Contacts of the helix formed by residues 69 - 79 (chain B) in PDB entry 3U7X
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 VAL 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B HIS* 2.9 31.7 + - + +
39B LEU* 3.7 10.7 - - + +
68B THR* 1.3 73.5 - - - +
70B GLU* 1.3 69.0 + - - +
72B PHE* 3.3 6.2 + - - +
73B TRP* 3.1 41.8 + - + +
138B ILE* 5.3 1.6 - - + -
54D TYR* 3.7 27.6 - - + -
58D PHE* 5.0 2.7 - - + -
59D LEU* 3.8 25.6 - - + +
62D CYS* 4.3 18.8 - - + -
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ILE 4.5 0.3 - - - +
36B LYS* 3.5 24.4 - - + +
37B HIS* 2.6 57.4 + - - +
68B THR* 3.3 3.8 - - - +
69B VAL* 1.3 78.1 + - + +
71B ASP* 1.3 59.5 + - - +
73B TRP* 3.6 8.4 + - - +
74B ALA* 3.2 26.0 + - - +
62D CYS* 5.4 10.2 - - + +
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Residues in contact with ASP 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LYS* 2.9 32.1 + - - -
66B PHE* 3.7 23.2 - - + +
67B ASP* 4.4 6.1 + - - +
68B THR* 2.7 28.1 + - - +
70B GLU* 1.3 73.5 - - - +
72B PHE* 1.3 67.9 + - - +
74B ALA* 3.5 6.9 + - - +
75B LEU* 3.1 22.2 + - - +
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B PHE* 3.6 40.7 - + + -
68B THR 3.0 14.7 + - - +
69B VAL 3.3 8.3 + - - +
71B ASP* 1.3 78.4 - - - +
73B TRP* 1.3 98.2 + + - +
75B LEU* 3.1 4.9 + - + +
76B TYR* 2.9 35.3 + - + +
93B LEU* 5.4 1.1 - - + -
131B LEU* 4.1 8.5 - - + -
134B LEU* 3.9 44.2 - - + -
135B LEU* 4.0 13.2 - - + -
138B ILE* 3.5 26.7 - - + -
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Residues in contact with TRP 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B VAL* 3.1 35.5 + - + +
70B GLU* 3.6 8.5 + - - +
72B PHE* 1.3 100.0 - + - +
74B ALA* 1.3 58.4 + - - +
76B TYR* 3.8 29.2 - + - -
77B ASN* 3.0 38.3 + - - -
131B LEU* 3.9 22.0 - - + -
135B LEU* 4.1 7.2 - - + -
59D LEU* 2.8 31.4 + - - +
60D MET* 3.8 28.3 - - + -
62D CYS* 4.0 4.9 - - + -
63D ARG* 3.5 58.9 - - + +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLU 3.2 17.3 + - - +
71B ASP* 3.5 8.3 + - - +
72B PHE 3.3 0.2 - - - -
73B TRP* 1.3 75.1 - - - +
75B LEU* 1.3 62.6 + - - +
77B ASN* 4.7 2.7 - - - +
78B HIS* 3.3 9.9 + - - +
226B UNX 4.2 4.4 - - - -
231B UNX 2.9 29.3 - - - -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 3.8 29.6 - - + -
63B ILE* 4.0 16.8 - - + -
64B SER* 3.9 29.2 - - - +
66B PHE* 3.7 33.4 - - + -
71B ASP 3.1 12.4 + - - +
72B PHE* 3.3 9.0 - - + +
74B ALA* 1.3 74.7 - - - +
76B TYR* 1.3 66.1 + - - +
78B HIS* 3.1 19.4 + - + +
79B ILE* 3.5 26.1 + - + +
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PHE* 2.9 29.4 + + + +
73B TRP* 3.8 29.4 - + + +
75B LEU* 1.3 76.4 - - - +
77B ASN* 1.3 71.6 + - - +
78B HIS 3.3 1.0 + - - -
79B ILE* 3.4 33.8 + - + +
81B LEU* 3.5 28.9 - - + +
127B ASP* 4.6 5.4 + - - +
130B TRP* 5.0 8.3 - + - -
131B LEU* 3.9 35.1 - - + +
134B LEU* 3.9 24.7 - - + -
63D ARG* 5.6 3.4 - - - -
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B TRP* 3.0 27.4 + - - +
74B ALA* 4.3 6.3 - - - +
76B TYR* 1.3 86.8 - - - +
78B HIS* 1.3 58.7 + - - +
79B ILE 3.5 2.0 + - - +
230B UNX 4.0 6.8 - - - -
231B UNX 4.3 5.8 - - - -
63D ARG* 3.5 46.5 + - - +
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 6.0 1.6 - - + -
74B ALA 3.3 9.8 + - - +
75B LEU* 3.1 10.4 + - + +
77B ASN* 1.3 77.3 - - - +
79B ILE* 1.3 74.3 + - + +
226B UNX 4.5 7.9 - - - -
229B UNX 2.7 38.9 - - - -
230B UNX 3.8 4.6 - - - -
231B UNX 3.2 21.2 - - - -
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU* 3.4 31.2 - - + -
63B ILE* 4.8 12.8 - - + -
75B LEU* 3.5 22.0 - - + +
76B TYR* 3.4 31.2 + - + +
77B ASN 4.8 1.4 - - - +
78B HIS* 1.3 99.3 - - + +
80B GLN* 1.3 67.7 + - - +
81B LEU* 3.5 4.2 + - - +
91B TYR* 3.7 27.4 - - + +
130B TRP* 6.3 0.7 - - - +
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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