Contacts of the strand formed by residues 64 - 70 (chain B) in PDB entry 3SBW
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 MET 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ASP 4.4 5.6 - - - +
63B LEU* 1.3 77.2 - - - +
65B LEU* 1.3 61.2 + - - +
66B ASN* 4.0 14.6 + - - +
78B LYS* 5.5 0.7 - - - +
81B ALA* 4.8 9.4 - - + -
82B PHE 3.4 5.2 - - - -
83B SER* 3.8 27.4 - - - +
124B GLY 3.7 0.7 - - - +
125B ALA* 3.4 4.4 - - - +
126B ILE* 2.9 47.6 + - + +
128B LEU* 5.1 14.6 - - + -
18C MET* 5.7 3.4 - - + -
117C SER* 6.1 0.2 - - - -
120C GLY* 5.2 4.5 - - - -
121C ALA* 3.9 39.0 - - + +
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Residues in contact with LEU 65 (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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35B LEU* 4.0 25.1 - - + -
54B CYS* 4.0 9.2 - - - -
56B LEU* 4.1 12.1 - - + -
59B TRP* 4.6 11.2 - - + -
63B LEU 4.2 0.4 - - - -
64B MET* 1.3 73.1 - - - +
66B ASN* 1.3 63.9 + - - +
81B ALA* 3.3 1.4 - - - -
82B PHE* 2.7 45.3 + - + +
97B ILE* 3.9 7.5 - - + +
106B PHE* 3.5 49.6 - - + -
108B MET* 4.2 17.9 - - + -
123B CYS* 4.4 0.2 - - + -
124B GLY 3.4 17.3 - - - +
125B ALA* 4.3 2.5 - - + +
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Residues in contact with ASN 66 (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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64B MET* 4.3 7.0 - - - +
65B LEU* 1.3 83.9 + - - +
67B TRP* 1.3 60.8 + - - +
68B ASN* 3.7 19.2 + - - +
78B LYS* 3.7 23.5 - - + +
80B ALA 3.7 3.6 - - - +
81B ALA* 3.4 13.9 - - - +
108B MET* 4.9 0.7 - - - -
123B CYS* 3.2 7.4 - - - +
124B GLY 2.7 39.3 + - - +
126B ILE* 3.2 30.7 - - - +
121C ALA 3.8 6.3 + - - -
122C ASP* 4.3 9.9 + - - -
123C TYR* 4.5 5.8 - - + -
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Residues in contact with TRP 67 (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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37B PHE* 4.0 4.6 - + - -
52B PHE* 4.8 3.6 - + - -
65B LEU 4.0 0.8 + - - -
66B ASN* 1.3 72.0 - - - +
68B ASN* 1.3 61.7 - - - +
79B GLN* 2.7 36.7 + - + +
80B ALA* 2.8 18.4 + - + +
95B PHE* 3.7 23.1 - + + -
96B GLN 3.4 16.2 - - - -
97B ILE* 4.0 17.9 - - + +
108B MET* 3.4 40.4 - - + +
109B ASN 3.0 46.4 - - - -
110B ILE* 3.3 29.4 - - + -
121B TYR* 3.6 28.2 - + - +
122B LEU 3.6 11.7 - - - -
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Residues in contact with ASN 68 (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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66B ASN* 3.7 13.0 + - - +
67B TRP* 1.3 75.6 - - - +
69B ARG* 1.3 64.0 + - - +
76B THR* 4.2 12.6 - - - -
77B GLU 3.6 1.7 + - - +
78B LYS* 3.0 32.6 + - - +
79B GLN* 4.3 0.9 - - - -
121B TYR* 3.2 12.1 - - - +
122B LEU* 2.8 53.7 + - + +
124B GLY 4.7 0.4 - - - +
122C ASP* 4.8 2.6 - - - +
123C TYR* 2.7 42.8 + - - -
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Residues in contact with ARG 69 (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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68B ASN* 1.3 75.1 - - - +
70B LEU* 1.3 76.7 + - - +
75B GLN 3.5 0.5 - - - +
76B THR* 3.4 4.0 - - - -
77B GLU* 2.8 43.4 + - - +
79B GLN* 3.4 29.5 + - - +
95B PHE* 5.0 4.8 - - - -
116B ASN 2.8 29.4 + - - -
117B ASP* 3.7 7.9 + - - +
118B SER 3.0 22.3 + - - -
119B GLY* 4.7 3.2 - - - -
120B ILE 3.7 9.4 - - - +
121B TYR* 3.6 34.6 + - + -
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Residues in contact with LEU 70 (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* 1.3 85.8 + - - +
71B SER* 1.3 68.9 - - - +
72B PRO* 4.7 0.7 - - - +
74B ASN* 3.5 26.0 - - - +
75B GLN 3.2 8.3 - - - +
76B THR* 3.7 29.2 - - + -
77B GLU* 4.9 1.3 - - - +
119B GLY* 5.7 0.9 - - - -
120B ILE* 2.9 53.8 + - + +
122B LEU* 4.4 17.9 - - + -
139B GLY* 5.6 1.1 - - - -
125C ARG* 4.0 14.8 - - - +
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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