Contacts of the helix formed by residues 38 - 51 (chain A) in PDB entry 3FZ7
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 ARG 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A MET* 1.3 76.9 - - - +
39A ASP* 1.3 67.2 + - - +
40A ASP* 3.2 11.2 - - + +
41A VAL* 2.9 41.1 + - + +
42A ALA* 2.9 11.3 + - - +
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Residues in contact with ASP 39 (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 MET 3.3 4.9 + - - +
38A ARG* 1.3 71.7 - - - +
40A ASP* 1.3 59.5 + - - +
42A ALA 3.1 2.1 + - - -
43A PHE* 2.9 23.0 + - - +
69F ASP* 4.9 3.3 - - - +
71F ASN* 3.8 7.9 - - - +
329F TYR* 3.3 26.6 + - - +
333F ARG* 2.8 48.9 + - - +
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Residues in contact with ASP 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 ARG* 3.2 12.2 - - + +
39A ASP* 1.3 78.3 - - - +
41A VAL* 1.3 61.1 + - + +
43A PHE* 3.8 7.0 - - + +
44A GLN* 3.0 45.6 + - + +
71F ASN* 2.9 27.9 + - - +
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Residues in contact with VAL 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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18A PHE* 3.9 33.7 - - + -
23A ILE* 4.3 11.4 - - + -
37A MET* 4.3 12.6 - - + -
38A ARG* 2.9 46.6 + - + +
40A ASP* 1.3 77.0 - - + +
42A ALA* 1.3 59.5 + - - +
44A GLN* 3.4 6.8 + - - +
45A ILE* 2.9 52.3 + - + +
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Residues in contact with ALA 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 MET* 3.8 23.3 - - - -
38A ARG 2.9 7.9 + - - +
39A ASP 3.5 7.4 - - - +
41A VAL* 1.3 75.9 - - - +
43A PHE* 1.3 62.9 + - - +
45A ILE* 3.4 4.6 + - - +
46A ILE* 3.0 29.5 + - - +
329F TYR* 3.9 11.7 - - + -
332F LEU* 4.2 8.1 - - + -
333F ARG* 3.8 29.4 - - + +
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Residues in contact with PHE 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 ASP 2.9 15.7 + - - +
40A ASP* 3.8 8.1 - - + +
41A VAL 3.2 0.2 - - - -
42A ALA* 1.3 75.5 - - - +
44A GLN* 1.3 69.2 + - + +
46A ILE* 3.3 3.6 + - - +
47A ASN* 2.7 56.7 + - + +
71F ASN* 3.8 31.2 - - + +
74F LYS* 3.8 47.6 - - + -
75F LEU* 3.8 31.4 - - + -
78F LEU* 4.9 4.3 - - + -
329F TYR* 3.9 8.5 - - + -
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Residues in contact with GLN 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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18A PHE* 3.8 29.0 - - + -
40A ASP* 3.0 35.7 + - + +
41A VAL* 4.5 2.2 - - - +
43A PHE* 1.3 89.8 - - + +
45A ILE* 1.4 57.0 + - - +
47A ASN* 3.7 6.0 - - + +
48A ASP* 2.9 41.0 + - - +
67B TRP* 3.7 28.2 - - + -
68B ASP 5.2 0.9 - - - +
69B ASP* 5.7 2.6 - - - -
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Residues in contact with ILE 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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17A ARG* 4.2 15.8 + - - +
18A PHE* 4.0 17.5 - - + -
23A ILE* 4.2 35.4 - - + +
25A THR* 3.4 30.3 - - + -
37A MET* 4.2 9.2 - - + -
41A VAL* 2.9 36.6 + - + +
42A ALA* 3.6 5.4 - - - +
44A GLN* 1.4 75.5 - - - +
46A ILE* 1.3 63.6 + - + +
48A ASP* 3.4 2.9 + - - +
49A GLU* 3.1 24.9 + - - +
432B ASP* 5.5 1.6 - - - +
433B PHE* 5.4 0.5 - - - -
332F LEU* 4.2 7.0 - - + -
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Residues in contact with ILE 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 ALA 3.0 19.1 + - - +
43A PHE 3.9 2.2 - - - +
45A ILE* 1.3 72.4 - - + +
47A ASN* 1.3 68.4 + - - +
49A GLU* 3.0 8.5 + - - +
50A LEU* 3.0 28.4 + - + +
75F LEU* 3.7 21.8 - - + -
96F ILE* 4.4 9.0 - - + -
325F ILE* 3.7 18.2 - - + +
328F TYR* 3.5 32.8 - - + -
329F TYR* 3.4 41.7 - - + +
332F LEU* 4.2 10.3 - - + -
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Residues in contact with ASN 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 PHE* 2.7 45.5 + - + +
44A GLN* 3.7 8.5 + - - +
46A ILE* 1.3 74.5 - - - +
48A ASP* 1.3 69.4 + - - +
50A LEU* 3.2 20.8 + - - +
51A TYR* 3.5 27.7 + - - -
57B ARG* 5.4 0.8 - - - +
68B ASP* 6.3 0.6 - - - +
75F LEU* 4.5 2.4 - - - +
78F LEU* 3.4 28.8 - - + +
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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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17A ARG* 2.4 49.8 + - - +
44A GLN* 2.9 20.3 + - - +
45A ILE 3.8 1.8 - - - +
47A ASN* 1.3 84.8 + - - +
49A GLU* 1.3 62.6 + - - +
51A TYR* 3.3 18.2 + - - +
52A LEU 4.6 0.2 + - - -
57B ARG* 2.9 31.9 + - - +
67B TRP* 3.1 13.5 + - - -
68B ASP 5.6 0.2 - - - +
428B GLY 5.7 0.9 - - - -
433B PHE* 3.8 17.7 - - + -
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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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25A THR* 2.9 31.3 + - - +
45A ILE* 3.1 18.8 + - - +
46A ILE* 3.0 16.5 + - - +
48A ASP* 1.3 76.8 - - - +
50A LEU* 1.3 61.5 - - - +
52A LEU* 3.1 13.9 + - - +
432B ASP* 4.6 4.2 - - - +
433B PHE* 4.0 18.2 - - + -
92F GLN* 2.8 48.8 + - + +
96F ILE* 3.7 13.8 - - + +
99F ARG* 2.7 28.1 + - - -
328F TYR* 5.1 1.1 - - - -
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Residues in contact with LEU 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 ILE* 3.0 33.1 + - + +
47A ASN* 3.4 12.3 - - - +
48A ASP 3.2 0.4 - - - -
49A GLU* 1.3 77.6 - - - +
51A TYR* 1.3 55.1 + - - +
52A LEU 3.1 0.2 - - - -
53A ASP* 3.0 44.2 + - - +
75F LEU* 4.1 10.3 - - + -
78F LEU* 4.9 10.3 - - + -
79F SER* 4.5 2.9 - - - +
82F LYS* 3.6 18.8 + - - +
92F GLN* 4.5 2.7 - - + -
93F SER* 4.1 4.9 - - - +
96F ILE* 4.0 19.1 - - + -
325F ILE* 3.8 35.2 - - + -
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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 ASN* 3.5 35.1 + - - -
48A ASP 3.3 9.0 + - - +
49A GLU 3.1 1.4 + - - -
50A LEU* 1.3 75.8 - - - +
52A LEU* 1.3 59.1 + - + +
53A ASP 3.1 14.3 - - - +
55B ASN* 3.3 38.7 + - + +
57B ARG* 3.4 64.4 + - + -
58B GLN* 5.0 0.3 - - - +
68B ASP* 3.2 23.1 + - - +
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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