Contacts of the helix formed by residues 70 - 77 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ASN* 3.9 1.8 - - - -
58A GLN 6.0 0.2 - - - -
67A TYR 5.8 2.3 + - - -
68A GLY 5.1 3.8 - - - -
69A ARG* 1.3 81.4 - - - +
71A ALA* 1.3 61.3 + - - +
72A ALA 3.2 1.7 + - - +
73A LEU* 3.3 7.7 + - - +
74A ARG* 2.9 23.6 + - - +
101A CYS* 3.1 16.6 - - + -
104A TRP* 3.8 27.8 - + + +
106A CYS* 3.5 11.1 - - - -
130A TYR* 5.2 1.6 - + - -
201A ZN 2.0 38.7 - - - -
0E C 3.2 51.5 + + + +
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Residues in contact with ALA 71 (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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31A THR* 4.0 26.9 - - + +
32A TYR 4.7 0.2 - - - -
33A LEU* 3.6 23.0 - - + +
55A LEU* 3.5 19.5 - - + +
57A ASN* 3.8 12.4 - - - +
70A HIS* 1.3 75.5 - - - +
72A ALA* 1.3 57.5 + - - +
74A ARG* 3.2 11.4 + - - +
75A PHE 2.9 23.0 + - - -
96A ILE* 4.5 2.0 - - + -
0E C 3.3 6.5 + - - -
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Residues in contact with ALA 72 (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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33A LEU* 4.1 4.4 - - - +
70A HIS* 3.2 1.4 - - + +
71A ALA* 1.3 77.5 - - - +
73A LEU* 1.3 58.3 + - - +
75A PHE* 3.1 5.4 + - - +
76A LEU* 2.9 31.7 + - - +
94A TRP* 3.7 32.2 - - + -
96A ILE* 4.7 5.3 - - + +
100A PRO* 4.8 8.5 - - + -
106A CYS* 4.1 24.0 - - + -
110A VAL* 4.3 8.3 - - + -
0E C 5.4 1.3 + - - +
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Residues in contact with LEU 73 (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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69A ARG* 3.8 37.9 - - - +
70A HIS* 3.3 12.3 + - + +
72A ALA* 1.3 77.7 - - + +
74A ARG* 1.3 56.4 + - - +
76A LEU* 3.1 11.0 + - + -
77A ASP* 2.9 38.6 + - - +
104A TRP 4.9 9.2 - - - +
105A GLY 4.9 1.3 - - - +
106A CYS* 3.8 24.4 - - - +
109A GLU* 3.7 38.4 - - + +
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Residues in contact with ARG 74 (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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55A LEU* 3.6 29.5 - - + +
56A HIS 3.9 17.7 + - - +
57A ASN* 4.3 0.2 - - - -
58A GLN* 3.2 43.5 - - - +
69A ARG* 3.6 17.9 - - - +
70A HIS 2.9 19.7 + - - +
71A ALA 3.4 9.2 - - - +
73A LEU* 1.3 76.0 - - - +
75A PHE* 1.3 60.1 + - - +
77A ASP* 3.7 17.6 + - - +
78A LEU* 3.6 13.6 + - - +
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Residues in contact with PHE 75 (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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33A LEU* 4.4 4.7 - - + -
35A TYR* 3.5 51.8 - + + -
37A VAL* 4.7 0.4 - - + -
55A LEU* 3.9 8.7 - - + +
71A ALA 2.9 12.0 + - - +
72A ALA 3.1 6.9 + - - +
74A ARG* 1.3 74.6 - - - +
76A LEU* 1.3 66.1 + - + +
77A ASP 3.1 2.0 - - - -
78A LEU* 2.9 28.3 + - + +
79A VAL* 3.2 27.7 + - + +
82A LEU* 4.5 18.6 - - + -
92A VAL* 3.5 28.9 - - + -
94A TRP* 3.4 35.2 - + + -
113A PHE* 5.6 4.9 - + - -
122A LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 76 (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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72A ALA 2.9 16.0 + - - +
73A LEU* 3.1 17.7 + - + +
75A PHE* 1.3 87.8 - - + +
77A ASP* 1.3 63.8 + - - +
78A LEU 3.5 0.3 + - - -
79A VAL* 3.6 15.4 + - + +
80A PRO* 3.8 7.8 - - - +
94A TRP* 4.9 3.6 - - + -
109A GLU* 3.8 44.6 - - + +
110A VAL* 3.9 18.6 - - + +
113A PHE* 4.0 35.9 - - + -
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Residues in contact with ASP 77 (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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69A ARG* 2.8 33.0 + - - -
73A LEU* 2.9 16.7 + - - +
74A ARG* 3.9 23.7 + - - +
75A PHE 3.1 0.2 - - - -
76A LEU* 1.3 79.1 - - - +
78A LEU* 1.3 58.7 + - - +
79A VAL 3.4 0.2 - - - -
80A PRO* 3.5 12.2 - - - +
81A 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