Contacts of the helix formed by residues 48 - 63 (chain A) in PDB entry 7NG0
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 ASP 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A MET 4.3 1.2 + - - -
47A PHE* 1.3 67.5 - - - +
49A GLU* 1.3 68.8 + - - +
50A GLU* 3.4 27.3 + - - +
51A LYS* 3.3 24.8 + - + +
52A ILE* 3.1 22.8 + - - +
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Residues in contact with GLU 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 PHE* 3.4 19.5 + - - +
48A ASP* 1.3 71.4 + - - +
50A GLU* 1.3 66.5 + - - +
52A ILE* 3.1 14.6 + - - +
53A ASP* 2.9 32.3 + - - +
88A ARG* 3.8 20.7 + - - -
92A LYS* 3.4 34.4 + - - +
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Residues in contact with GLU 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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48A ASP* 3.4 19.2 + - - +
49A GLU* 1.3 78.6 - - - +
51A LYS* 1.3 59.8 + - - +
53A ASP* 3.6 5.6 + - - +
54A GLU* 3.0 31.1 + - - +
152A GLY 4.5 2.6 - - - +
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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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48A ASP* 3.3 28.2 + - + +
49A GLU 3.2 0.4 - - - -
50A GLU* 1.3 73.5 - - - +
52A ILE* 1.3 66.8 + - - +
53A ASP 3.0 2.0 - - - -
54A GLU* 3.0 33.6 + - - +
55A LEU* 3.1 11.7 + - - +
85A ARG* 4.2 24.8 + - - +
123A GLU* 4.5 16.0 + - - -
129A GLU* 6.1 0.7 - - - -
153A LYS* 4.1 23.3 - - - +
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Residues in contact with ILE 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 PHE* 4.0 31.0 - - + -
48A ASP 3.1 11.2 + - - +
49A GLU* 3.1 30.8 + - - +
51A LYS* 1.3 79.4 - - + +
53A ASP* 1.3 67.9 + - - +
55A LEU* 3.3 9.0 - - - +
56A ALA* 3.1 21.7 + - - +
85A ARG* 4.1 32.1 - - + +
88A ARG* 4.1 20.2 - - + +
89A ALA* 3.6 14.8 - - - +
92A LYS* 4.1 11.7 - - + -
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Residues in contact with ASP 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 GLU* 2.9 22.7 + - - +
50A GLU* 3.8 6.0 - - - +
52A ILE* 1.3 75.6 - - - +
54A GLU* 1.3 67.9 + - - +
55A LEU 3.1 1.6 - - - -
56A ALA* 3.1 7.7 + - - +
57A LEU* 2.8 33.1 + - + +
92A LYS* 2.8 41.8 + - - +
152A GLY 6.0 0.7 - - - +
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Residues in contact with GLU 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 GLU* 3.0 29.1 - - - +
51A LYS* 3.0 26.8 + - - +
53A ASP* 1.3 78.2 - - - +
55A LEU* 1.3 47.7 + - - +
57A LEU* 3.4 7.1 - - - +
58A THR* 2.7 42.2 + - + +
151A LEU 3.2 23.6 - - - +
152A GLY* 3.2 17.7 + - - +
153A LYS* 3.4 41.9 + - - +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LYS 3.1 10.9 + - - +
52A ILE* 3.3 11.7 - - - +
53A ASP 3.1 0.2 - - - -
54A GLU* 1.3 71.4 - - - +
56A ALA* 1.3 54.5 + - - +
58A THR* 2.6 28.0 + - - +
59A ILE* 2.7 43.3 + - + +
85A ARG* 3.5 65.7 - - + +
86A ARG* 3.8 11.7 - - + +
89A ALA* 4.1 0.7 - - + -
301A SO4 4.7 0.4 - - - +
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Residues in contact with ALA 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 ILE 3.1 9.6 + - - +
53A ASP* 3.6 10.8 - - - +
55A LEU* 1.3 74.7 - - - +
57A LEU* 1.3 58.3 + - + +
59A ILE* 3.4 2.6 + - - -
60A ARG 2.9 22.7 + - - -
89A ALA* 3.2 39.6 - - + +
92A LYS* 4.6 9.9 - - + -
93A LEU* 3.2 23.9 - - + +
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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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53A ASP* 2.8 21.0 + - + +
54A GLU* 3.4 8.7 - - - +
56A ALA* 1.3 73.9 - - + +
58A THR* 1.3 60.2 + - - +
60A ARG* 2.9 25.7 + - + +
61A THR* 3.2 12.0 + - - -
93A LEU* 6.2 2.0 - - + -
149A GLN 4.4 11.7 - - - +
150A ARG 4.6 8.5 - - - +
152A GLY* 3.7 29.8 - - - +
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Residues in contact with THR 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 GLU* 2.7 21.6 + - + +
55A LEU* 2.6 33.1 + - - +
57A LEU* 1.3 72.2 - - - +
59A ILE* 1.3 54.6 + - - +
61A THR* 3.5 6.5 + - - +
62A HIS* 3.2 54.9 + - + +
150A ARG* 4.2 16.4 - - + +
151A LEU* 4.9 15.5 - - + +
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Residues in contact with ILE 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 LEU* 2.7 36.6 + - + +
56A ALA 3.7 4.9 - - - +
58A THR* 1.3 71.7 - - - +
60A ARG* 1.3 62.0 + - - +
61A THR 3.2 0.4 - - - -
62A HIS* 5.7 1.3 - - + -
63A GLY* 2.8 39.8 + - - +
64A ILE* 3.7 16.6 - - + +
86A ARG* 4.2 13.7 - - + +
89A ALA* 3.9 23.6 - - + -
90A VAL* 4.1 16.2 - - + -
93A LEU* 3.7 10.8 - - + -
95A TRP* 3.4 31.9 - - + -
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Residues in contact with ARG 60 (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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56A ALA 2.9 15.0 + - - +
57A LEU* 2.9 15.6 + - + +
59A ILE* 1.3 75.8 - - - +
61A THR* 1.3 61.9 + - - +
63A GLY* 4.5 0.7 + - - -
93A LEU* 3.8 21.0 - - + +
95A TRP* 5.0 5.3 - - - -
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Residues in contact with THR 61 (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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57A LEU 3.2 10.4 + - - -
58A THR* 3.8 10.8 - - - -
59A ILE 3.2 0.4 - - - -
60A ARG* 1.3 80.0 - - - +
62A HIS* 1.3 66.1 + - - +
150A ARG* 5.1 19.3 - - - -
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Residues in contact with HIS 62 (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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58A THR* 3.2 38.0 + - + +
59A ILE* 4.9 1.6 - - + -
61A THR* 1.3 82.4 - - - +
63A GLY* 1.3 86.8 + - - +
65A ILE* 3.4 36.2 - - + +
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Residues in contact with GLY 63 (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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59A ILE* 2.8 34.1 + - - +
60A ARG 4.5 0.6 + - - -
61A THR 3.6 0.6 - - - -
62A HIS* 1.3 98.4 + - - +
64A ILE* 1.3 63.4 + - - -
65A ILE 3.5 1.9 + - - -
95A TRP* 4.2 8.3 - - - -
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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