Contacts of the strand formed by residues 67 - 80 (chain B) in PDB entry 4SBV
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 THR 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B SER* 3.8 7.4 - - - +
63B SER 5.1 0.3 + - - -
65B ASP 5.3 0.7 + - - -
66B VAL* 1.3 77.6 + - - +
68B ILE* 1.3 75.7 + - - +
69B LEU* 4.7 6.3 - - + -
107B TRP* 4.2 23.5 + - + -
249B ARG 3.7 2.1 - - - -
250B LEU* 2.9 59.7 + - + +
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Residues in contact with ILE 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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62B SER* 3.1 50.2 + - - +
63B SER 4.7 0.4 - - - +
66B VAL* 4.6 12.8 - - + -
67B THR* 1.3 81.9 - - - +
69B LEU* 1.3 68.2 - - - +
70B SER* 4.8 1.6 - - - +
113B VAL* 5.7 5.2 - - + -
247B THR* 3.7 26.0 - - + -
248B ILE 3.7 7.4 - - - +
249B ARG* 4.9 9.9 - - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B THR* 4.0 5.6 - - + -
68B ILE* 1.3 77.9 - - - +
70B SER* 1.3 69.9 + - - +
99B TRP* 3.6 39.0 - - + -
100B LEU* 4.1 7.4 - - + -
103B VAL* 5.1 8.7 - - + -
107B TRP* 6.5 0.2 - - + -
246B TYR* 3.7 14.7 - - + +
247B THR* 3.2 2.5 - - - -
248B ILE* 2.7 64.2 + - + +
250B LEU* 3.6 14.6 - - + -
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 4.8 1.4 - - - +
69B LEU* 1.3 80.0 - - - +
71B HIS* 1.3 69.7 + - - +
99B TRP* 5.6 0.2 - - - -
246B TYR 3.0 8.7 - - - -
247B THR* 2.9 33.3 + - - +
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Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.8 0.2 - - + -
70B SER* 1.3 78.6 - - - +
72B CYS* 1.3 96.7 + - + +
73B GLU* 5.0 1.8 - - + -
99B TRP* 3.0 63.6 + + + -
245B SER* 3.2 5.7 - - - -
246B TYR* 2.9 55.7 + - + +
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Residues in contact with CYS 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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71B HIS* 1.3 114.8 + - + +
73B GLU* 1.3 65.1 + - - +
170B PHE 4.3 1.3 - - - +
171B VAL* 3.2 49.6 - - + +
243B TYR* 4.4 2.9 - - - -
244B ALA 3.0 17.9 - - - -
245B SER* 3.4 17.3 - - - -
246B TYR* 4.7 0.2 - - - -
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B HIS* 5.4 0.7 - - + -
72B CYS* 1.3 80.4 - - - +
74B LEU* 1.4 73.8 + - + +
96B VAL 5.1 0.3 - - - -
97B GLY* 3.6 16.1 + - - -
98B THR* 3.2 3.2 + - - +
99B TRP* 2.3 50.0 + - - +
100B LEU* 3.4 9.7 + - - +
243B TYR* 3.0 11.7 - - - +
244B ALA* 2.8 33.6 + - + +
246B TYR* 2.7 31.7 + - + +
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Residues in contact with LEU 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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73B GLU* 1.4 83.7 - - + +
75B SER* 1.3 64.5 - - - +
76B THR* 3.8 10.3 - - - +
77B GLU* 3.6 34.3 - - + +
97B GLY* 4.2 4.9 - - - -
98B THR* 5.1 0.9 + - - -
241B ARG* 3.7 21.1 - - - -
242B LEU 3.6 11.7 - - - +
243B TYR* 3.7 20.2 - - + -
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Residues in contact with SER 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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73B GLU 3.3 3.0 + - - -
74B LEU* 1.3 77.3 - - - +
76B THR* 1.3 70.7 + - - +
89B GLU* 5.4 6.9 - - - +
95B THR 4.2 6.8 + - - +
96B VAL* 2.8 32.3 + - - +
97B GLY* 5.2 1.4 - - - -
117B TYR* 3.7 24.1 - - - -
242B LEU 2.8 10.3 + - - -
244B ALA* 4.1 19.1 - - - -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.3 8.9 - - - +
75B SER* 1.3 90.2 - - - +
77B GLU* 1.3 78.7 + - - +
78B LEU* 5.2 5.9 - - + +
89B GLU* 4.1 26.5 + - + +
117B TYR* 6.3 0.2 - - + -
226B THR* 5.7 4.7 - - + -
241B ARG* 3.6 3.5 - - - +
242B LEU* 2.8 57.3 + - + +
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Residues in contact with GLU 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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74B LEU* 3.6 22.6 - - + +
76B THR* 1.3 82.1 + - - +
78B LEU* 1.3 65.9 + - - +
238B ASN* 6.2 1.3 - - - +
240B GLY 4.3 0.7 - - - +
241B ARG* 2.8 41.6 + - + -
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Residues in contact with LEU 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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76B THR* 4.8 5.6 - - + +
77B GLU* 1.3 80.6 - - - +
79B ALA* 1.4 62.8 - - - +
119B TYR* 3.8 17.3 - - + -
131B ILE* 4.1 11.4 - - + -
226B THR* 3.9 24.9 - - + +
228B MET* 3.2 28.7 - - + -
238B ASN* 3.6 12.2 + - - +
239B THR 3.0 18.9 + - - -
240B GLY* 3.1 35.3 + - - +
241B ARG* 3.8 7.6 - - - +
242B LEU* 4.4 10.8 - - + +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 1.4 76.4 - - - +
80B VAL* 1.3 64.4 + - - +
81B THR* 5.7 0.2 - - - -
85B VAL* 5.6 3.3 - - - +
228B MET* 3.4 21.0 - - - +
236B ALA* 3.7 20.6 - - + -
237B VAL 2.7 32.3 - - - +
238B ASN* 3.5 11.0 - - - +
239B THR 3.9 2.7 - - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA* 1.3 82.9 - - - +
81B THR* 1.4 72.8 - - - +
127B THR* 4.6 4.7 - - + -
128B SER 4.4 15.9 - - - +
130B ALA 4.8 0.7 - - - +
161B VAL* 3.8 16.4 - - + -
228B MET* 3.8 32.1 - - + +
229B GLU 4.0 13.9 - - - +
231B GLY* 4.7 8.1 - - - +
233B SER 4.4 1.2 + - - +
235B THR 4.0 2.1 - - - +
236B ALA* 3.7 0.5 - - - -
237B VAL* 3.1 27.7 + - + +
239B THR* 3.2 22.9 - - + -
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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