Contacts of the helix formed by residues 39 - 55 (chain A) in PDB entry 1OZ6
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 ASP 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A TYR* 3.1 29.3 + - - -
37A PRO* 3.2 4.9 - - - +
38A LYS* 1.3 81.9 - - - +
40A ALA* 1.3 56.5 + - - +
41A THR* 3.4 9.0 + - - -
42A ASP* 2.8 25.3 + - - +
43A ARG* 2.7 37.6 + - - +
112A THR* 3.7 18.4 + - - +
117A TYR* 3.9 15.1 - - + +
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Residues in contact with ALA 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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39A ASP* 1.3 74.9 - - - +
41A THR* 1.3 64.2 + - - +
43A ARG* 2.9 35.7 + - - +
44A CYS* 2.9 18.1 + - - -
109A ASN* 3.3 31.1 + - + +
112A THR* 4.4 9.9 - - - +
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Residues in contact with THR 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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22A TYR* 3.6 21.6 + - + -
25A TYR* 3.6 24.0 - - + -
29A CYS* 4.3 2.7 - - - -
39A ASP* 3.3 13.8 + - - -
40A ALA* 1.3 77.0 - - - +
42A ASP* 1.3 59.7 + - - +
44A CYS* 2.9 34.9 + - - +
45A CYS* 3.2 5.2 + - - -
106A LEU* 3.5 21.7 + - + +
109A ASN* 3.7 24.3 + - - +
110A VAL* 5.1 0.3 - - - -
112A THR* 5.0 0.2 + - - -
113A TYR* 4.5 11.0 - - + -
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Residues in contact with ASP 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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25A TYR* 3.7 4.8 - - + +
26A GLY* 3.5 11.2 - - - -
27A CYS* 3.0 21.5 + - - +
28A TYR* 2.9 29.4 + - - +
29A CYS* 3.9 8.4 + - - -
37A PRO* 3.3 8.7 - - - +
38A LYS* 2.5 26.6 + - + +
39A ASP* 2.8 32.3 + - - +
41A THR* 1.3 72.5 - - - +
43A ARG* 1.3 62.3 + - - +
45A CYS* 3.1 4.5 + - - +
46A LEU* 3.1 18.5 + - - +
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Residues in contact with ARG 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 PRO* 4.1 18.8 - - + +
39A ASP 2.7 15.5 + - - +
40A ALA* 2.9 28.7 + - - +
42A ASP* 1.3 69.6 - - - +
44A CYS* 1.3 65.1 + - - +
46A LEU* 3.0 24.1 + - + +
47A VAL* 3.1 23.9 + - + +
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Residues in contact with CYS 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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40A ALA 2.9 16.2 + - - -
41A THR* 2.9 14.0 + - - +
43A ARG* 1.3 79.9 - - - +
45A CYS* 1.3 58.6 + - - +
47A VAL* 3.5 7.1 + - - +
48A HIS* 3.2 22.0 + - - +
102A ALA* 4.6 8.8 - - - +
105A CYS* 2.0 70.0 - - + -
106A LEU* 3.6 18.4 - - + -
109A ASN* 3.5 5.6 - - - -
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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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22A TYR* 5.2 2.0 - - - -
28A TYR* 3.4 5.8 - - - +
29A CYS* 2.0 64.8 - - - +
41A THR 3.2 5.6 + - - -
42A ASP 3.1 7.4 + - - +
44A CYS* 1.3 77.4 - - - +
46A LEU* 1.3 63.3 + - - +
48A HIS* 3.8 7.5 - - - +
49A ASP* 2.8 31.4 + - - +
102A ALA* 6.2 0.2 - - - -
106A LEU* 4.5 15.3 - - - -
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Residues in contact with LEU 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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28A TYR* 3.9 31.0 - - + -
37A PRO* 3.4 30.7 - - + -
42A ASP 3.1 8.8 + - - +
43A ARG* 3.0 18.7 + - + +
45A CYS* 1.3 73.2 - - - +
47A VAL* 1.3 64.4 + - + +
49A ASP* 2.7 33.1 + - - +
50A CYS* 3.1 26.7 + - - -
130A GLN* 3.8 23.6 - - + -
131A GLU 4.0 11.9 - - - +
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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 ARG* 3.1 21.3 + - + +
44A CYS* 3.7 9.2 - - - +
46A LEU* 1.3 89.6 - - + +
48A HIS* 1.3 56.0 + - - +
50A CYS* 3.3 7.2 + - - +
51A CYS* 2.9 27.1 + - + +
54A ARG* 4.9 0.3 + - - -
101A GLU* 3.8 25.1 - - - +
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Residues in contact with HIS 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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5A PHE* 3.5 25.4 - + - -
44A CYS 3.2 14.2 + - - +
45A CYS* 3.8 9.6 - - - +
46A LEU 3.1 0.6 - - - -
47A VAL* 1.3 78.6 - - - +
49A ASP* 1.3 67.4 + - - +
51A CYS* 3.1 7.6 + - - +
52A TYR* 2.9 57.9 + + - +
98A CYS* 2.9 28.9 - - + -
99A ASP* 2.9 21.2 + - - -
101A GLU* 4.1 3.6 - - - -
102A ALA* 3.4 20.2 - - + -
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Residues in contact with ASP 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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28A TYR* 3.7 15.7 - - + +
32A GLY 3.1 11.4 - - - +
33A GLY* 4.8 0.2 - - - -
45A CYS 2.8 18.1 + - - +
46A LEU* 2.7 15.3 + - - +
48A HIS* 1.3 77.5 + - - +
50A CYS* 1.3 63.1 - - - +
52A TYR* 3.0 18.8 + - - +
53A THR* 3.2 18.2 + - - +
134A CA 2.7 28.6 - - - -
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Residues in contact with CYS 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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46A LEU* 3.1 29.4 + - - +
47A VAL* 3.6 10.1 - - + +
49A ASP* 1.3 80.9 - - - +
51A CYS* 1.3 57.4 + - - +
53A THR* 2.5 23.1 + - - -
54A ARG* 2.7 29.5 + - - +
130A GLN* 6.0 0.4 - - - -
131A GLU 3.8 0.9 - - - -
133A CYS* 2.0 60.8 - - + -
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Residues in contact with CYS 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 VAL* 2.9 15.3 + - + +
48A HIS 3.2 10.5 - - - +
50A CYS* 1.3 78.9 - - - +
52A TYR* 1.3 61.2 + - - +
54A ARG* 3.2 15.5 + - - +
55A VAL* 3.2 25.8 + - - +
97A GLU* 5.1 0.9 - - - -
98A CYS* 2.0 44.9 - - + -
101A GLU* 3.0 25.8 - - - +
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Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ASN 5.8 1.4 - - - -
2A LEU* 5.9 1.0 - - - -
5A PHE* 4.8 4.9 - - - +
48A HIS* 2.9 43.5 + + - +
49A ASP* 3.0 11.4 + - - +
51A CYS* 1.3 78.5 - - - +
53A THR* 1.3 63.9 + - + +
55A VAL* 3.1 23.9 + - + +
56A GLY* 4.0 0.9 + - - -
68A PRO* 3.2 52.4 + - + +
69A LYS* 4.2 15.8 - - + -
95A VAL* 4.5 6.5 - - + -
98A CYS* 4.0 13.5 - - + -
99A ASP* 2.9 26.0 + - - -
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Residues in contact with THR 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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49A ASP* 3.2 13.8 + - + +
50A CYS* 2.5 26.4 + - - +
52A TYR* 1.3 77.1 - - + +
54A ARG* 1.3 68.3 + - - +
55A VAL 3.2 0.9 + - - -
56A GLY* 3.4 13.0 + - - -
133A CYS* 4.7 9.7 - - - +
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Residues in contact with ARG 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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47A VAL 4.9 0.4 + - - -
50A CYS* 2.7 44.6 + - - +
51A CYS* 3.2 19.7 - - - +
52A TYR 3.3 0.4 - - - -
53A THR* 1.3 84.5 + - - +
55A VAL* 1.3 59.6 + - + +
56A GLY 3.2 5.5 + - - -
133A CYS* 2.5 31.7 + - - -
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Residues in contact with VAL 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 CYS 3.2 15.5 - - - +
52A TYR* 3.1 13.3 + - + +
53A THR 3.0 1.4 - - - -
54A ARG* 1.3 78.1 - - + +
56A GLY* 1.3 63.5 + - - +
59A ASP 3.6 1.3 - - - -
61A CYS* 3.3 31.2 - - + +
68A PRO* 3.3 23.2 - - + +
91A CYS 4.8 0.4 - - - +
94A ALA* 4.2 19.1 - - + -
95A VAL* 3.4 21.5 - - + +
98A CYS* 4.0 16.6 - - - -
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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