Contacts of the helix formed by residues 47 - 58 (chain A) in PDB entry 1NN1
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 THR 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLU* 3.8 7.2 + - + -
46A SER* 1.3 87.7 - - - +
48A GLU* 1.3 67.8 + - - +
49A ILE 3.6 0.7 + - - -
50A GLY 2.9 14.9 + - - -
51A LYS* 2.9 23.6 + - - +
75A ASN* 3.4 3.3 + - - -
78A GLU* 2.6 40.1 + - - +
79A GLN* 4.0 17.9 - - - +
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Residues in contact with GLU 48 (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* 1.3 76.9 - - - +
49A ILE* 1.3 65.5 + - + +
51A LYS* 3.1 17.6 + - + +
52A LEU* 3.3 19.0 + - + +
78A GLU* 5.2 0.4 + - - -
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Residues in contact with ILE 49 (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* 3.3 1.0 + - - -
48A GLU* 1.3 80.2 - - + +
50A GLY* 1.3 63.7 + - - +
52A LEU* 3.0 22.4 + - + +
53A LEU* 3.1 13.3 + - + +
71A LEU* 3.4 48.5 - - + +
74A ALA* 4.0 24.0 - - + +
75A ASN* 4.0 10.1 - - + -
78A GLU* 3.8 29.6 + - + +
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Residues in contact with GLY 50 (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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43A PRO* 5.5 0.2 - - - -
44A GLU 3.3 24.7 - - - -
45A ARG* 3.5 12.1 - - - +
47A THR* 2.9 14.6 + - - -
49A ILE* 1.3 78.1 - - - +
51A LYS* 1.3 58.2 + - - +
53A LEU* 3.3 8.6 + - - +
54A SER* 2.9 28.8 + - - -
75A ASN* 3.8 5.1 - - - +
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Residues in contact with LYS 51 (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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45A ARG 3.5 11.2 - - - +
46A SER* 2.7 33.5 + - - +
47A THR 2.9 12.9 + - - +
48A GLU* 3.6 12.1 - - + +
49A ILE 3.1 0.4 - - - -
50A GLY* 1.3 76.1 - - - +
52A LEU* 1.3 64.8 + - + +
54A SER* 3.8 5.4 - - - +
55A SER* 3.1 24.8 + - - -
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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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48A GLU* 3.6 15.9 - - + +
49A ILE* 3.0 14.6 + - + +
51A LYS* 1.3 77.8 - - + +
53A LEU* 1.3 58.4 + - - +
55A SER* 3.5 5.4 + - - -
56A TYR* 3.0 28.6 + - - +
61A SER* 4.3 2.8 + - - -
63A VAL* 4.9 4.8 - - + +
71A LEU* 4.3 29.6 - - + -
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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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43A PRO* 3.9 9.4 - - + -
49A ILE* 3.1 17.2 + - + +
50A GLY* 3.6 8.7 - - - +
51A LYS 3.3 0.2 - - - -
52A LEU* 1.3 74.3 - - - +
54A SER* 1.3 59.4 + - - +
56A TYR* 3.3 4.8 + - - +
57A LEU* 2.8 36.1 + - - +
68A VAL* 3.8 22.4 - - + -
71A LEU* 3.6 28.3 - - + +
72A PHE* 3.7 42.0 - - + +
75A ASN* 3.8 35.9 - - + +
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Residues in contact with SER 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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45A ARG* 2.6 50.0 + - - +
50A GLY 2.9 17.6 + - - -
51A LYS* 3.8 7.4 - - - -
53A LEU* 1.3 73.1 - - - +
55A SER* 1.3 65.8 + - - +
57A LEU* 3.2 2.0 + - - +
58A GLN* 2.7 48.8 + - - +
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Residues in contact with SER 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 LYS 3.1 15.9 + - - -
52A LEU* 3.8 4.7 - - - -
54A SER* 1.3 79.8 - - - +
56A TYR* 1.3 61.2 + - - +
58A GLN* 3.4 6.3 + - - +
59A LYS 3.1 3.8 + - - -
60A LYS* 2.9 46.1 + - - +
61A SER* 2.9 24.3 + - - -
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Residues in contact with TYR 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 3.0 15.5 + - - +
53A LEU* 3.4 9.2 - - - +
55A SER* 1.3 76.2 - - - +
57A LEU* 1.3 75.1 + - + +
59A LYS 3.1 2.6 + - - -
61A SER* 3.3 10.4 + - - -
62A ASP* 4.8 0.4 - - - -
63A VAL* 3.6 46.9 - - + -
65A ASP* 4.1 4.0 + - - -
68A VAL* 3.7 25.6 - - + +
72A PHE* 4.7 4.7 - + - -
109A LYS* 3.1 24.8 + - - -
150A ARG* 2.7 72.7 + - + -
151A TYR* 3.2 22.4 + + - -
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Residues in contact with LEU 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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43A PRO* 4.1 11.2 - - + -
45A ARG* 3.7 22.9 - - - +
53A LEU 2.8 24.7 + - - +
54A SER 3.2 3.1 + - - +
56A TYR* 1.3 82.9 - - + +
58A GLN* 1.3 57.8 + - - +
59A LYS 3.2 0.8 + - - -
72A PHE* 4.1 12.8 - - + -
149A GLU* 3.0 26.1 - - - +
150A ARG* 2.9 38.8 + - + +
151A TYR* 4.1 22.4 - - + -
301A 2DT 3.6 37.9 - - - +
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Residues in contact with GLN 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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45A ARG* 4.1 1.8 - - - +
54A SER* 2.7 44.3 + - - +
55A SER* 3.8 5.4 - - - +
57A LEU* 1.3 75.7 - - - +
59A LYS* 1.3 71.4 + - - +
60A LYS* 2.4 51.1 + - + +
148A HIS 5.0 1.7 - - - +
149A GLU* 3.7 21.5 - - + +
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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