Contacts of the helix formed by residues 46 - 55 (chain A) in PDB entry 4I7H
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 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PRO* 1.3 75.8 - - - +
47A ALA* 1.3 65.1 + - - +
48A ASP* 3.5 8.2 + - - +
49A LYS* 3.1 24.3 + - - +
50A ILE* 3.2 22.0 + - - +
52A ARG* 4.9 2.1 + - - -
89A THR* 3.7 28.3 - - - -
90A THR 3.6 9.0 - - - -
91A TYR* 3.7 15.3 - - - -
92A TYR* 4.3 2.5 - - - -
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Residues in contact with ALA 47 (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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46A SER* 1.3 74.7 - - - +
48A ASP* 1.3 57.3 + - - +
50A ILE* 3.3 4.0 + - - +
51A TYR* 2.9 29.5 + - - +
63A LEU* 3.8 4.0 - - + -
66A VAL* 3.7 12.2 - - + +
67A TYR* 3.4 51.7 + - + +
70A LEU* 4.1 16.6 - - + -
89A THR* 5.4 0.4 - - - +
90A THR 4.2 0.8 + - - -
92A TYR* 3.8 8.2 - - + -
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Residues in contact with ASP 48 (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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46A SER* 3.2 8.1 + - - +
47A ALA* 1.3 75.8 - - - +
49A LYS* 1.3 60.7 + - - +
51A TYR* 3.7 18.4 - - - -
52A ARG* 2.9 57.6 + - - +
63A LEU* 4.0 20.5 - - + +
67A TYR* 5.1 1.8 + - - +
89A THR* 6.4 0.2 - - + -
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Residues in contact with LYS 49 (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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37A TYR* 3.3 13.0 - - - +
43A GLU* 4.8 13.7 - - - +
45A PRO* 4.1 11.2 - - + -
46A SER* 3.1 28.6 + - - +
48A ASP* 1.3 75.9 - - - +
50A ILE* 1.3 66.1 + - - +
52A ARG* 3.7 29.0 - - - +
53A ASP* 3.1 48.5 + - - +
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Residues in contact with ILE 50 (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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34A ILE* 4.4 11.4 - - + -
37A TYR* 3.6 32.3 - - + -
38A MET* 3.7 29.8 - - + -
45A PRO* 3.9 7.9 - - + +
46A SER 3.2 15.3 + - - +
47A ALA 3.7 5.2 - - - +
49A LYS* 1.3 74.5 - - - +
51A TYR* 1.3 58.4 + - - +
53A ASP* 3.2 1.9 + - - +
54A LEU* 2.9 52.9 + - + +
66A VAL* 3.9 14.6 - - + -
70A LEU* 4.1 26.9 - - + -
92A TYR* 5.1 1.1 - - + -
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Residues in contact with TYR 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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47A ALA 2.9 19.2 + - - +
48A ASP* 3.6 21.5 - - - +
50A ILE* 1.3 77.2 - - - +
52A ARG* 1.3 63.7 + - + +
55A GLN* 2.8 57.9 + - + +
61A MET* 3.7 25.0 + - + -
62A SER* 3.5 24.4 - - - -
63A LEU* 3.7 34.7 + - + -
66A VAL* 3.9 9.6 - - + +
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Residues in contact with ARG 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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46A SER* 4.9 2.0 + - - -
48A ASP* 2.9 49.7 + - - +
49A LYS* 3.7 41.6 - - - +
51A TYR* 1.3 80.1 - - + +
53A ASP* 1.3 64.6 + - - +
55A GLN* 4.8 4.1 - - - +
56A PRO* 3.5 17.8 - - - +
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Residues in contact with ASP 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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37A TYR* 2.6 41.8 + - + -
49A LYS* 3.1 44.6 + - - +
50A ILE 3.8 0.4 - - - +
52A ARG* 1.3 82.2 + - - +
54A LEU* 1.3 64.9 + - - +
56A PRO* 3.8 8.0 - - - +
57A ASN* 4.9 6.1 + - - -
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Residues in contact with LEU 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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33A ALA* 3.9 31.9 - - + +
34A ILE* 3.7 30.7 - - + -
37A TYR* 4.1 20.9 - - + -
50A ILE* 2.9 29.4 + - + +
53A ASP* 1.3 79.5 - - - +
55A GLN* 1.3 64.9 + - - +
56A PRO* 3.3 3.8 - - - -
57A ASN* 3.0 22.5 + - - +
58A PHE* 3.2 19.7 - - + -
61A MET* 4.0 16.8 - - + -
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Residues in contact with GLN 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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51A TYR* 2.8 50.8 + - + +
52A ARG* 4.8 4.0 - - - +
54A LEU* 1.3 72.7 - - - +
56A PRO* 1.4 72.2 - - + +
58A PHE 2.8 34.1 + - - +
59A PRO* 3.8 7.0 - - - +
61A MET* 3.9 18.5 - - + +
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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