Contacts of the helix formed by residues 42 - 52 (chain A) in PDB entry 1IJZ
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 GLY 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASN 5.9 0.2 - - - -
40A THR* 4.1 4.7 + - - -
41A ALA* 1.3 76.7 - - - +
43A MET* 1.3 56.5 + - - -
44A TYR* 3.3 2.7 - - - -
45A CYS* 3.3 12.8 + - - +
46A ALA* 2.8 34.0 + - - +
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Residues in contact with MET 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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37A ILE* 4.3 3.5 - - - +
38A ASN 5.2 1.8 - - - -
39A LEU* 3.7 23.1 - - + -
40A THR 3.2 46.9 - - - +
41A ALA 2.4 19.3 + - - +
42A GLY* 1.3 73.2 - - - +
44A TYR* 1.3 68.4 + - + +
46A ALA* 4.5 4.9 - - - -
47A ALA* 2.5 39.2 + - - +
99A LEU* 4.7 10.3 - - + -
102A HIS* 3.7 37.0 - - + +
103A LEU* 5.1 2.9 - - + +
106A LEU* 4.3 20.0 - - + -
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Residues in contact with TYR 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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10A LEU* 3.5 19.6 - - - +
13A LEU* 4.3 4.0 - - + -
41A ALA 4.5 9.6 - - - -
42A GLY* 3.3 0.6 - - - -
43A MET* 1.3 92.3 - - + +
45A CYS* 1.3 57.2 + - - +
47A ALA* 3.8 4.8 - - - +
48A LEU* 2.8 30.5 + - - +
67A LEU* 3.7 32.9 - - + +
70A PHE* 3.4 66.7 - + + +
71A CYS* 4.3 2.6 - - + +
99A LEU* 6.2 1.8 - - + -
103A LEU* 3.4 30.8 - - + +
106A LEU* 5.9 4.7 - - + +
113A ASN* 4.4 19.1 - - - -
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Residues in contact with CYS 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 GLY* 3.3 13.5 + - - +
43A MET 3.2 0.2 - - - -
44A TYR* 1.3 78.3 - - - +
46A ALA* 1.3 67.4 + - - +
48A LEU* 3.1 12.0 + - - +
49A GLU* 3.1 16.0 + - - +
70A PHE 4.6 3.6 - - - -
71A CYS* 2.0 54.5 - - - -
72A PRO* 5.4 0.9 - - - -
73A HIS* 3.3 20.6 + - - +
75A VAL* 5.2 1.7 - - - +
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Residues in contact with ALA 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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37A ILE* 3.9 19.6 - - + +
38A ASN 5.3 4.3 - - - +
42A GLY 2.8 21.9 + - - +
43A MET* 3.9 1.3 - - - +
45A CYS* 1.3 72.8 - - - +
47A ALA* 1.3 61.3 + - - +
49A GLU* 2.8 32.2 - - - +
50A SER* 2.9 11.1 + - - -
82A SER* 3.9 21.8 - - - +
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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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37A ILE* 3.6 13.4 - - + +
43A MET 2.5 26.7 + - - +
44A TYR* 3.8 5.2 - - - +
46A ALA* 1.3 75.6 - - - +
48A LEU* 1.3 61.4 + - - +
50A SER* 3.2 3.7 + - - -
51A LEU* 3.1 26.3 + - - +
67A LEU* 4.9 7.4 - - + -
95A PHE* 3.7 23.2 - - + -
99A LEU* 4.7 15.9 - - + -
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Residues in contact with LEU 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 TYR 2.8 20.5 + - - +
45A CYS* 3.1 6.0 + - - +
47A ALA* 1.3 76.1 - - - +
49A GLU* 1.3 64.5 - - - +
51A LEU* 2.9 17.5 + - - +
52A ILE* 2.9 30.7 + - + +
64A GLN* 3.9 39.3 - - + +
67A LEU* 4.5 8.5 - - + +
68A SER* 3.6 25.8 - - - +
71A CYS* 4.6 7.4 - - + +
73A HIS 4.3 17.9 - - - +
74A LYS* 5.1 2.2 - - - -
75A VAL* 4.5 13.9 - - + +
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Residues in contact with GLU 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 CYS 3.1 8.4 + - - +
46A ALA* 2.8 24.5 - - - +
48A LEU* 1.3 77.4 - - - +
50A SER* 1.3 55.7 + - - +
52A ILE* 3.3 17.8 + - - +
53A ASN* 2.5 27.4 - - - +
73A HIS* 6.5 0.2 - - - -
75A VAL* 3.7 25.7 - - + +
80A PHE* 3.7 2.9 - - + -
81A SER* 2.7 33.1 + - - -
82A SER* 2.6 42.3 + - - -
83A LEU* 3.2 20.1 - - + +
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Residues in contact with SER 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 VAL* 3.9 18.4 - - - +
35A TRP* 3.9 19.2 + - - +
37A ILE* 3.4 20.4 - - - +
46A ALA 2.9 13.7 + - - -
47A ALA* 3.4 8.2 - - - -
48A LEU 3.0 0.4 - - - -
49A GLU* 1.3 81.9 - - - +
51A LEU* 1.3 61.9 + - - +
53A ASN* 3.2 24.2 + - - +
54A VAL 4.1 0.2 + - - -
83A LEU* 4.9 7.6 - - - +
95A PHE* 4.3 13.2 - - - -
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Residues in contact with LEU 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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34A VAL* 4.8 5.8 - - + -
47A ALA 3.1 12.5 + - - +
48A LEU* 2.9 8.3 + - - +
50A SER* 1.3 73.1 - - - +
52A ILE* 1.3 54.5 + - - +
53A ASN 2.8 4.9 - - - -
54A VAL* 2.6 38.9 + - + +
60A ILE* 4.6 20.2 - - + -
63A THR* 4.7 8.7 - - + -
64A GLN* 3.3 32.3 + - + +
67A LEU* 3.3 35.0 - - + -
92A VAL* 5.3 7.2 - - + -
95A PHE* 4.3 27.4 - - + -
96A VAL* 6.1 1.1 - - + -
99A LEU* 6.1 0.2 - - + -
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Residues in contact with ILE 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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48A LEU* 2.9 35.0 + - + +
49A GLU* 3.4 17.3 - - - +
50A SER 3.2 0.2 - - - -
51A LEU* 1.3 76.3 - - - +
53A ASN* 1.3 61.2 + - - +
54A VAL 3.2 3.6 + - - +
55A SER* 4.4 6.4 + - - -
64A GLN* 4.0 19.1 - - + +
75A VAL* 3.7 24.5 - - + +
76A SER* 3.9 4.0 - - - +
77A ALA* 3.8 38.5 - - + +
80A PHE* 5.3 1.6 - - + -
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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