Contacts of the helix formed by residues 49 - 63 (chain A) in PDB entry 1NHX
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 SER 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ASP* 2.9 30.9 + - - -
48A GLY* 1.3 82.2 - - - +
50A GLU* 1.3 63.8 + - - +
51A GLU* 3.2 17.7 + - - +
52A GLU* 3.2 17.3 + - - +
53A ASN 3.1 16.3 + - - -
55A ARG* 5.3 0.7 + - - -
171A ARG* 3.6 5.9 + - - -
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Residues in contact with GLU 50 (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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49A SER* 1.3 70.6 - - - +
51A GLU* 1.3 66.7 + - - +
53A ASN* 3.1 3.5 + - - +
54A GLY* 2.9 28.2 + - - -
171A ARG* 3.4 25.6 - - - +
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Residues in contact with GLU 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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49A SER* 3.2 22.4 - - - +
50A GLU* 1.3 83.3 + - + +
52A GLU* 1.3 61.5 + - - +
54A GLY* 3.6 1.7 + - - -
55A ARG* 3.1 43.5 + - - +
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Residues in contact with GLU 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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17A GLN* 2.9 13.6 + - - +
44A HIS* 2.7 34.7 + - + +
46A CYS* 3.2 13.6 - - - +
47A ASP* 2.9 18.2 + - - +
48A GLY* 3.0 25.3 + - - -
49A SER* 3.2 22.4 + - - +
51A GLU* 1.3 72.1 - - - +
53A ASN* 1.3 65.9 + - - +
55A ARG* 3.3 21.9 + - - +
56A LEU* 3.0 35.1 + - + +
171A ARG* 5.9 0.5 - - - -
176A MET* 4.0 7.3 - - - +
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Residues in contact with ASN 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 SER 3.1 13.2 + - - +
50A GLU* 3.1 9.2 + - - +
52A GLU* 1.3 77.2 - - - +
54A GLY* 1.3 62.8 + - - +
56A LEU* 3.0 9.8 + - - +
57A LEU* 3.0 47.9 + - - +
74A ASN* 4.9 8.9 - - - +
168A ALA* 4.0 24.4 - - - +
171A ARG* 3.5 40.2 - - - +
172A ILE* 6.4 0.2 - - - +
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Residues in contact with GLY 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 2.9 14.9 + - - -
51A GLU* 3.9 2.2 - - - -
53A ASN* 1.3 75.7 - - - +
55A ARG* 1.3 56.7 + - - +
57A LEU* 3.6 12.6 + - - +
58A GLY* 3.0 24.9 + - - -
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Residues in contact with ARG 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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17A GLN* 2.7 32.3 + - - +
44A HIS* 5.0 1.6 - - - -
47A ASP* 5.3 1.4 + - - -
49A SER* 5.3 0.6 + - - -
51A GLU* 3.1 42.7 + - - +
52A GLU* 3.6 25.3 - - - +
53A ASN 3.2 0.4 - - - -
54A GLY* 1.3 75.1 - - - +
56A LEU* 1.3 60.0 + - + +
58A GLY* 3.5 1.5 + - - -
59A GLN* 3.0 44.2 + - - +
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Residues in contact with LEU 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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44A HIS* 4.6 11.0 - - + +
52A GLU* 3.0 33.5 + - + +
53A ASN* 3.0 10.9 + - - +
55A ARG* 1.3 75.0 - - + +
57A LEU* 1.3 55.7 + - + +
59A GLN* 3.3 19.6 + - - +
60A MET* 2.8 50.7 + - + +
140A TYR* 3.8 36.3 - - + +
164A PRO* 5.1 7.0 - - + +
167A VAL* 3.7 33.4 - - + -
168A ALA* 5.4 2.5 - - + +
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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 ASN* 3.0 43.4 + - - +
54A GLY* 3.7 9.6 - - - +
56A LEU* 1.3 76.2 - - - +
58A GLY* 1.3 52.1 + - - +
60A MET* 3.1 15.5 + - + +
61A GLU* 2.7 35.3 + - - +
66A LEU* 3.7 23.4 - - + +
74A ASN* 3.8 11.7 - - - +
76A TRP* 3.6 47.2 - - + +
168A ALA* 4.5 12.8 - - + -
356A ILE* 5.0 6.5 - - + -
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Residues in contact with GLY 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 GLY 3.0 16.9 + - - -
55A ARG* 3.8 1.8 - - - -
56A LEU 3.3 0.2 - - - -
57A LEU* 1.3 76.0 - - - +
59A GLN* 1.3 56.3 + - - +
61A GLU* 3.3 16.2 + - - +
62A GLU* 3.1 32.2 + - - +
76A TRP* 4.9 2.8 - - - -
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Residues in contact with GLN 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 ARG* 3.0 33.7 + - - +
56A LEU* 3.6 24.3 - - + +
58A GLY* 1.3 72.5 - - - +
60A MET* 1.3 63.4 + - + +
62A GLU* 3.3 11.2 + - + +
63A GLU* 3.1 25.6 + - - +
65A ILE* 5.9 0.2 - - - -
140A TYR* 4.3 8.0 + - - -
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Residues in contact with MET 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 LEU* 2.8 38.0 + - + +
57A LEU* 3.5 6.3 - - + +
59A GLN* 1.3 71.4 - - + +
61A GLU* 1.3 63.6 + - - +
63A GLU 3.6 0.3 + - - -
64A GLY 3.2 1.9 + - - -
65A ILE* 2.8 60.8 + - + -
66A LEU* 3.1 31.4 + - + -
164A PRO* 3.5 37.0 - - + +
165A TYR* 3.5 27.1 - - - -
168A ALA* 3.9 17.9 - - + -
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Residues in contact with GLU 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 2.7 16.8 + - - +
58A GLY* 3.4 14.1 - - - +
59A GLN 3.2 0.2 - - - -
60A MET* 1.3 70.3 - - - +
62A GLU* 1.3 64.2 + - + +
64A GLY* 3.2 12.8 + - - -
66A LEU* 3.4 17.8 - - - +
67A ARG* 5.3 0.7 - - - -
68A ARG* 3.8 25.3 + - - +
76A TRP* 3.8 23.9 - - + -
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Residues in contact with GLU 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 GLY 3.1 19.9 + - - +
59A GLN* 3.4 12.1 - - - +
61A GLU* 1.3 77.7 - - - +
63A GLU* 1.3 60.5 + - + +
64A GLY* 3.3 3.5 + - - -
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Residues in contact with GLU 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 GLN 3.1 13.7 + - - +
60A MET 3.6 0.4 + - - +
61A GLU 3.3 0.2 - - - -
62A GLU* 1.3 79.4 - - + +
64A GLY* 1.3 59.5 + - - +
65A ILE* 3.2 23.9 + - + +
137A ARG* 6.0 0.2 + - - -
209A ASN* 2.9 29.3 - - - +
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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