Contacts of the helix formed by residues 56 - 64 (chain D) in PDB entry 2IHC
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D LEU 3.1 11.9 + - - +
53D ALA 3.3 9.7 - - - +
54D ALA 3.5 1.6 - - - -
55D CYS* 1.3 82.1 - - - +
57D SER* 1.3 57.1 + - - +
58D TYR 3.4 4.9 + - - -
59D PHE* 3.5 21.4 + - - -
60D HIS* 3.0 22.2 + - - +
113D LEU* 2.3 39.9 + - - +
114D SER 3.5 5.8 - - - -
115D VAL* 4.5 4.3 - - - -
116D HIS* 3.5 4.2 - - - -
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D SER* 1.3 68.1 - - - +
58D TYR* 1.3 66.8 + - - +
60D HIS* 3.2 9.8 + - - +
61D SER* 3.0 29.4 + - - -
114D SER* 3.3 23.7 + - - -
116D HIS* 3.4 22.1 + - - -
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Residues in contact with TYR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D SER* 3.7 0.4 - - - +
57D SER* 1.3 79.7 - - - +
59D PHE* 1.3 71.8 + + - +
61D SER* 3.3 6.3 + - - -
62D ARG* 3.3 24.7 + - + +
73D ILE* 4.9 17.2 - - + +
74D THR 4.6 5.4 + - - -
75D LEU* 5.6 3.8 - - + -
76D PRO* 3.9 14.1 - - + +
112D PHE* 3.4 44.8 - + - +
113D LEU* 3.2 48.1 + - + +
114D SER* 4.5 0.8 - - - -
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Residues in contact with PHE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ILE* 3.9 36.3 - - + -
52D LEU* 3.4 46.4 - - + +
53D ALA* 4.1 1.8 - - - +
56D SER* 3.5 23.9 + - - -
58D TYR* 1.3 88.0 - + - +
60D HIS* 1.3 62.1 + - - +
62D ARG* 3.4 3.9 + - + +
63D ILE* 3.1 30.0 + - + +
73D ILE* 4.2 22.0 - - + -
84D PHE* 3.8 23.6 - + - -
113D LEU* 3.5 31.4 - - + -
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Residues in contact with HIS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLN* 5.3 4.2 + - + -
32C VAL* 5.8 3.6 - - + -
33C LEU* 5.3 2.9 - - + -
53D ALA* 3.7 28.9 + - + +
56D SER 3.0 15.4 + - - +
57D SER* 3.2 15.7 + - - +
59D PHE* 1.3 76.7 - - - +
61D SER* 1.3 62.0 + - - +
64D VAL* 3.1 62.3 + - + +
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Residues in contact with SER 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D SER* 3.0 13.5 + - - -
58D TYR* 3.7 9.3 - - - -
59D PHE 3.3 0.2 - - - -
60D HIS* 1.3 80.8 - - - +
62D ARG* 1.3 62.0 + - - +
63D ILE 3.4 0.9 + - - -
64D VAL* 4.2 5.7 + - - +
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Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TYR* 3.3 21.8 + - + +
59D PHE* 4.2 5.4 - - + +
60D HIS 3.4 0.4 - - - -
61D SER* 1.3 78.0 - - - +
63D ILE* 1.3 58.0 + - - +
71D LEU* 5.7 1.6 - - - +
73D ILE* 3.9 34.0 - - + +
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 4.0 20.3 - - + +
49D ARG* 4.6 22.0 - - + +
53D ALA* 4.8 3.6 - - + -
59D PHE* 3.1 18.8 + - + +
60D HIS 4.2 0.9 - - - +
61D SER 4.7 0.2 - - - -
62D ARG* 1.3 79.8 - - - +
64D VAL* 1.3 66.1 + - - +
71D LEU* 4.7 17.1 - - + +
73D ILE* 5.5 4.3 - - + -
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C VAL* 4.9 18.2 - - + +
33C LEU* 4.1 29.5 + - + +
53D ALA* 5.1 0.2 - - + -
60D HIS* 3.1 57.7 + - + +
61D SER* 4.2 5.1 + - - +
63D ILE* 1.3 81.8 - - - +
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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