Contacts of the strand formed by residues 307 - 312 (chain B) in PDB entry 1U0O
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 LYS 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ASN* 4.2 9.6 - - - +
96A VAL* 3.5 33.9 - - + +
300B ALA 3.6 0.2 - - - +
302B LYS* 3.2 21.7 + - + +
305B ASN* 3.1 47.2 + - + +
306B ASN* 1.3 76.3 - - - +
308B TRP* 1.3 62.8 + - - +
309B TRP* 3.3 21.3 - - - +
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Residues in contact with TRP 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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79A GLN* 6.4 0.7 - - + -
84A TRP* 3.1 40.6 - + - -
90A VAL* 5.6 1.1 - - + -
92A TYR* 3.2 21.3 - + - -
93A GLU* 3.3 24.9 - - + -
94A ASN* 3.3 32.4 + - + +
95A VAL* 3.4 19.7 - - + +
96A VAL* 2.6 34.5 + - - +
242B PHE* 3.9 24.3 - + + -
266B ILE* 5.4 1.8 - - + -
268B LEU* 3.7 11.2 - - + -
299B VAL* 3.6 26.7 - - + -
300B ALA 3.3 3.8 - - - -
301B SER* 4.0 14.3 - - - -
306B ASN* 3.7 21.0 + - - +
307B LYS* 1.3 76.3 - - - +
309B TRP* 1.3 61.3 + - - +
310B ILE* 4.1 0.6 + - - -
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Residues in contact with TRP 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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96A VAL* 3.8 25.0 - - + +
98A ARG* 4.8 14.6 - - + -
99A THR* 3.3 29.2 - - + -
263B VAL* 3.8 23.3 - - + +
299B VAL* 3.3 2.8 - - - -
300B ALA* 2.5 43.5 + - + +
302B LYS* 4.2 25.4 - - + +
307B LYS* 3.3 25.4 + - + +
308B TRP* 1.3 73.2 - - - +
310B ILE* 1.3 58.8 + - - +
311B ILE* 2.7 30.8 - - + +
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Residues in contact with ILE 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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78A LYS 4.0 3.4 - - - +
79A GLN* 3.9 17.0 - - + -
95A VAL* 3.3 42.0 - - + -
99A THR* 3.3 26.3 + - - +
100A VAL* 4.6 1.1 - - + -
101A LYS* 3.3 20.3 + - - -
271B VAL* 3.6 24.5 - - + -
272B TRP* 3.8 19.3 - - + +
297B GLU* 3.5 21.1 - - + +
298B CYS 3.4 6.7 - - - +
299B VAL* 4.6 11.2 - - + -
308B TRP 5.1 0.2 - - - +
309B TRP* 1.3 72.4 - - - +
311B ILE* 1.3 63.6 + - - +
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Residues in contact with ILE 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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99A THR* 5.5 0.4 - - + -
263B VAL* 5.1 0.7 - - + -
265B TRP* 3.7 18.2 - - + -
297B GLU* 2.9 7.8 - - - +
298B CYS 2.6 40.3 + - - +
300B ALA* 3.2 26.9 - - + +
309B TRP* 2.7 52.0 - - + +
310B ILE* 1.3 79.0 - - - +
312B PRO* 1.3 74.0 - - + +
315B ARG* 4.1 23.8 - - - +
317B LYS* 5.2 6.3 - - - -
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Residues in contact with PRO 312 (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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101A LYS* 5.7 0.2 - - - +
265B TRP* 3.5 7.3 - - - -
295B GLU* 4.0 15.9 - - - +
296B TYR 3.7 8.1 - - - +
297B GLU* 3.2 19.1 - - + +
311B ILE* 1.3 93.2 - - + +
313B CYS* 1.3 58.3 + - - +
314B THR* 3.1 21.3 + - + +
315B ARG* 3.2 46.1 + - + +
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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