Contacts of the strand formed by residues 71 - 81 (chain B) in PDB entry 3A46
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 ASP 71 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B ASP* 2.6 28.7 + - + +
70B ASN* 1.3 74.9 - - + +
72B LYS* 1.3 51.7 + - - +
73B SER* 3.0 8.0 + - - -
74B ASN* 2.6 63.2 + - + +
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Residues in contact with LYS 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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67B PHE* 3.6 36.4 - - + +
68B ASP 2.8 14.1 + - - +
69B PRO 4.1 6.7 + - - +
70B ASN 3.7 2.0 - - - -
71B ASP* 1.3 69.7 - - - +
73B SER* 1.3 78.1 + - - +
74B ASN 3.4 0.9 + - - -
75B LYS* 4.2 6.4 - - - +
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Residues in contact with SER 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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71B ASP* 2.8 10.3 + - - -
72B LYS* 1.3 91.3 + - - +
74B ASN* 1.3 57.1 + - - -
75B LYS* 3.1 22.3 + - - +
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Residues in contact with ASN 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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47B ASN* 4.5 7.4 - - - +
50B LEU* 5.4 1.0 - - - +
67B PHE* 3.7 17.7 - - - -
68B ASP* 4.0 7.2 + - + +
71B ASP* 2.6 42.8 + - + +
72B LYS 4.4 1.3 - - - -
73B SER* 1.3 67.0 - - - +
75B LYS* 1.3 65.5 + - - +
76B TRP* 3.5 28.9 + - - +
123B ASN* 4.2 15.0 + - - +
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Residues in contact with LYS 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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65B GLU* 3.3 26.1 + - + +
66B LEU 3.3 7.4 - - - +
67B PHE* 4.7 3.8 - - + -
72B LYS 4.2 11.4 - - - +
73B SER* 3.1 17.1 + - - +
74B ASN* 1.3 74.9 + - - +
76B TRP* 1.3 62.4 + - - +
77B TYR* 3.2 23.9 + - + +
123B ASN* 3.4 28.9 - - - +
125B GLU* 2.7 37.1 + - - -
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Residues in contact with TRP 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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40B GLY 4.7 2.0 - - - -
43B ASP* 3.6 33.2 - - + -
44B PHE* 3.7 37.0 - + + -
47B ASN* 3.2 33.2 - - + +
50B LEU* 3.8 35.2 - - + +
65B GLU* 3.5 1.0 - - - +
66B LEU* 2.7 39.7 + - + +
74B ASN* 3.5 31.2 + - - +
75B LYS* 1.3 76.6 - - - +
77B TYR* 1.3 67.5 + - - +
121B PHE 4.9 0.4 - - - -
122B SER* 3.4 17.7 - - - -
123B ASN* 3.3 42.4 - - + -
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Residues in contact with TYR 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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44B PHE* 5.0 1.7 - - - -
63B TRP* 4.1 7.9 - + + -
64B PHE 3.2 12.8 - - - +
65B GLU* 3.5 26.4 + - + -
66B LEU* 4.7 0.4 - - - -
75B LYS* 3.2 51.8 + - + +
76B TRP* 1.3 78.4 - - - +
78B ILE* 1.3 65.1 + - - +
79B TRP* 4.0 18.6 - - + +
120B LYS 3.7 0.5 - - - +
121B PHE* 3.3 6.1 - - - +
122B SER* 2.6 44.3 + - - +
124B SER 4.1 10.3 - - - -
125B GLU* 3.4 37.4 + - + +
128B LEU* 3.7 26.7 - - + -
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Residues in contact with ILE 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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23B LEU* 4.2 12.3 - - + -
26B ILE* 5.4 2.2 - - + -
44B PHE* 3.8 26.2 - - + -
63B TRP* 3.1 7.8 - - - +
64B PHE* 3.0 51.8 + - + -
66B LEU* 4.1 14.8 - - + -
77B TYR* 1.3 75.4 - - - +
79B TRP* 1.3 63.4 + - - +
80B ASN* 5.1 0.4 - - + -
100B LEU* 4.9 11.2 - - + -
119B PHE* 4.0 25.1 - - + -
120B LYS 3.5 3.8 - - - +
121B PHE* 3.7 30.5 - - + -
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Residues in contact with TRP 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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61B PHE* 3.7 27.1 - + + -
62B LEU 3.9 3.6 - - - -
63B TRP* 4.4 0.9 - - + -
77B TYR* 4.0 18.3 - - + +
78B ILE* 1.3 78.2 - - - +
80B ASN* 1.3 60.8 + - - +
118B THR* 4.3 0.4 - - - -
119B PHE* 3.2 9.8 - - - -
120B LYS* 2.7 79.4 + - + +
122B SER* 4.0 16.7 - - - -
127B GLU* 3.6 30.1 - - + -
128B LEU* 3.7 40.2 - - + +
131B LYS* 3.6 24.9 - - + -
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Residues in contact with ASN 80 (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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61B PHE* 3.7 2.3 - - - -
62B LEU* 2.8 53.7 + - + +
64B PHE* 5.3 0.4 - - + -
78B ILE* 4.8 3.6 - - + +
79B TRP* 1.3 77.3 - - - +
81B THR* 1.3 76.0 + - - +
82B PHE* 3.3 16.1 - - - -
88B TRP* 3.0 30.7 + - + -
110B PHE* 4.1 4.9 - - - -
118B THR* 2.9 23.7 + - - -
119B PHE* 3.4 32.8 - - + -
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Residues in contact with THR 81 (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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60B LYS* 4.3 6.5 - - - +
61B PHE* 3.9 24.9 - - + -
80B ASN* 1.3 86.3 + - - +
82B PHE* 1.3 65.6 + - - +
83B GLY* 4.6 4.0 + - - -
110B PHE* 4.2 0.5 - - - -
116B PHE 4.6 1.2 + - - -
117B GLY* 3.1 4.9 - - - -
118B THR* 2.3 62.9 + - - +
131B LYS* 5.5 5.6 - - - +
22F T 6.1 6.7 - - - +
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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