Contacts of the strand formed by residues 301 - 311 (chain B) in PDB entry 1U5U
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 PHE 301 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B LYS* 3.5 39.7 - - + -
85B PHE* 3.9 25.1 - - + +
86B PRO* 5.1 1.8 - - + -
272B GLN* 3.2 5.3 - - - -
273B ILE* 2.8 52.9 + - + +
275B ILE* 3.8 28.0 - - + -
299B PRO* 3.8 32.1 - - + -
300B TRP* 1.3 77.7 - - - +
302B ASP* 1.3 66.5 + - - +
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Residues in contact with ASP 302 (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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80B VAL* 3.7 29.7 - - + +
83B PRO* 5.1 1.4 - - - +
84B LYS 5.2 0.9 + - - -
85B PHE* 3.8 9.2 - - - -
270B ARG* 3.1 35.8 + - - +
271B LEU 3.9 3.4 - - - +
272B GLN* 3.0 27.3 + - - +
300B TRP 4.2 1.0 + - - -
301B PHE* 1.3 73.2 - - - +
303B LEU* 1.3 60.1 + - - +
304B ALA 5.1 0.7 - - - +
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Residues in contact with LEU 303 (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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79B ILE* 3.4 9.4 - - + +
80B VAL* 3.2 19.0 + - - +
85B PHE* 3.5 30.1 - - + -
91B PHE* 3.6 37.0 - - + -
212B TYR* 3.8 31.9 - - + -
271B LEU* 2.7 44.1 + - + +
272B GLN* 4.1 4.7 - - - +
273B ILE* 4.1 13.2 - - + -
301B PHE 3.3 1.0 + - - -
302B ASP* 1.3 73.9 - - - +
304B ALA* 1.3 66.2 + - + +
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Residues in contact with ALA 304 (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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77B ILE* 3.9 15.3 - - + -
78B THR 3.1 22.2 - - - +
79B ILE* 3.6 14.4 - - + +
80B VAL* 4.0 8.7 - - - +
270B ARG* 3.8 2.3 - - - -
271B LEU* 2.8 42.5 + - + +
302B ASP* 3.8 1.2 - - - +
303B LEU* 1.3 83.0 - - - +
305B LYS* 1.3 61.5 + - - +
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Residues in contact with LYS 305 (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 GLU 3.7 1.4 - - - +
77B ILE* 3.5 4.0 - - - +
78B THR* 2.8 42.7 + - + +
80B VAL* 5.0 1.8 - - + +
268B ASN* 3.4 35.4 + - + +
269B TYR 3.7 8.7 - - - +
270B ARG* 5.2 0.4 - - - +
304B ALA* 1.3 73.2 - - - +
306B VAL* 1.3 67.3 + - - +
307B SER* 4.0 7.8 - - - +
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Residues in contact with VAL 306 (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 GLU 3.7 5.6 - - - +
77B ILE* 4.3 23.3 - - + -
99B ALA* 6.1 0.7 - - + -
101B LEU* 4.5 7.9 - - + -
119B PHE* 4.6 8.1 - - + -
121B ILE* 4.6 15.7 - - + -
267B VAL 3.6 1.2 - - - +
268B ASN* 3.1 6.6 - - - +
269B TYR* 2.8 53.9 + - + +
271B LEU* 4.1 23.3 - - + -
305B LYS* 1.3 77.6 - - - +
307B SER* 1.3 63.9 + - - +
308B ILE* 3.9 23.1 - - + -
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Residues in contact with SER 307 (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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75B GLY* 3.1 3.1 - - - -
76B GLU* 2.9 39.4 + - - -
266B PRO* 4.1 7.3 - - - +
267B VAL 3.6 0.2 - - - -
268B ASN* 2.8 23.7 + - - -
305B LYS* 4.0 10.2 - - - -
306B VAL* 1.3 73.4 - - - +
308B ILE* 1.3 62.4 + - - +
309B LYS* 3.5 28.3 + - - +
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Residues in contact with ILE 308 (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 GLY* 3.8 25.4 - - - +
74B ILE 3.7 9.4 - - - +
75B GLY* 4.3 11.9 - - - +
76B GLU 5.1 0.4 - - - +
99B ALA* 5.4 3.4 - - + +
100B ARG 5.3 1.6 - - - -
101B LEU* 3.7 37.5 - - + +
258B TYR* 3.6 26.5 - - - +
262B LEU* 3.7 16.1 - - + +
266B PRO* 3.1 6.1 - - - +
267B VAL 2.8 36.5 + - - +
269B TYR* 3.8 9.4 - - + -
306B VAL* 3.9 11.4 - - + -
307B SER* 1.3 78.9 - - - +
309B LYS* 1.3 61.8 + - - +
310B THR 4.5 0.2 - - - +
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Residues in contact with LYS 309 (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 ILE 3.0 8.2 + - - +
75B GLY* 4.8 5.6 - - - -
76B GLU* 3.7 28.3 + - - +
262B LEU* 4.1 20.8 - - - +
266B PRO* 4.1 15.4 - - + +
307B SER* 3.5 33.1 - - - +
308B ILE* 1.3 78.8 - - - +
310B THR* 1.3 68.7 + - - +
311B PRO* 4.3 1.2 - - - +
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Residues in contact with THR 310 (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 GLY* 3.0 3.4 - - - -
74B ILE* 2.8 57.4 + - + +
262B LEU* 4.1 3.1 - - - +
308B ILE 4.0 0.2 - - - -
309B LYS* 1.3 87.1 + - - +
311B PRO* 1.3 83.1 - - + +
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Residues in contact with PRO 311 (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 GLY 3.6 8.5 - - - +
74B ILE* 5.5 0.5 - - - +
259B VAL* 4.0 31.4 - - + -
262B LEU* 3.8 24.6 - - + -
263B GLN* 4.9 12.1 - - + +
309B LYS 4.3 4.0 - - - +
310B THR* 1.3 100.0 - - + +
312B LEU* 1.3 64.6 + - - +
313B SER 3.9 0.9 + - - -
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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