Contacts of the helix formed by residues 56 - 64 (chain A) in PDB entry 1I43
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASN* 1.3 78.6 - - - +
57A ASP* 1.3 66.9 + - - +
58A GLY 3.3 6.1 + - - -
59A SER* 3.3 4.2 + - - -
60A VAL* 3.2 24.6 + - - +
430D ASP* 2.8 49.4 + - - -
432D ASP* 6.4 0.4 - - - -
433D ASP* 2.9 9.0 + - - -
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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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55A ASN 4.0 3.1 + - - +
56A SER* 1.3 75.4 + - - +
58A GLY* 1.3 58.4 + - - +
60A VAL* 3.2 9.7 + - - +
61A ALA* 2.8 31.0 + - - +
126A LEU* 3.6 8.7 - - + +
243A LEU* 3.3 33.6 - - + +
246A LYS* 2.9 36.9 + - - -
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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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56A SER* 3.2 8.7 + - - -
57A ASP* 1.3 81.0 - - - +
59A SER* 1.3 60.8 + - - +
60A VAL 3.3 0.2 + - - -
61A ALA* 3.4 3.7 + - - +
62A ILE* 3.2 28.3 + - - +
311A HIS* 3.5 43.0 - - - +
430D ASP* 4.7 2.2 - - - -
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Residues in contact with SER 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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54A LEU* 3.8 23.4 - - - +
56A SER* 3.3 5.5 + - - -
58A GLY* 1.3 75.3 - - - +
60A VAL* 1.3 58.0 + - - +
62A ILE* 3.4 1.3 + - - +
63A HIS* 3.1 32.7 + - - +
429D GLU* 3.8 17.1 - - - +
430D ASP* 3.2 23.4 + - - +
433D ASP* 2.7 32.5 + - - +
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Residues in contact with VAL 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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50A TYR* 5.5 7.4 - - + +
54A LEU* 4.2 26.2 - - + +
55A ASN 5.3 0.7 - - - -
56A SER 3.2 15.5 + - - +
57A ASP* 3.4 11.9 - - - +
58A GLY 3.2 0.4 - - - -
59A SER* 1.3 74.0 - - - +
61A ALA* 1.3 54.6 + - - +
62A ILE 2.7 11.8 + - - -
64A ALA* 2.7 52.2 + - + +
125A ALA* 3.8 19.7 - - + +
126A LEU* 3.8 20.0 - - + +
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Residues in contact with ALA 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 ASP 2.8 20.4 + - - +
58A GLY* 3.8 9.0 - - - +
60A VAL* 1.3 72.6 - - - +
62A ILE* 1.3 57.8 + - + +
122A LYS* 3.0 27.2 + - - +
126A LEU* 4.1 25.6 - - + -
243A LEU* 5.5 1.6 - - + -
307A MET* 3.5 28.9 - - + +
310A LEU* 4.4 12.1 - - + -
311A HIS* 5.1 2.5 - - - +
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Residues in contact with ILE 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 3.2 16.4 + - - +
59A SER 3.7 5.6 - - - +
60A VAL 2.7 5.9 + - - -
61A ALA* 1.3 75.8 - - - +
63A HIS* 1.3 78.4 + - + +
66A GLU* 3.5 1.2 - - - +
122A LYS* 2.7 23.3 + - - +
308A LYS* 3.0 52.8 + - + +
311A HIS* 3.9 2.2 - - + -
392D CYS* 4.3 8.5 - - + +
393D GLU* 4.3 10.1 - - + -
428D VAL* 3.3 34.5 - - + -
429D GLU* 3.8 20.9 - - + +
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Residues in contact with HIS 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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50A TYR* 3.2 8.8 - - - -
54A LEU* 3.9 16.0 - - + +
59A SER 3.1 15.4 + - - +
62A ILE* 1.3 91.5 - - + +
64A ALA* 1.3 65.0 + - - +
65A GLY 3.1 0.9 + - - -
66A GLU* 3.1 17.4 + - + -
67A ARG* 3.1 46.9 + - + +
308A LYS* 5.8 0.4 - - - -
382D ILE* 3.8 18.6 + - + +
384D TYR* 4.2 10.2 - + - -
393D GLU* 4.0 18.4 - - + +
394D SER 4.6 0.2 + - - -
429D GLU* 2.9 41.5 + - + +
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Residues in contact with ALA 64 (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 TYR* 3.9 11.6 - - + -
60A VAL* 2.7 46.4 + - + +
62A ILE 3.6 0.8 - - - -
63A HIS* 1.3 69.8 - - - +
65A GLY* 1.3 59.9 + - - +
66A GLU* 4.2 0.2 - - - +
118A VAL 4.2 0.2 - - - +
122A LYS* 3.0 46.1 - - + +
125A ALA* 3.8 18.2 - - + -
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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