Contacts of the helix formed by residues 70 - 77 (chain B) in PDB entry 5SWW
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 HIS 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ASN* 4.0 0.9 - - - -
67B TYR 6.1 0.2 - - - -
68B GLY 5.3 4.0 - - - -
69B ARG* 1.3 83.0 - - - +
71B ALA* 1.3 61.9 + - - +
72B ALA 3.2 1.9 + - - +
73B LEU* 3.3 6.7 + - + +
74B ARG* 3.0 24.3 + - - +
101B CYS* 3.1 17.0 - - + -
104B TRP* 3.8 27.3 - + + +
106B CYS* 3.5 12.9 - - - -
130B TYR* 5.1 1.6 - + - -
201B ZN 2.0 40.3 - - - -
0F C 3.2 51.5 + + + +
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Residues in contact with ALA 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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31B THR* 4.0 27.4 - - + +
33B LEU* 3.7 20.6 - - + +
55B LEU* 3.5 18.4 - - + +
57B ASN* 3.8 11.7 - - - +
70B HIS* 1.3 75.3 - - - +
72B ALA* 1.3 57.2 + - - +
74B ARG* 3.3 10.8 + - - +
75B PHE* 2.9 26.5 + - - +
96B ILE* 4.5 2.9 - - + -
0F C 3.3 5.9 + - - -
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Residues in contact with ALA 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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33B LEU* 4.2 3.7 - - - +
70B HIS* 3.2 2.0 - - + +
71B ALA* 1.3 77.7 - - - +
73B LEU* 1.3 57.7 + - + +
75B PHE* 3.1 5.0 + - - +
76B LEU* 2.9 33.0 + - - +
94B TRP* 3.8 31.9 - - + -
96B ILE* 4.8 5.1 - - + +
100B PRO* 4.9 8.1 - - + -
106B CYS* 4.0 24.7 - - + -
110B VAL* 4.3 8.3 - - + -
0F C 5.4 1.1 + - - +
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Residues in contact with LEU 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 ARG* 3.8 43.5 - - + +
70B HIS* 3.3 8.5 + - + +
72B ALA* 1.3 78.7 - - + +
74B ARG* 1.3 62.3 + - - +
76B LEU* 3.2 12.7 + - + +
77B ASP* 3.0 31.7 + - - +
104B TRP 5.0 9.2 - - - +
106B CYS* 3.9 23.1 - - - -
109B GLU* 3.8 37.2 - - + +
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Residues in contact with ARG 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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55B LEU* 3.6 29.8 - - + +
56B HIS 4.0 16.5 + - - +
57B ASN* 4.4 0.7 - - - -
58B GLN* 3.1 42.1 - - - +
69B ARG* 3.7 23.8 - - + +
70B HIS 3.0 20.3 + - - +
71B ALA 3.4 9.4 - - - +
72B ALA 3.2 0.2 - - - -
73B LEU* 1.3 77.4 - - - +
75B PHE* 1.3 60.7 + - - +
77B ASP* 3.8 13.0 + - - +
78B LEU* 3.7 13.1 + - - +
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Residues in contact with PHE 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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33B LEU* 4.3 7.0 - - + -
35B TYR* 3.4 51.1 - + + -
37B VAL* 4.8 0.7 - - + -
55B LEU* 3.9 11.2 - - + +
71B ALA 2.9 13.1 + - - +
72B ALA 3.1 7.2 + - - +
74B ARG* 1.3 74.6 - - - +
76B LEU* 1.3 67.2 + - + +
77B ASP 3.1 2.0 - - - -
78B LEU* 2.9 26.6 + - + +
79B VAL* 3.3 30.1 + - + +
82B LEU* 4.6 13.9 - - + -
92B VAL* 3.6 28.7 - - + -
94B TRP* 3.4 34.1 - + + -
113B PHE* 5.6 5.4 - + - -
122B LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 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 ALA 2.9 16.9 + - - +
73B LEU* 3.2 19.2 + - + +
75B PHE* 1.3 88.0 - - + +
77B ASP* 1.3 63.2 + - - +
78B LEU 3.5 0.3 + - - -
79B VAL* 3.6 15.7 + - + +
80B PRO* 3.8 7.4 - - - +
94B TRP* 4.8 3.6 - - + -
109B GLU* 3.9 40.2 - - + +
110B VAL* 4.1 17.3 - - + +
113B PHE* 4.0 36.3 - - + -
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Residues in contact with ASP 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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69B ARG* 2.6 47.2 + - - -
73B LEU 3.0 11.4 + - - +
74B ARG* 3.9 19.0 + - - +
75B PHE 3.1 0.2 - - - -
76B LEU* 1.3 78.5 - - - +
78B LEU* 1.3 60.6 + - - +
80B PRO* 3.5 12.8 - - - +
81B SER* 5.1 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