Contacts of the helix formed by residues 50 - 63 (chain A) in PDB entry 5IHC
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A THR 5.0 0.9 - - - +
47A LEU* 3.2 32.2 + - - +
49A SER* 1.4 82.7 + - - +
51A LEU* 1.4 61.7 + - - +
52A PRO* 3.5 1.3 - - - -
53A ARG* 3.2 25.9 + - + +
54A ILE* 3.4 23.6 + - + +
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Residues in contact with LEU 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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44A LYS* 3.8 35.4 - - + +
47A LEU* 4.0 28.9 - - + +
48A GLY* 3.5 20.8 + - - +
49A SER 3.2 0.2 - - - -
50A ASP* 1.4 74.8 - - - +
52A PRO* 1.4 67.3 - - + +
54A ILE* 3.1 14.3 + - + +
55A LYS* 3.2 34.9 + - - +
82A ILE* 3.8 29.6 - - + -
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Residues in contact with PRO 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 GLY 4.5 2.7 - - - +
49A SER* 3.3 18.2 - - - +
50A ASP 3.7 0.9 - - - -
51A LEU* 1.4 94.4 - - + +
53A ARG* 1.3 63.7 + - - +
55A LYS* 3.4 14.3 + - + +
56A THR* 3.2 31.6 + - - +
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Residues in contact with ARG 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 4.7 6.6 + - - -
50A ASP* 3.2 23.2 + - + +
51A LEU 3.2 1.2 - - - -
52A PRO* 1.3 81.3 - - - +
54A ILE* 1.4 64.9 + - + +
56A THR* 2.7 24.6 + - + +
57A GLU* 2.9 22.8 + - - +
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Residues in contact with ILE 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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42A MET* 3.8 35.0 - - + -
47A LEU* 3.8 35.7 - - + -
50A ASP* 3.4 26.8 + - + +
51A LEU 3.1 9.2 + - - +
53A ARG* 1.4 77.4 - - + +
55A LYS* 1.3 58.7 + - - +
57A GLU* 3.3 9.7 + - + +
58A ILE* 3.1 45.9 + - + +
82A ILE* 4.3 9.9 - - + -
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Residues in contact with LYS 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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44A LYS* 5.3 0.2 - - - -
51A LEU* 3.2 44.0 + - + +
52A PRO* 3.5 14.4 - - + +
54A ILE* 1.3 77.4 - - - +
56A THR* 1.4 56.2 + - + +
58A ILE* 3.7 11.1 + - + +
59A GLU* 3.2 30.8 + - - +
77A GLU* 3.9 31.4 + - - +
82A ILE* 4.3 9.4 - - + -
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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 PRO 3.2 13.9 + - - +
53A ARG* 2.7 26.7 + - + +
55A LYS* 1.4 74.0 - - - +
57A GLU* 1.3 65.6 + - - +
59A GLU* 3.5 8.2 + - - +
60A ALA* 3.1 25.6 + - - +
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Residues in contact with GLU 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 ARG* 2.9 31.8 + - - +
54A ILE* 3.3 13.2 + - + +
56A THR* 1.3 80.6 + - - +
58A ILE* 1.4 58.8 + - + +
60A ALA* 3.2 7.9 + - + +
61A LEU* 3.0 30.0 + - - +
84A MET* 6.0 0.2 - - - -
151A PHE* 3.4 36.2 - - + +
152A GLY* 4.4 12.6 - - - -
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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 ILE* 3.1 37.4 + - + +
55A LYS* 3.8 11.0 - - + +
56A THR 3.4 0.2 - - - -
57A GLU* 1.4 74.5 - - + +
59A GLU* 1.4 60.7 + - - +
61A LEU* 3.2 10.1 + - - +
62A LYS* 3.0 39.3 + - - +
72A LEU* 4.1 2.2 - - + +
75A VAL* 3.8 32.1 - - + -
82A ILE* 3.8 32.3 - - + -
84A MET* 3.5 27.1 - - + -
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Residues in contact with GLU 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 LYS 3.2 18.5 + - - +
56A THR* 3.7 8.3 - - - +
57A GLU 3.3 0.2 - - - -
58A ILE* 1.4 80.3 - - - +
60A ALA* 1.4 54.5 + - - +
62A LYS* 3.0 50.5 + - - +
63A ASN* 2.8 29.6 + - - +
128A TYR* 4.9 0.2 - - - -
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Residues in contact with ALA 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 THR 3.1 15.1 + - - +
57A GLU* 3.2 15.0 + - + +
59A GLU* 1.4 71.1 - - - +
61A LEU* 1.3 60.8 + - - +
63A ASN* 2.9 20.3 + - - +
64A LEU* 3.3 21.9 + - + +
128A TYR* 3.6 40.4 - - + -
151A PHE* 5.9 5.6 - - + -
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Residues in contact with LEU 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 GLU 3.0 13.8 + - - +
58A ILE 3.2 9.8 + - - +
60A ALA* 1.3 73.6 - - - +
62A LYS* 1.4 62.7 + - - +
64A LEU* 3.0 31.1 + - + +
69A ILE* 4.2 17.3 - - + -
70A CYS 4.0 17.9 - - - +
71A GLN* 5.7 0.2 + - - -
72A LEU* 4.0 20.4 - - + +
84A MET* 3.6 29.4 - - + -
86A LEU* 4.0 18.2 - - + -
151A PHE* 4.5 23.0 - - + -
310A TYR* 4.6 1.0 + - - -
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Residues in contact with LYS 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 ILE* 3.0 30.9 + - - +
59A GLU* 3.0 45.3 + - - +
60A ALA 3.2 0.4 - - - -
61A LEU* 1.4 75.7 - - - +
63A ASN* 1.4 62.5 + - - +
64A LEU 3.5 0.2 - - - -
72A LEU* 4.0 7.9 - - + -
75A VAL* 4.3 9.5 - - - +
279A PHE* 3.3 14.7 - - - -
308A TRP 5.5 0.2 - - - +
309A GLN 4.6 9.7 + - - -
310A TYR* 3.0 61.4 + - + -
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Residues in contact with ASN 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 GLU* 2.8 26.0 + - - +
60A ALA 2.9 9.2 + - - +
62A LYS* 1.4 82.2 - - - +
64A LEU* 1.3 58.0 + - - +
122A TYR* 3.8 2.1 + - - -
126A GLN* 2.9 29.4 + - - +
128A TYR* 3.1 27.4 + - + +
279A PHE* 3.9 12.1 - - - -
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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