Contacts of the helix formed by residues 48 - 56 (chain B) 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 HIS 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A SER* 3.7 19.7 - - - -
24B LEU* 3.4 31.9 - - + -
27B GLN* 3.0 25.8 + - + +
28B ARG 4.3 0.4 - - - -
33B LEU 3.3 27.0 + - - -
34B CYS* 4.0 15.3 - - - -
35B ASP* 3.6 9.2 - - - +
36B VAL* 3.9 1.3 - - - -
47B ALA* 1.3 72.1 - - - +
49B ARG* 1.3 65.8 + - - +
50B SER* 4.0 9.0 - - - +
51B VAL* 3.2 17.1 + - + +
52B LEU* 3.1 23.4 + - - +
92B TYR* 2.7 34.4 + + - +
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.0 20.3 - - + +
35A ASP* 6.1 0.7 - - - -
35B ASP* 2.6 57.2 + - - +
36B VAL* 3.7 15.1 - - + +
48B HIS* 1.3 72.5 - - - +
50B SER* 1.3 60.3 + - - +
52B LEU* 3.4 0.6 + - - -
53B ALA* 3.0 28.1 + - - +
63B ILE* 3.3 45.7 + - + +
66B GLN* 3.9 32.1 - - - +
70B GLU* 4.1 17.4 + - - +
71B LEU* 4.0 21.3 - - + +
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Residues in contact with SER 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.6 12.8 - - - +
27A GLN* 3.1 34.0 + - - -
33A LEU* 4.0 11.9 - - - -
48A HIS* 3.4 23.6 - - - -
50A SER* 4.8 5.4 + - - -
51A VAL* 6.0 0.2 - - - +
35B ASP* 5.0 1.9 + - - -
48B HIS* 4.0 10.7 - - - +
49B ARG* 1.3 81.7 - - - +
51B VAL* 1.3 60.1 + - - +
53B ALA 3.6 0.2 + - - -
54B ALA* 3.0 25.1 + - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.7 11.9 - - + -
24A LEU* 4.8 4.3 - - + -
21B LEU* 5.4 1.1 - - + -
24B LEU* 3.8 29.4 - - + -
48B HIS* 3.2 18.9 + - + +
50B SER* 1.3 82.0 + - - +
52B LEU* 1.3 66.1 + - - +
54B ALA* 3.3 7.6 + - - +
55B CYS* 3.0 35.3 + - - -
91B ALA* 4.4 9.6 - - + +
92B TYR* 3.7 39.9 - - + +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B VAL* 3.9 16.4 - - + -
38B ILE* 3.4 37.5 - - + -
47B ALA* 3.9 15.5 - - + -
48B HIS 3.1 12.1 + - - +
49B ARG 3.9 4.7 - - - +
51B VAL* 1.3 77.2 - - + +
53B ALA* 1.3 58.8 + - - +
55B CYS* 3.2 4.4 + - + +
56B SER* 2.9 34.7 + - - +
59B PHE* 3.6 34.9 - - + +
63B ILE* 3.9 5.2 - - + -
84B PHE* 5.7 1.1 - - + -
88B ILE* 4.8 11.2 - - + -
91B ALA* 5.4 5.4 - - + -
92B TYR* 4.5 13.7 - - + -
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLN* 4.3 2.2 - - - +
33A LEU* 3.5 25.6 - - + -
49B ARG 3.0 18.1 + - - +
50B SER 3.8 1.1 - - - +
52B LEU* 1.3 76.0 - - - +
54B ALA* 1.3 61.3 + - - +
56B SER 3.2 13.5 + - - +
60B HIS* 3.6 45.6 + - - +
63B ILE* 4.0 6.0 - - + +
116B HIS* 4.9 2.3 + - - -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.5 14.5 - - + +
23A SER* 3.4 38.8 + - - -
24A LEU* 5.0 1.3 - - + +
27A GLN* 4.0 5.2 - - - +
50B SER 3.0 18.8 + - - +
51B VAL* 3.4 9.9 - - - +
53B ALA* 1.3 77.2 - - - +
55B CYS* 1.3 62.1 + - - +
116B HIS* 3.3 18.4 - - - +
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Residues in contact with CYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A HIS* 3.8 15.9 - - - -
20A VAL* 3.6 30.7 - - - -
51B VAL* 3.0 22.6 + - - +
52B LEU* 4.0 4.3 - - + +
54B ALA* 1.3 77.0 - - - +
56B SER* 1.3 59.6 + - - +
90B PHE* 6.6 0.2 - - + -
91B ALA* 4.1 23.6 - - + -
115B VAL* 3.3 14.3 - - + +
116B HIS* 2.9 33.0 + - - +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU 2.9 11.7 + - - +
53B ALA 3.2 11.1 - - - +
54B ALA 3.5 1.2 - - - -
55B CYS* 1.3 81.1 - - - +
57B SER* 1.3 57.2 + - - +
58B TYR* 3.7 1.0 - - - +
59B PHE* 3.1 31.1 + - - -
60B HIS 3.0 21.8 + - - -
113B LEU* 2.4 29.4 + - - +
114B SER 3.5 5.4 - - - -
115B VAL* 4.5 9.9 - - - -
116B HIS* 4.0 2.9 - - - -
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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