Contacts of the strand formed by residues 277 - 282 (chain B) in PDB entry 1SZU
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 ALA 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 3.7 10.0 - - - +
108B VAL* 3.0 29.2 + - + +
109B THR 3.4 2.2 + - - -
110B THR 3.2 38.4 - - - +
111B GLY* 4.1 1.3 - - - -
114B ALA* 4.3 1.3 - - + -
266B PHE* 3.2 24.2 - - - +
267B ALA* 3.5 6.7 - - + +
276B LEU* 1.3 79.0 - - - +
278B GLY* 1.3 60.1 + - - +
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Residues in contact with GLY 278 (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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106B LEU 3.2 12.1 - - - -
108B VAL* 3.8 8.4 - - - +
114B ALA* 3.4 5.6 - - - +
265B THR* 3.1 5.9 - - - -
266B PHE* 2.9 45.7 + - - -
277B ALA* 1.3 79.0 - - - +
279B VAL* 1.3 62.9 + - - -
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 3.2 2.6 - - - -
106B LEU* 2.8 43.3 + - + +
108B VAL* 5.6 0.7 - - + -
114B ALA* 3.3 32.3 - - - +
117B ASN* 4.3 8.7 - - + -
118B ALA* 4.0 20.0 - - + +
121B ILE* 4.4 1.6 - - + -
263B LEU* 3.7 29.2 - - + -
264B THR 3.3 8.7 - - - +
265B THR* 4.1 3.6 - - + -
266B PHE* 3.8 1.2 - - - -
278B GLY* 1.3 79.5 - - - +
280B THR* 1.3 63.2 + - - +
286B MET* 3.5 15.4 - - + +
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Residues in contact with THR 280 (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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93B MET* 3.6 13.1 - - - +
94B ASN* 4.0 0.7 - - - +
97B VAL* 3.6 36.6 - - + +
103B LYS* 3.9 21.1 - - + -
104B LYS 3.5 3.4 - - - -
105B THR* 2.6 24.9 + - - +
263B LEU* 3.4 1.1 - - - -
264B THR* 2.7 43.0 + - - -
266B PHE* 3.4 18.7 - - - -
279B VAL* 1.3 74.0 - - - +
281B GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 281 (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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101B PHE* 5.3 0.4 - - - -
103B LYS* 3.1 12.7 - - - -
104B LYS 2.9 27.3 + - - -
262B ASP 3.0 14.6 - - - -
263B LEU* 4.0 8.7 - - - -
280B THR* 1.3 78.1 - - - +
282B ARG* 1.3 69.7 + - - +
286B MET* 3.4 6.3 - - - +
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Residues in contact with ARG 282 (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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101B PHE* 3.2 58.9 - - + +
102B ALA 3.7 7.0 - - - -
226B ARG* 4.7 9.1 - - - +
230B ASP* 5.4 3.0 + - - -
235B MET* 5.5 1.5 - - - +
260B ALA 5.4 1.0 + - - -
262B ASP* 2.7 41.4 + - - +
281B GLY* 1.3 70.6 - - - +
283B ALA* 1.3 61.9 + - - +
284B GLU* 3.6 24.9 + - - +
285B VAL* 3.0 26.0 + - + +
286B MET* 2.8 25.1 + - - +
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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