Contacts of the helix formed by residues 71 - 78 (chain A) in PDB entry 5WN0
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 GLY 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A VAL 3.5 3.7 - - - +
70A ASP* 1.3 72.4 - - - +
72A LEU* 1.3 59.2 + - - -
73A ARG 3.2 2.9 - - - -
74A ALA* 3.0 5.9 + - - +
75A TRP* 2.8 28.8 + - - +
96A GLU 2.9 13.1 + - - -
97A THR 3.5 7.9 - - - -
98A LYS* 4.3 9.0 - - - +
14E G 3.8 5.2 - - - -
15E C 3.3 15.5 - - - -
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Residues in contact with LEU 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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69A VAL* 3.7 15.1 - - + +
71A GLY* 1.3 72.6 - - - +
73A ARG* 1.3 58.2 + - - +
75A TRP* 3.1 38.4 + - + +
76A ILE* 2.8 45.0 + - + +
94A LEU* 4.2 12.3 - - + -
97A THR* 2.8 35.0 + - + +
99A CYS* 4.4 8.1 - - + -
104A LEU* 3.4 33.2 - - + -
105A PRO* 5.1 2.0 - - + -
108A LEU* 3.9 10.3 - - + -
119A TRP* 3.9 11.4 - - + -
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Residues in contact with ARG 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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71A GLY 3.2 1.0 - - - -
72A LEU* 1.3 76.2 - - + +
74A ALA* 1.3 61.6 + - - +
76A ILE* 3.9 6.3 - - - +
77A LYS* 3.2 38.9 + - - +
97A THR 4.7 0.2 + - - -
98A LYS 3.1 23.6 + - - -
99A CYS* 3.5 26.1 - - - +
103A LYS* 3.9 36.8 - - - +
105A PRO* 4.0 24.7 - - + -
15E C 3.5 22.6 + - - +
16E A 3.4 31.0 + - - -
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Residues in contact with ALA 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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70A ASP 4.9 0.4 - - - +
71A GLY* 3.0 8.3 + - - +
73A ARG* 1.3 74.7 - - - +
75A TRP* 1.3 54.5 + - - +
77A LYS* 3.1 9.6 + - - +
78A LYS* 2.7 49.2 + - - +
14E G 3.5 45.3 - - - +
15E C 3.1 10.4 + - - +
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Residues in contact with TRP 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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67A TRP* 3.1 41.5 - + - -
69A VAL* 3.4 32.1 - - + +
71A GLY 2.8 16.2 + - - +
72A LEU* 3.1 40.4 - - + +
74A ALA* 1.3 71.2 - - - +
76A ILE* 1.3 81.5 + - + +
78A LYS* 3.2 10.8 + - - +
79A LYS 3.2 0.3 + - - -
80A GLY* 2.8 47.1 + - - -
81A LEU* 3.7 24.9 - - + -
84A VAL* 3.7 15.5 - - + -
92A LEU* 4.4 3.8 - - + -
94A LEU* 4.4 17.5 - - + -
108A LEU* 5.0 1.3 - - + -
306A GLY* 3.6 22.8 + - - +
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Residues in contact with ILE 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 LEU* 2.8 28.8 + - + +
73A ARG* 3.9 4.9 - - - +
74A ALA 3.2 0.2 - - - -
75A TRP* 1.3 88.7 - - + +
77A LYS* 1.3 62.0 + - + +
79A LYS* 2.8 25.1 + - - +
80A GLY 3.8 4.2 + - - +
81A LEU* 4.2 15.6 + - + +
105A PRO* 3.6 34.8 - - + -
107A GLU* 3.6 32.5 - - + +
108A LEU* 3.9 25.4 - - + -
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Residues in contact with LYS 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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73A ARG* 3.2 23.2 + - - +
74A ALA* 3.1 10.4 + - - +
76A ILE* 1.3 81.4 - - + +
78A LYS* 1.3 61.0 + - + +
79A LYS* 3.0 22.2 + - - +
15E C 5.9 1.3 + - - +
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Residues in contact with LYS 78 (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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70A ASP 5.5 0.8 + - - -
74A ALA* 2.7 28.8 + - - +
75A TRP 3.2 5.6 + - - +
77A LYS* 1.3 73.1 - - + +
79A LYS* 1.3 69.8 + - - +
80A GLY* 3.4 1.4 + - - -
269A TYR* 4.2 10.3 + - - -
305A LEU* 4.6 5.4 - - - +
306A GLY* 3.1 43.6 + - - -
13E C 3.9 2.4 + - - -
14E G 2.4 49.1 + - - +
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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