Contacts of the helix formed by residues 42 - 51 (chain A) in PDB entry 3IOT
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 LYS 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PRO 3.6 1.2 + - - -
41A ASP* 1.3 81.7 + - + +
43A LEU* 1.3 57.3 + - - +
44A GLU* 3.2 17.9 - - - +
45A GLU* 2.9 28.3 + - + +
46A LYS* 3.2 9.9 + - + +
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Residues in contact with LEU 43 (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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10A TRP* 4.3 12.1 - - + -
11A ILE 3.5 34.3 - - - +
12A ASN* 3.9 11.2 - - - +
13A GLY 5.1 0.2 - - - +
39A HIS* 4.6 0.4 - - - -
40A PRO* 3.5 40.3 + - + +
41A ASP 2.7 8.0 + - - -
42A LYS* 1.3 73.2 - - - +
44A GLU* 1.3 60.9 + - - +
45A GLU 3.0 0.4 - - - -
46A LYS* 3.6 7.7 - - - +
47A PHE* 2.9 33.3 + - - +
60A ILE* 3.6 29.6 - - + -
61A PHE 4.8 2.7 - - - +
62A TRP* 3.8 22.9 - - + -
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Residues in contact with GLU 44 (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 LYS* 3.4 12.6 - - - +
43A LEU* 1.3 86.1 + - - +
45A GLU* 1.3 74.6 + - - +
47A PHE* 4.9 1.1 - - - -
48A PRO* 3.3 11.2 - - - +
60A ILE* 5.0 1.3 - - - -
62A TRP* 3.0 59.0 - - + +
66A ARG* 3.9 15.8 + - + +
70A TYR* 2.6 31.4 + - - +
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Residues in contact with GLU 45 (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 LYS* 2.9 19.2 + - + +
44A GLU* 1.3 90.6 - - - +
46A LYS* 1.3 64.3 + - - +
47A PHE 3.3 1.3 - - - -
48A PRO* 3.2 15.8 - - + +
49A GLN* 3.2 24.5 + - - +
66A ARG* 2.6 35.2 + - - -
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Residues in contact with LYS 46 (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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10A TRP* 4.2 14.6 - - + -
40A PRO* 4.1 22.2 - - + +
41A ASP* 3.4 41.3 + - - +
42A LYS* 3.2 6.6 + - + +
43A LEU* 3.1 9.3 + - - +
45A GLU* 1.3 76.3 - - - +
47A PHE* 1.3 63.0 + - - +
49A GLN* 3.0 22.1 + - - +
50A VAL* 3.1 18.3 + - + +
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Residues in contact with PHE 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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10A TRP* 4.3 3.1 - + + -
43A LEU 2.9 15.5 + - - +
46A LYS* 1.3 76.6 - - - +
48A PRO* 1.4 65.8 - - + +
50A VAL* 3.7 5.8 - - + -
51A ALA* 2.8 57.6 + - + +
57A PRO* 3.7 37.0 - - + -
59A ILE 5.7 0.2 - - - -
60A ILE* 3.8 36.8 - - + -
70A TYR* 4.2 28.9 - + - +
75A LEU* 4.2 24.5 - - + -
76A LEU* 4.5 5.4 - - + -
267A ASN* 4.0 21.8 - - + -
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Residues in contact with PRO 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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44A GLU 3.3 18.6 - - - +
45A GLU* 3.2 17.7 - - + +
47A PHE* 1.4 95.8 - - + +
49A GLN* 1.3 64.0 + - - +
51A ALA 4.4 0.2 - - - -
52A ALA* 3.3 22.0 + - - +
66A ARG* 4.9 4.3 - - - +
70A TYR* 3.6 20.9 - - + -
75A LEU* 4.0 19.1 - - + +
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Residues in contact with GLN 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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45A GLU* 3.2 24.6 + - - +
46A LYS* 3.0 12.4 + - - +
48A PRO* 1.3 88.0 - - - +
50A VAL* 1.3 66.9 + - + +
52A ALA* 3.5 13.3 + - - +
53A THR* 3.7 12.3 + - - +
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Residues in contact with VAL 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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10A TRP* 4.3 13.9 - - + -
46A LYS* 3.3 20.4 - - + +
47A PHE* 3.5 12.1 - - - +
49A GLN* 1.3 79.6 - - + +
51A ALA* 1.3 65.2 + - + +
52A ALA 3.2 1.8 - - - -
53A THR* 2.7 22.5 + - - +
55A ASP* 2.9 24.4 + - + -
56A GLY* 3.9 26.7 - - - +
57A PRO* 4.8 1.1 - - + -
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Residues in contact with ALA 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 PHE* 2.8 50.0 + - + +
50A VAL* 1.3 74.7 - - - +
52A ALA* 1.3 60.7 + - - +
54A GLY* 3.1 13.0 + - - -
55A ASP 3.3 9.6 - - - +
75A LEU* 3.5 24.8 - - + +
267A ASN* 4.0 16.1 - - - +
269A ALA* 4.9 1.4 - - - +
356B THR* 4.1 5.7 - - - +
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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