Contacts of the helix formed by residues 71 - 78 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B VAL* 3.6 3.5 - - - +
70B ASP* 1.3 74.3 - - - +
72B LEU* 1.3 60.2 + - - -
73B ARG* 3.2 3.8 - - - -
74B ALA* 3.1 8.2 + - - -
75B TRP* 2.8 30.8 + - - +
96B GLU 2.8 13.3 + - - -
97B THR 3.3 8.3 - - - -
98B LYS* 3.9 12.9 - - - +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 3.8 9.8 - - + +
71B GLY* 1.3 71.8 - - - +
73B ARG* 1.3 61.6 + - - +
75B TRP* 3.2 37.1 + - + +
76B ILE* 3.0 32.6 + - + +
94B LEU* 4.2 14.6 - - + -
97B THR* 2.8 28.3 + - - +
98B LYS 5.2 0.2 + - - -
99B CYS* 4.6 4.9 - - + -
104B LEU* 4.1 17.5 - - + -
105B PRO* 4.3 5.8 - - + -
108B LEU* 3.7 28.3 - - + -
119B TRP* 3.8 20.2 - - + -
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLY* 3.2 0.8 - - - -
72B LEU* 1.3 76.9 - - - +
74B ALA* 1.3 57.0 + - - +
76B ILE* 3.1 4.9 + - - +
77B LYS* 3.0 36.4 + - + +
98B LYS 2.8 27.5 + - - -
99B CYS* 3.9 16.4 - - - +
103B LYS* 3.8 42.0 - - - +
105B PRO* 3.9 28.9 - - + -
127B GLY* 5.4 5.1 - - - -
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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 ASP 5.1 3.8 - - - +
71B GLY* 3.1 10.9 + - - +
73B ARG* 1.3 75.2 - - - +
75B TRP* 1.3 66.1 + - - +
77B LYS* 3.4 10.5 + - - +
78B LYS* 3.1 45.2 + - - +
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Residues in contact with TRP 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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67B TRP* 3.2 51.3 - + - -
69B VAL* 3.3 36.7 + - + +
71B GLY 2.8 18.4 + - - +
72B LEU* 3.2 37.2 - - + +
74B ALA* 1.3 77.8 - - - +
76B ILE* 1.3 71.7 + - + +
78B LYS* 3.2 9.7 + - - +
79B LYS 3.4 0.2 + - - -
80B GLY* 3.1 39.7 + - - -
81B LEU* 3.5 33.0 - - + -
84B VAL* 3.8 8.7 - - + -
92B LEU* 5.2 1.1 - - + -
94B LEU* 4.2 13.7 - - + -
108B LEU* 5.2 0.4 - - + -
306B GLY* 3.7 29.4 + - - +
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Residues in contact with ILE 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 LEU* 3.0 24.2 + - + +
73B ARG* 3.1 5.6 + - - +
75B TRP* 1.3 91.4 - - + +
77B LYS* 1.3 68.4 + - + +
78B LYS 3.0 1.3 - - - -
79B LYS* 3.0 21.9 + - - +
80B GLY 4.5 2.9 - - - +
81B LEU* 3.8 30.2 + - + +
105B PRO* 4.1 21.8 - - + -
107B GLU* 3.9 27.5 - - + +
108B LEU* 4.0 24.0 - - + -
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Residues in contact with LYS 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 ARG* 3.0 19.9 + - + +
74B ALA* 3.4 10.3 + - - +
76B ILE* 1.3 78.1 - - + +
78B LYS* 1.4 58.3 + - + +
79B LYS* 3.3 23.8 + - - +
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Residues in contact with LYS 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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69B VAL 5.8 0.2 + - - -
70B ASP 5.7 2.2 + - - -
74B ALA* 3.1 39.3 + - - +
75B TRP 3.6 4.7 - - - +
76B ILE 3.0 1.4 - - - -
77B LYS* 1.4 77.9 - - + +
79B LYS* 1.3 68.8 + - - +
80B GLY* 3.3 4.5 + - - -
269B TYR* 4.2 14.1 + - - -
305B LEU* 4.8 7.6 - - - +
306B GLY* 3.3 39.3 + - - +
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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