Contacts of the helix formed by residues 39 - 48 (chain A) in PDB entry 1Z83
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 THR 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU 4.1 1.0 + - - -
38A SER* 1.3 70.9 - - - +
40A GLY* 1.3 55.7 + - - +
42A LEU* 3.3 9.5 + - + +
43A LEU* 2.9 34.7 + - - +
72A VAL* 3.4 28.9 - - + +
76A LEU* 4.1 23.8 - - + -
92A ILE* 5.7 0.2 - - + -
93A ASP 3.4 5.7 + - - +
94A GLY* 3.2 18.5 + - - -
95A TYR* 3.8 21.3 - - + -
631A AP5 2.8 27.1 + - - -
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Residues in contact with GLY 40 (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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38A SER* 3.2 3.6 + - - -
39A THR* 1.3 76.7 + - - +
41A ASP* 1.3 58.9 + - - +
43A LEU* 3.3 3.5 + - - +
44A ARG* 2.9 43.5 + - - +
631A AP5 3.5 42.8 + - - -
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Residues in contact with ASP 41 (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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36A HIS* 4.6 8.0 - - - -
38A SER* 3.2 32.0 + - - +
40A GLY* 1.3 75.1 - - - +
42A LEU* 1.3 64.9 + - + +
44A ARG* 2.6 32.6 + - - +
45A SER* 3.0 23.9 + - - -
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Residues in contact with LEU 42 (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 LEU* 5.0 12.8 - - + -
38A SER 3.1 22.2 + - - +
39A THR* 3.7 13.9 - - + +
40A GLY 3.3 0.4 - - - -
41A ASP* 1.3 77.7 - - + +
43A LEU* 1.3 63.5 + - - +
45A SER* 3.3 10.4 + - - -
46A GLU* 3.2 19.1 + - - +
75A MET* 4.2 36.7 - - + +
76A LEU* 4.3 21.5 - - + +
79A ALA* 4.3 18.4 - - + -
83A LYS* 6.0 0.9 - - - +
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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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39A THR 2.9 22.1 + - - +
40A GLY 3.6 3.6 - - - +
42A LEU* 1.3 76.3 - - - +
44A ARG* 1.3 63.9 + - - +
46A GLU* 2.9 14.9 + - - +
47A VAL* 3.0 16.2 + - - +
57A LEU* 4.1 16.8 - - + +
61A MET* 4.0 13.0 - - + -
67A VAL* 3.9 26.5 - - + -
71A THR* 4.6 2.9 - - + -
72A VAL* 4.8 9.6 - - + -
75A MET* 3.7 28.7 - - + -
631A AP5 3.5 43.7 - - + +
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Residues in contact with ARG 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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38A SER* 4.7 0.8 + - - -
40A GLY 2.9 22.4 + - - +
41A ASP* 2.6 38.4 + - - +
43A LEU* 1.3 71.7 - - - +
45A SER* 1.3 56.0 + - - +
47A VAL* 3.3 11.3 + - + +
48A SER* 2.9 32.0 + - - +
61A MET* 3.8 15.0 - - + +
138A ARG* 3.3 51.6 - - - +
139A VAL* 6.5 0.9 - - - -
140A ASP* 4.9 1.3 + - - -
631A AP5 2.9 32.3 + - - -
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Residues in contact with SER 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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41A ASP 3.0 13.6 + - - -
42A LEU* 3.5 14.8 - - - -
43A LEU 3.1 0.2 - - - -
44A ARG* 1.3 72.7 - - - +
46A GLU* 1.3 65.0 + - - +
48A SER* 3.4 19.2 + - - -
49A SER* 3.6 5.4 + - - -
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Residues in contact with GLU 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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42A LEU 3.2 3.6 + - - +
43A LEU 2.9 9.1 + - - +
45A SER* 1.3 76.6 - - - +
47A VAL* 1.3 63.4 + - - +
49A SER* 2.8 31.7 + - - +
51A SER* 4.1 6.2 + - - +
53A ARG* 3.0 37.3 - - - +
54A GLY* 4.3 8.3 - - - +
57A LEU* 4.1 13.8 - - + +
71A THR* 5.3 1.2 - - - +
75A MET* 2.7 41.3 - - + +
107B ARG* 5.9 0.7 - - - +
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Residues in contact with VAL 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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43A LEU 3.0 13.4 + - - +
44A ARG* 3.6 14.8 - - + +
46A GLU* 1.3 73.6 - - - +
48A SER* 1.3 58.0 + - - +
50A GLY* 3.0 22.9 + - - -
51A SER 4.6 0.2 + - - -
54A GLY* 3.6 26.5 - - - +
55A LYS* 5.7 0.4 - - + -
57A LEU* 4.4 4.9 - - + -
58A SER* 3.7 36.3 - - - +
61A MET* 4.2 11.4 - - - -
139A VAL* 6.4 0.7 - - + -
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Residues in contact with SER 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 ARG 2.9 16.9 + - - -
45A SER* 3.4 15.1 - - - -
46A GLU 3.2 0.2 - - - -
47A VAL* 1.3 76.5 - - - +
49A SER* 1.3 60.3 + - - +
50A GLY* 3.1 0.9 + - - -
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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