residues in contact with ASP 57 (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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53A PRO* 2.8 27.0 + - - +
54A PHE* 3.5 1.1 + - - +
56A THR* 1.3 86.0 - - - +
58A THR* 1.3 63.3 + - - +
59A ILE* 4.3 2.9 + - - +
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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